mothur_summary_single: tool_test_output

annotate tool_test_output_all.html @ 4:c4db2a4fdb42 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4

author	iuc
date	Wed, 14 Feb 2018 10:10:10 -0500
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4 c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	1 <!DOCTYPE html>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	2 <html lang="en">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	3 <head>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	4 <meta charset="utf-8">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	5 <meta http-equiv="X-UA-Compatible" content="IE=edge">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	6 <meta name="viewport" content="width=device-width, initial-scale=1">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	7 <title>Tool Test Results (powered by Planemo)</title>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	8
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	9 <!-- Bootstrap -->
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	10 <style>/*!
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	11 * Bootstrap v3.3.1 (http://getbootstrap.com)
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	12 * Copyright 2011-2014 Twitter, Inc.
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	13 * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	14 //! normalize.css v3.0.2 \| MIT License \| git.io/normalize /html{font-family:sans-serif;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%}body{margin:0}article,aside,details,figcaption,figure,footer,header,hgroup,main,menu,nav,section,summary{display:block}audio,canvas,progress,video{display:inline-block;vertical-align:baseline}audio:not([controls]){display:none;height:0}[hidden],template{display:none}a{background-color:transparent}a:active,a:hover{outline:0}abbr[title]{border-bottom:1px dotted}b,strong{font-weight:700}dfn{font-style:italic}h1{margin:.67em 0;font-size:2em}mark{color:#000;background:#ff0}small{font-size:80%}sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline}sup{top:-.5em}sub{bottom:-.25em}img{border:0}svg:not(:root){overflow:hidden}figure{margin:1em 40px}hr{height:0;-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box}pre{overflow:auto}code,kbd,pre,samp{font-family:monospace,monospace;font-size:1em}button,input,optgroup,select,textarea{margin:0;font:inherit;color:inherit}button{overflow:visible}button,select{text-transform:none}button,html input[type=button],input[type=reset],input[type=submit]{-webkit-appearance:button;cursor:pointer}button[disabled],html input[disabled]{cursor:default}button::-moz-focus-inner,input::-moz-focus-inner{padding:0;border:0}input{line-height:normal}input[type=checkbox],input[type=radio]{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;padding:0}input[type=number]::-webkit-inner-spin-button,input[type=number]::-webkit-outer-spin-button{height:auto}input[type=search]{-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;-webkit-appearance:textfield}input[type=search]::-webkit-search-cancel-button,input[type=search]::-webkit-search-decoration{-webkit-appearance:none}fieldset{padding:.35em .625em .75em;margin:0 2px;border:1px solid silver}legend{padding:0;border:0}textarea{overflow:auto}optgroup{font-weight:700}table{border-spacing:0;border-collapse:collapse}td,th{padding:0}/! 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c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	15 <style>/* bootstrap custom style stuff - taken from demo template. */
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	16 /*
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	17 * Base structure
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	18 */
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	19
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	20 /* Move down content because we have a fixed navbar that is 50px tall */
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	21 body {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	22 padding-top: 50px;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	23 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	24
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	25
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	26 /*
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	27 * Global add-ons
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	28 */
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	29
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	30 .sub-header {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	31 padding-bottom: 10px;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	32 border-bottom: 1px solid #eee;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	33 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	34
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	35 /*
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	36 * Top navigation
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	37 * Hide default border to remove 1px line.
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	38 */
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	39 .navbar-fixed-top {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	40 border: 0;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	41 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	42
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	43 /*
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	44 * Sidebar
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	45 */
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	46
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	47 /* Hide for mobile, show later */
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	48 .sidebar {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	49 display: none;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	50 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	51 @media (min-width: 768px) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	52 .sidebar {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	53 position: fixed;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	54 top: 51px;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	55 bottom: 0;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	56 left: 0;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	57 z-index: 1000;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	58 display: block;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	59 padding: 20px;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	60 overflow-x: hidden;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	61 overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	62 background-color: #f5f5f5;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	63 border-right: 1px solid #eee;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	64 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	65 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	66
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	67 /* Sidebar navigation */
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	68 .nav-sidebar {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	69 margin-right: -21px; /* 20px padding + 1px border */
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	70 margin-bottom: 20px;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	71 margin-left: -20px;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	72 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	73 .nav-sidebar > li > a {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	74 padding-right: 20px;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	75 padding-left: 20px;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	76 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	77 .nav-sidebar > .active > a,
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	78 .nav-sidebar > .active > a:hover,
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	79 .nav-sidebar > .active > a:focus {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	80 color: #fff;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	81 background-color: #428bca;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	82 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	83
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	84
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	85 /*
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	86 * Main content
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	87 */
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	88
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	89 .main {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	90 padding: 20px;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	91 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	92 @media (min-width: 768px) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	93 .main {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	94 padding-right: 40px;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	95 padding-left: 40px;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	96 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	97 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	98 .main .page-header {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	99 margin-top: 0;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	100 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	101
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	102
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	103 /*
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	104 * Placeholder dashboard ideas
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	105 */
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	106
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	107 .placeholders {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	108 margin-bottom: 30px;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	109 text-align: center;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	110 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	111 .placeholders h4 {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	112 margin-bottom: 0;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	113 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	114 .placeholder {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	115 margin-bottom: 20px;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	116 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	117 .placeholder img {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	118 display: inline-block;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	119 border-radius: 50%;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	120 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	121
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	122 .text-success-custom{
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	123 color: rgba(6, 108, 8, 1);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	124 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	125 .text-danger-custom{
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	126 font-weight: bold;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	127 color: rgba(213, 24, 20, 1);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	128 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	129 .panel-danger-custom .panel-title{
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	130 font-weight: bold;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	131 color: rgba(213, 24, 20, 1);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	132 }t status
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	133
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	134 .panel-success-custom .panel-title{
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	135 color: rgba(6, 108, 8, 1);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	136 }t status
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	137 </style>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	138
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	139 <!-- HTML5 shim and Respond.js for IE8 support of HTML5 elements and media queries -->
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	140 <!-- WARNING: Respond.js doesn't work if you view the page via file:// -->
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	141 <!--[if lt IE 9]>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	142 <script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	143 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	144 <![endif]-->
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	145
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	146 </head>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	147 <body>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	148
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	149 <nav class="navbar navbar-inverse navbar-fixed-top" role="navigation">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	150 <div class="container-fluid">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	151 <div class="navbar-header">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	152
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	153 <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false" aria-controls="navbar">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	154 <span class="sr-only">Toggle navigation</span>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	155 <span class="icon-bar"></span>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	156 <span class="icon-bar"></span>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	157 <span class="icon-bar"></span>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	158 </button>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	159 <a class="navbar-brand" href="#">Tool Test Results (powered by Planemo)</a>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	160 </div>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	161 <div id="navbar" class="navbar-collapse collapse">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	162 <ul class="nav navbar-nav navbar-right">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	163 <li><a href="https://galaxyproject.org">Galaxy</a></li>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	164 <li><a href="https://planemo.readthedocs.org">Planemo</a></li>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	165 </ul>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	166 <div class="navbar-form navbar-right">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	167 </div>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	168 </div>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	169 </div>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	170 </nav>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	171
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	172 <div class="container-fluid">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	173 <div class="row">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	174 <div class="col-sm-3 col-md-2 sidebar">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	175 <ul class="nav nav-sidebar">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	176 <li><a href="#overview" class="text-success"><strong>Overview</strong></a></li>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	177 </ul>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	178 <ul class="nav nav-sidebar" id="nav-sidebar-tests">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	179 </ul>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	180 </div>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	181 <div class="col-sm-9 col-sm-offset-3 col-md-10 col-md-offset-2 main">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	182 <!-- <h1 class="page-header">Tests</h1> -->
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	183 <h2 id="overview">Overview</h2>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	184 <div id="overview-content"></div>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	185 <div class="progress">
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	186 </div>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	187 <h2 id="tests">Tests</h2>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	188 <p>The remainder of this contains a description for each test executed to run these jobs.</p>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	189 </div>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	190 </div>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	191 </div>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	192
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	193 <script>/! jQuery v2.1.1 \| (c) 2005, 2014 jQuery Foundation, Inc. \| jquery.org/license /
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c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	197 //# sourceMappingURL=jquery.min.map</script>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	198 <script>/*!
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	199 * Bootstrap v3.3.1 (http://getbootstrap.com)
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	200 * Copyright 2011-2014 Twitter, Inc.
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	201 * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	202 */
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c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	204 })}}},c.prototype.activate=function(b,d,e){function f(){g.removeClass("active").find("> .dropdown-menu > .active").removeClass("active").end().find('[data-toggle="tab"]').attr("aria-expanded",!1),b.addClass("active").find('[data-toggle="tab"]').attr("aria-expanded",!0),h?(b[0].offsetWidth,b.addClass("in")):b.removeClass("fade"),b.parent(".dropdown-menu")&&b.closest("li.dropdown").addClass("active").end().find('[data-toggle="tab"]').attr("aria-expanded",!0),e&&e()}var g=d.find("> .active"),h=e&&a.support.transition&&(g.length&&g.hasClass("fade")\|\|!!d.find("> .fade").length);g.length&&h?g.one("bsTransitionEnd",f).emulateTransitionEnd(c.TRANSITION_DURATION):f(),g.removeClass("in")};var d=a.fn.tab;a.fn.tab=b,a.fn.tab.Constructor=c,a.fn.tab.noConflict=function(){return a.fn.tab=d,this};var e=function(c){c.preventDefault(),b.call(a(this),"show")};a(document).on("click.bs.tab.data-api",'[data-toggle="tab"]',e).on("click.bs.tab.data-api",'[data-toggle="pill"]',e)}(jQuery),+function(a){"use strict";function b(b){return this.each(function(){var d=a(this),e=d.data("bs.affix"),f="object"==typeof b&&b;e\|\|d.data("bs.affix",e=new c(this,f)),"string"==typeof b&&e[b]()})}var c=function(b,d){this.options=a.extend({},c.DEFAULTS,d),this.$target=a(this.options.target).on("scroll.bs.affix.data-api",a.proxy(this.checkPosition,this)).on("click.bs.affix.data-api",a.proxy(this.checkPositionWithEventLoop,this)),this.$element=a(b),this.affixed=this.unpin=this.pinnedOffset=null,this.checkPosition()};c.VERSION="3.3.1",c.RESET="affix affix-top affix-bottom",c.DEFAULTS={offset:0,target:window},c.prototype.getState=function(a,b,c,d){var e=this.$target.scrollTop(),f=this.$element.offset(),g=this.$target.height();if(null!=c&&"top"==this.affixed)return c>e?"top":!1;if("bottom"==this.affixed)return null!=c?e+this.unpin<=f.top?!1:"bottom":a-d>=e+g?!1:"bottom";var h=null==this.affixed,i=h?e:f.top,j=h?g:b;return null!=c&&c>=i?"top":null!=d&&i+j>=a-d?"bottom":!1},c.prototype.getPinnedOffset=function(){if(this.pinnedOffset)return this.pinnedOffset;this.$element.removeClass(c.RESET).addClass("affix");var a=this.$target.scrollTop(),b=this.$element.offset();return this.pinnedOffset=b.top-a},c.prototype.checkPositionWithEventLoop=function(){setTimeout(a.proxy(this.checkPosition,this),1)},c.prototype.checkPosition=function(){if(this.$element.is(":visible")){var b=this.$element.height(),d=this.options.offset,e=d.top,f=d.bottom,g=a("body").height();"object"!=typeof d&&(f=e=d),"function"==typeof e&&(e=d.top(this.$element)),"function"==typeof f&&(f=d.bottom(this.$element));var h=this.getState(g,b,e,f);if(this.affixed!=h){null!=this.unpin&&this.$element.css("top","");var i="affix"+(h?"-"+h:""),j=a.Event(i+".bs.affix");if(this.$element.trigger(j),j.isDefaultPrevented())return;this.affixed=h,this.unpin="bottom"==h?this.getPinnedOffset():null,this.$element.removeClass(c.RESET).addClass(i).trigger(i.replace("affix","affixed")+".bs.affix")}"bottom"==h&&this.$element.offset({top:g-b-f})}};var d=a.fn.affix;a.fn.affix=b,a.fn.affix.Constructor=c,a.fn.affix.noConflict=function(){return a.fn.affix=d,this},a(window).on("load",function(){a('[data-spy="affix"]').each(function(){var c=a(this),d=c.data();d.offset=d.offset\|\|{},null!=d.offsetBottom&&(d.offset.bottom=d.offsetBottom),null!=d.offsetTop&&(d.offset.top=d.offsetTop),b.call(c,d)})})}(jQuery);</script>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	205 <script>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	206 var renderTestResults = function(testData) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	207 var summary = testData["summary"];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	208 var numTests = summary["num_tests"];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	209 var numProblems = summary["num_errors"] + summary["num_failures"] + summary["num_skips"];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	210 var $overview = $("#overview-content");
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	211 var $progress = $(".progress");
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	212 if(numTests == 0) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	213 $overview.addClass("alert").addClass("alert-danger").text("No tests were executed.");
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	214 $progress.append($('<div class="progress-bar progress-bar-warning" role="progressbar" style="width: 100%" />'));
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	215 } else if(numProblems > 0) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	216 $overview.addClass("alert").addClass("alert-danger").text("There were problems with " + numProblems + " test(s) out of " + numTests + ".");
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	217 var problemPercent = (numProblems/(1.0 * numTests)) * 100.0;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	218 var successPercent = 100.0 - problemPercent;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	219 $progress.append($('<div class="progress-bar progress-bar-success" role="progressbar" style="width: ' + successPercent + '%" />'));
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	220 $progress.append($('<div class="progress-bar progress-bar-danger" role="progressbar" style="width: ' + problemPercent + '%" />'));
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	221 } else {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	222 $overview.addClass("alert").addClass("alert-success").text("All " + numTests + " test(s) successfully executed.");
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	223 $progress.append($('<div class="progress-bar progress-bar-success" role="progressbar" style="width: 100%" />'));
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	224 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	225
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	226 var $sidebar = $("#nav-sidebar-tests");
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	227 for(var index in testData["tests"]) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	228 var test = testData["tests"][index];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	229 var testResult = new TestResult(test);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	230 var rawId = testResult.rawId;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	231
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	232 var panelType = testResult.passed ? "panel-success panel-success-custom" : "panel-danger panel-danger-custom";
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	233 var $panel = $('<div class="panel">');
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	234 $panel.addClass(panelType);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	235
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	236 var $panelHeading = $('<div class="panel-heading">');
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	237 var $panelTitle = $('<div class="panel-title">');
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	238 var $a = $('<a class="collapsed" data-toggle="collapse">');
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	239 $a.attr("id", rawId);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	240 $a.attr("data-target", "#collapse" + index);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	241 var testName = testResult.toolName + " (Test #" + (testResult.testIndex + 1) + (testResult.passed ? "" : ", Failed") + ")";
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	242 $a.text(testName);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	243 var $navLink = $('<a>').attr('href', '#' + rawId).text(testName)
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	244 if(!testResult.passed) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	245 $navLink.addClass("text-danger text-danger-custom");
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	246 } else {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	247 $navLink.addClass("text-success text-success-custom");
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	248 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	249 $sidebar.append($('<li>').append( $navLink ) );
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	250 $panelTitle.append($a)
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	251 $panelHeading.append($panelTitle);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	252
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	253 var $panelBody = $('<div class="panel-body panel-collapse collapse" >');
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	254 $panelBody.attr("id", "collapse" + index);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	255
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	256 var $status = $('<div>').text("status: " + testResult.status);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	257 $panelBody.append($status);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	258 if(testResult.problems.length > 0) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	259 var $problemsLabel = $('<div>').text("problems: ");
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	260 var $problemsDiv = $('<div style="margin-left:10px;">');
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	261 var $problemsUl = $('<ul>');
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	262 for(var problemIndex in testResult.problems) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	263 $problemsUl.append($('<li>').append($('<pre>').text(testResult.problems[problemIndex])));
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	264 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	265 $problemsDiv.append($problemsUl);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	266 $panelBody.append($problemsLabel).append($problemsDiv);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	267 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	268 var $commandLabel = $('<div>command:</div>');
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	269 var $stdoutLabel = $('<div>job standard output:</div>');
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	270 var $stderrLabel = $('<div>job standard error:</div>');
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	271 var $command;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	272 if(testResult.command !== null) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	273 $command = $('<pre class="pre-scrollable" style="margin-left:10px;">').text(testResult.command);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	274 } else {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	275 $command = $('<div class="alert alert-warning" style="margin-left:10px;">').text("No command recorded.");
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	276 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	277 var $stdout;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	278 if(testResult.stdout !== null) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	279 $stdout = $('<pre class="pre-scrollable" style="margin-left:10px;">').text(testResult.stdout);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	280 } else {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	281 $stdout = $('<div class="alert alert-warning" style="margin-left:10px;">').text("No standard output recorded.");
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	282 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	283 var $stderr;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	284 if(testResult.stderr !== null) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	285 $stderr = $('<pre class="pre-scrollable" style="margin-left:10px;">').text(testResult.stderr);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	286 } else {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	287 $stderr = $('<div class="alert alert-warning" style="margin-left:10px;">').text("No standard error recorded.");
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	288 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	289 $panelBody
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	290 .append($commandLabel)
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	291 .append($command)
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	292 .append($stdoutLabel)
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	293 .append($stdout)
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	294 .append($stderrLabel)
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	295 .append($stderr);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	296 if(!testResult.passed) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	297 var $logLabel = $('<div>log:</div>');
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	298 var $log = $('<pre class="pre-scrollable" style="margin-left: 10px;">').text(testResult.problemLog);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	299 $panelBody.append($logLabel).append($log);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	300 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	301
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	302 $panel.append($panelHeading).append($panelBody);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	303 $(".main").append($panel);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	304 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	305 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	306
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	307 var TestResult = function(data) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	308 this.rawId = data["id"];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	309
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	310 var idParts = this.rawId.split("TestForTool_");
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	311 var testMethod = idParts[idParts.length-1];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	312 var splitParts;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	313 if(testMethod.indexOf(".test_tool_") > -1) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	314 splitParts = testMethod.split(".test_tool_");
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	315 } else {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	316 splitParts = rSplit(testMethod, "_", 1);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	317 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	318 var toolName = splitParts[0];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	319 var testIndex = splitParts[1];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	320 this.toolName = toolName;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	321 this.testIndex = parseInt(testIndex);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	322 console.log(data);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	323 this.status = data["data"]["status"];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	324 var job = data["data"]["job"];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	325 if(job) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	326 this.stdout = data["data"]["job"]["stdout"];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	327 this.stderr = data["data"]["job"]["stderr"];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	328 this.command = data["data"]["job"]["command_line"];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	329 } else {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	330 this.stdout = null;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	331 this.stderr = null;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	332 this.command = null;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	333 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	334 this.problems = [];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	335 var outputProblems = data["data"]["output_problems"] \|\| [];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	336 var executionProblem = data["data"]["execution_problem"];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	337 this.problems.push.apply(this.problems, outputProblems);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	338 if(executionProblem) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	339 this.problems.push(executionProblem);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	340 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	341 this.problemLog = data["data"]["problem_log"];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	342 this.passed = (this.status == "success");
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	343 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	344
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	345 // http://stackoverflow.com/questions/5202085/javascript-equivalent-of-pythons-rsplit
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	346 function rSplit(str, sep, maxsplit) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	347 var split = str.split(sep);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	348 return maxsplit ? [ split.slice(0, -maxsplit).join(sep) ].concat(split.slice(-maxsplit)) : split;
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	349 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	350
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	351
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	352 // http://stackoverflow.com/questions/19491336/get-url-parameter-jquery
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	353 function getUrlParameter(sParam)
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	354 {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	355 var sPageURL = window.location.search.substring(1);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	356 var sURLVariables = sPageURL.split('&');
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	357 for (var i = 0; i < sURLVariables.length; i++)
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	358 {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	359 var sParameterName = sURLVariables[i].split('=');
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	360 if (sParameterName[0] == sParam)
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	361 {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	362 return sParameterName[1];
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	363 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	364 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	365 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	366 </script>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	367 <script>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	368 var testDataUrl = getUrlParameter("test_data_url");
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	369 if(testDataUrl) {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	370 $.ajax(
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	371 {'url': testDataUrl,
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	372 'type': 'GET',
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	373 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	374 )
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	375 .success(function(content) { renderTestResults( $.parseJSON(content) ); })
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	376 .failure(function() { alert("Failed to load test data.")} );
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	377 } else {
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	378 var test_data = {"tests": [{"data": {"status": "success", "inputs": {"ss\|source": "history", "fasta": {"src": "hda", "id": "2891970512fa2d5a"}, "ss\|map": {"src": "hda", "id": "5729865256bc2525"}}, "job": {"inputs": {"map": {"src": "hda", "id": "5729865256bc2525", "uuid": "053e2ad0-e168-4120-ad32-52e2416a299a"}, "fasta": {"src": "hda", "id": "2891970512fa2d5a", "uuid": "0941ec90-8b06-453f-a07d-7377fcc259fa"}}, "update_time": "2018-02-08T16:48:16.346086", "tool_id": "mothur_align_check", "outputs": {"align.check": {"src": "hda", "id": "8155e4b4bf1581ff", "uuid": "6f898177-0cce-4858-827e-c5f55957a447"}, "logfile": {"src": "hda", "id": "54f2a3a23292eb07", "uuid": "8bcb8390-ff8f-49ef-920e-edc5eea5af5e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > align.check(fasta=fasta.dat,map=map.dat)\n\n\t\tPound\tDash\tPlus\tEqual\tLoop\tTilde\tTotal\nMinimum:\t0\t0\t0\t0\t0\t0\t0\n2.5%-tile:\t0\t0\t0\t0\t0\t0\t0\n25%-tile:\t0\t0\t0\t0\t0\t0\t0\nMedian: \t0\t0\t0\t0\t0\t0\t0\n75%-tile:\t0\t0\t0\t0\t0\t0\t0\n97.5%-tile:\t0\t0\t0\t0\t0\t0\t0\nMaximum:\t0\t0\t0\t0\t0\t0\t0\n# of Seqs:\t3\n\nOutput File Names: \nfasta.align.check\n\n\nmothur > quit\nname\tpound\tdash\tplus\tequal\tloop\ttilde\ttotal\tnumseqs\nU68589\t0\t0\t0\t0\t0\t0\t0\t1\nU68590\t0\t0\t0\t0\t0\t0\t0\t1\nU68591\t0\t0\t0\t0\t0\t0\t0\t1\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_1.dat' fasta.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_2.dat' map.dat && echo 'align.check( fasta=fasta.dat, map=map.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && cat fasta.align.check", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:48:13.244725", "params": {"count": "null", "ss": "{\"source\": \"history\", \"__current_case__\": 1, \"map\": {\"values\": [{\"src\": \"hda\", \"id\": 2}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name": "null", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6024", "id": "54f2a3a23292eb07", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_align_check.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"ss\|source": "history", "fasta": {"src": "hda", "id": "7b55dbb89df8f4e5"}, "name": {"src": "hda", "id": "683bc220e21425bb"}, "ss\|map": {"src": "hda", "id": "fa6d20d0fb68383f"}}, "job": {"inputs": {"map": {"src": "hda", "id": "fa6d20d0fb68383f", "uuid": "097857e5-ed1d-4947-bce3-6fd2905a34d3"}, "fasta": {"src": "hda", "id": "7b55dbb89df8f4e5", "uuid": "bd1c7e31-c02d-42a6-aadc-13ca52654e33"}, "name": {"src": "hda", "id": "683bc220e21425bb", "uuid": "2e360511-c984-432e-85d3-1f609059f22b"}}, "update_time": "2018-02-08T16:48:40.077690", "tool_id": "mothur_align_check", "outputs": {"align.check": {"src": "hda", "id": "b842d972534ccb3e", "uuid": "a01d16ed-d559-4e00-b362-4037248e1858"}, "logfile": {"src": "hda", "id": "a90a30fafe298e1e", "uuid": "e866176f-3e93-4d33-b079-6bba2ce39eda"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > align.check(fasta=fasta.dat,name=name.dat,map=map.dat)\n\n\t\tPound\tDash\tPlus\tEqual\tLoop\tTilde\tTotal\nMinimum:\t0\t0\t0\t0\t0\t0\t0\n2.5%-tile:\t0\t0\t0\t0\t0\t0\t0\n25%-tile:\t0\t0\t0\t0\t0\t0\t0\nMedian: \t0\t0\t0\t0\t0\t0\t0\n75%-tile:\t0\t0\t0\t0\t0\t0\t0\n97.5%-tile:\t0\t0\t0\t0\t0\t0\t0\nMaximum:\t0\t0\t0\t0\t0\t0\t0\n# of unique seqs:\t3\ntotal # of seqs:\t3\n\nOutput File Names: \nfasta.align.check\n\n\nmothur > quit\nname\tpound\tdash\tplus\tequal\tloop\ttilde\ttotal\tnumseqs\nU68589\t0\t0\t0\t0\t0\t0\t0\t1\nU68590\t0\t0\t0\t0\t0\t0\t0\t1\nU68591\t0\t0\t0\t0\t0\t0\t0\t1\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_5.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_7.dat' name.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_6.dat' map.dat && echo 'align.check( fasta=fasta.dat, name=name.dat, map=map.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && cat fasta.align.check", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:48:36.966637", "params": {"count": "null", "ss": "{\"source\": \"history\", \"__current_case__\": 1, \"map\": {\"values\": [{\"src\": \"hda\", \"id\": 6}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6167", "id": "683bc220e21425bb", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_align_check.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "5449172d6ff5669b"}, "alignment\|reference": {"src": "hda", "id": "9ce08b2254e4d5ed"}, "alignment\|source": "history"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "5449172d6ff5669b", "uuid": "1511b135-9600-43ec-91ca-20164079249a"}, "reference": {"src": "hda", "id": "9ce08b2254e4d5ed", "uuid": "2ef10dca-7831-4e85-bab7-f42bbd443a69"}}, "update_time": "2018-02-08T16:49:00.881405", "tool_id": "mothur_align_seqs", "outputs": {"report": {"src": "hda", "id": "1ae74d26531588b0", "uuid": "5aec6e8b-0ee3-4a6f-aa99-cc598c48e677"}, "logfile": {"src": "hda", "id": "80b8022ff3f677b7", "uuid": "b8c8daf3-d155-49f0-8e41-c3be034495a8"}, "out_align": {"src": "hda", "id": "b54fb481e575bccc", "uuid": "50a15fa3-f47b-446b-b906-ca3c5b1d1d79"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > align.seqs(fasta=fasta.dat,reference=alignment.reference.dat,align=need \rleman,ksize=8,processors=1)\n\nUsing 1 processors.\n\nReading in the alignment.reference.dat template sequences...\tDONE.\nIt took 0 to read 32 sequences.\nAligning sequences from fasta.dat ...\n22\nIt took 0 secs to align 22 sequences.\n\n\nOutput File Names: \nfasta.align\nfasta.align.report\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s `dirname $(which mothur)`/* . && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_10.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_11.dat' alignment.reference.dat && echo 'align.seqs( fasta=fasta.dat, reference=alignment.reference.dat, align=needleman, ksize=8, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| ./mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:48:57.586073", "params": {"scoring": "{\"adjust\": \"no\", \"__current_case__\": 1}", "search": "{\"method\": \"kmer\", \"__current_case__\": 0, \"ksize\": \"8\"}", "reverse": "{\"flip\": \"no\", \"__current_case__\": 1}", "align": "\"needleman\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"history\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 11}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6286", "id": "5449172d6ff5669b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_align_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"scoring\|adjust": "yes", "alignment\|reference": {"src": "hda", "id": "ea0b941dfbe636f8"}, "search\|method": "kmer", "alignment\|source": "history", "scoring\|gapopen": "-6", "scoring\|mismatch": "-15", "scoring\|match": "2", "fasta": {"src": "hda", "id": "440a6c2b5d9efe20"}, "scoring\|gapextend": "-3"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "440a6c2b5d9efe20", "uuid": "3057b911-5600-4c3c-b9f6-35b7b93693e9"}, "reference": {"src": "hda", "id": "ea0b941dfbe636f8", "uuid": "1ed348d0-821e-41d1-ac7a-4318df4ccfb4"}}, "update_time": "2018-02-08T16:49:26.757457", "tool_id": "mothur_align_seqs", "outputs": {"report": {"src": "hda", "id": "d5b3e51b7b790121", "uuid": "6d8c3d0a-b428-4f86-ae91-09e4e56c859f"}, "logfile": {"src": "hda", "id": "27ee89e2e3d631e0", "uuid": "f47ef7f7-8a17-466f-8150-4a3aa88cab8d"}, "out_align": {"src": "hda", "id": "61f03d5eef6f1538", "uuid": "5c082a64-10a1-41aa-815a-75e92ba5145a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > align.seqs(fasta=fasta.dat,reference=alignment.reference.dat,align=need \rleman,ksize=8,match=2,mismatch=-15,gapopen=-6,gapextend=-3,processors=1)\n\nUsing 1 processors.\n\nReading in the alignment.reference.dat template sequences...\tDONE.\nIt took 0 to read 32 sequences.\nAligning sequences from fasta.dat ...\n22\nIt took 0 secs to align 22 sequences.\n\n\nOutput File Names: \nfasta.align\nfasta.align.report\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s `dirname $(which mothur)`/* . && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_15.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_16.dat' alignment.reference.dat && echo 'align.seqs( fasta=fasta.dat, reference=alignment.reference.dat, align=needleman, ksize=8, match=2, mismatch=-15, gapopen=-6, gapextend=-3, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| ./mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:49:23.290890", "params": {"scoring": "{\"gapopen\": \"-6\", \"mismatch\": \"-15\", \"adjust\": \"yes\", \"__current_case__\": 0, \"gapextend\": \"-3\", \"match\": \"2\"}", "search": "{\"method\": \"kmer\", \"__current_case__\": 0, \"ksize\": \"8\"}", "reverse": "{\"flip\": \"no\", \"__current_case__\": 1}", "align": "\"needleman\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"history\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 16}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6412", "id": "b54fb481e575bccc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_align_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"scoring\|adjust": "yes", "alignment\|reference": {"src": "hda", "id": "c18708cec3343c17"}, "search\|method": "suffix", "align": "gotoh", "alignment\|source": "history", "scoring\|gapopen": "-6", "scoring\|mismatch": "-15", "scoring\|match": "2", "fasta": {"src": "hda", "id": "b28067233c6d9fa0"}, "scoring\|gapextend": "-3"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "b28067233c6d9fa0", "uuid": "a898f88c-9854-45b4-b978-8f6e8c19a035"}, "reference": {"src": "hda", "id": "c18708cec3343c17", "uuid": "69a4e7a8-77db-46bd-8b24-a45f4df43f0b"}}, "update_time": "2018-02-08T16:49:55.216327", "tool_id": "mothur_align_seqs", "outputs": {"report": {"src": "hda", "id": "a1e670e1ea0da54b", "uuid": "302f7300-55b1-4314-9556-7004d1c9fe2c"}, "logfile": {"src": "hda", "id": "5ca39fba41b940d1", "uuid": "ec2c6d47-b9a7-4d62-b5b9-7bf44a852e2c"}, "out_align": {"src": "hda", "id": "3e4e8de146a035f5", "uuid": "edca646b-7964-4384-8097-96d24e09046f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > align.seqs(fasta=fasta.dat,reference=alignment.reference.dat,align=goto \rh,search=suffix,match=2,mismatch=-15,gapopen=-6,gapextend=-3,processors=1)\n\nUsing 1 processors.\n\nReading in the alignment.reference.dat template sequences...\tDONE.\nIt took 0 to read 32 sequences.\nAligning sequences from fasta.dat ...\n22\nIt took 0 secs to align 22 sequences.\n\n\nOutput File Names: \nfasta.align\nfasta.align.report\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s `dirname $(which mothur)`/* . && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_20.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_21.dat' alignment.reference.dat && echo 'align.seqs( fasta=fasta.dat, reference=alignment.reference.dat, align=gotoh, search=suffix, match=2, mismatch=-15, gapopen=-6, gapextend=-3, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| ./mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:49:51.967514", "params": {"scoring": "{\"gapopen\": \"-6\", \"mismatch\": \"-15\", \"adjust\": \"yes\", \"__current_case__\": 0, \"gapextend\": \"-3\", \"match\": \"2\"}", "search": "{\"method\": \"suffix\", \"__current_case__\": 1}", "reverse": "{\"flip\": \"no\", \"__current_case__\": 1}", "align": "\"gotoh\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"history\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 21}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6539", "id": "ea0b941dfbe636f8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_align_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"reverse\|threshold": "0.5", "reverse\|flip": "yes", "search\|method": "blast", "alignment\|source": "history", "alignment\|reference": {"src": "hda", "id": "0535d515f68130b3"}, "fasta": {"src": "hda", "id": "9a22496ee796fbfc"}, "align": "blast"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "9a22496ee796fbfc", "uuid": "bf930a57-cb72-465c-9544-d8fab031b1b9"}, "reference": {"src": "hda", "id": "0535d515f68130b3", "uuid": "82704b74-e2ca-4ce7-adec-4995d8f13f83"}}, "update_time": "2018-02-08T16:50:21.251688", "tool_id": "mothur_align_seqs", "outputs": {"report": {"src": "hda", "id": "073082a17e1b2f0b", "uuid": "6df7f08f-1df2-4678-9895-34a65f4be0a8"}, "flip_accnos": {"src": "hda", "id": "a908e285532ac9b0", "uuid": "8d49424e-a5ed-4167-bd8f-f1306b9ffebd"}, "logfile": {"src": "hda", "id": "238993350abc9bfd", "uuid": "6d52e61a-30c4-4bf8-bb2a-25d0aac7dcbc"}, "out_align": {"src": "hda", "id": "adba32ec9811aba7", "uuid": "d8f8e608-698b-471f-b7cb-777a2e7a7e53"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > align.seqs(fasta=fasta.dat,reference=alignment.reference.dat,align=blas \rt,search=blast,flip=true,threshold=0.5,processors=1)\n\nUsing 1 processors.\n\nReading in the alignment.reference.dat template sequences...\tDONE.\nIt took 0 to read 32 sequences.\nAligning sequences from fasta.dat ...\n22\nIt took 0 secs to align 22 sequences.\n\n\nOutput File Names: \nfasta.align\nfasta.align.report\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s `dirname $(which mothur)`/* . && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_25.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_26.dat' alignment.reference.dat && echo 'align.seqs( fasta=fasta.dat, reference=alignment.reference.dat, align=blast, search=blast, flip=true, threshold=0.5, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| ./mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:50:17.543144", "params": {"scoring": "{\"adjust\": \"no\", \"__current_case__\": 1}", "search": "{\"method\": \"blast\", \"__current_case__\": 2}", "reverse": "{\"threshold\": \"0.5\", \"flip\": \"yes\", \"__current_case__\": 0}", "align": "\"blast\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"history\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 26}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6655", "id": "d5b3e51b7b790121", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_align_seqs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"alignment\|source": "history", "reverse\|threshold": "0.5", "reverse\|flip": "yes", "fasta": {"src": "hda", "id": "27a22803849b1486"}, "alignment\|reference": {"src": "hda", "id": "3777da040b354424"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "27a22803849b1486", "uuid": "6f889445-9480-4dfe-99a4-640d4d6f292f"}, "reference": {"src": "hda", "id": "3777da040b354424", "uuid": "0d421449-2afb-4639-aa7d-92fe9f605482"}}, "update_time": "2018-02-08T16:50:51.061674", "tool_id": "mothur_align_seqs", "outputs": {"report": {"src": "hda", "id": "05f80801815deda8", "uuid": "0c8e178c-f0da-4eb3-9766-01c4c2d3416a"}, "flip_accnos": {"src": "hda", "id": "95a5ac7e4618a243", "uuid": "ff4586a2-2f5c-4ae4-9d13-3b32eccfe2b7"}, "logfile": {"src": "hda", "id": "2d785e48ad6d0148", "uuid": "676f6060-0b7f-41c4-be36-5774428ebebc"}, "out_align": {"src": "hda", "id": "840f77504195704d", "uuid": "6e22fcea-953a-4218-930d-853351145ba8"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > align.seqs(fasta=fasta.dat,reference=alignment.reference.dat,align=need \rleman,ksize=8,flip=true,threshold=0.5,processors=1)\n\nUsing 1 processors.\n\nReading in the alignment.reference.dat template sequences...\tDONE.\nIt took 0 to read 32 sequences.\nAligning sequences from fasta.dat ...\n98\n[WARNING]: Some of your sequences generated alignments that eliminated too many bases, a list is provided in fasta.flip.accnos. If the reverse compliment proved to be better it was reported.\nIt took 1 secs to align 98 sequences.\n\n\nOutput File Names: \nfasta.align\nfasta.align.report\nfasta.flip.accnos\n\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s `dirname $(which mothur)`/* . && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_31.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_32.dat' alignment.reference.dat && echo 'align.seqs( fasta=fasta.dat, reference=alignment.reference.dat, align=needleman, ksize=8, flip=true, threshold=0.5, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| ./mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:50:47.166993", "params": {"scoring": "{\"adjust\": \"no\", \"__current_case__\": 1}", "search": "{\"method\": \"kmer\", \"__current_case__\": 0, \"ksize\": \"8\"}", "reverse": "{\"threshold\": \"0.5\", \"flip\": \"yes\", \"__current_case__\": 0}", "align": "\"needleman\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"history\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 32}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6892", "id": "5ca39fba41b940d1", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_align_seqs.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"phylip": {"src": "hda", "id": "863b4912f43ba501"}, "design": {"src": "hda", "id": "a068cbb083194156"}}, "job": {"inputs": {"phylip": {"src": "hda", "id": "863b4912f43ba501", "uuid": "bd47e735-1d66-48e8-85b2-5cb23c5910da"}, "design": {"src": "hda", "id": "a068cbb083194156", "uuid": "b297c9ec-d075-46b6-a8b9-0a26269db239"}}, "update_time": "2018-02-08T16:51:24.191000", "tool_id": "mothur_amova", "outputs": {"logfile": {"src": "hda", "id": "bb70618268111ce1", "uuid": "ae1be271-e920-4241-82dc-c9c3086c860d"}, "amova": {"src": "hda", "id": "f16a54a3ef316466", "uuid": "8ee19962-9e76-40a7-8c8e-595fdc6b675a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > amova(phylip=phylip.dat,iters=1000,alpha=0.05,design=design.dat)\nA-B\tAmong\tWithin\tTotal\nSS\t0.04869\t4.72878\t4.77747\ndf\t1\t96\t97\nMS\t0.04869\t0.0492581\n\nFs:\t0.988466\np-value: 0.458\n\nExperiment-wise error rate: 0.05\nIf you have borderline P-values, you should try increasing the number of iterations\n\nOutput File Names: \nphylip.amova\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_37.dat' phylip.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_38.dat' design.dat && echo 'amova( phylip=phylip.dat, iters=1000, alpha=0.05, design=design.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:51:20.982934", "params": {"iters": "\"1000\"", "alpha": "\"0.05\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "sets": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7011", "id": "9a22496ee796fbfc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_amova.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"phylip": {"src": "hda", "id": "e511a12dc2cf12e1"}, "design": {"src": "hda", "id": "25f486d5fc93a1ce"}}, "job": {"inputs": {"phylip": {"src": "hda", "id": "e511a12dc2cf12e1", "uuid": "d9fa0ca2-ecc1-4a59-a245-4aa165e1ddd8"}, "design": {"src": "hda", "id": "25f486d5fc93a1ce", "uuid": "d8d23a72-a2c6-4587-8694-92d2d5d9694a"}}, "update_time": "2018-02-08T16:51:45.688705", "tool_id": "mothur_anosim", "outputs": {"logfile": {"src": "hda", "id": "244c246e3628fe4f", "uuid": "fd4ccc15-8aca-438d-a74b-13c4e3d53183"}, "anosim": {"src": "hda", "id": "8c9b639396181d1e", "uuid": "3fc29196-23fd-4ee4-a1cd-e44881657963"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > anosim(phylip=phylip.dat,iters=1000,alpha=0.05,design=design.dat)\n\ncomparison\tR-value\tP-value\nA-B\t-0.00786503\t0.803\n\nExperiment-wise error rate: 0.05\nIf you have borderline P-values, you should try increasing the number of iterations\n\nOutput File Names: \nphylip.anosim\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_41.dat' phylip.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_42.dat' design.dat && echo 'anosim( phylip=phylip.dat, iters=1000, alpha=0.05, design=design.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:51:42.659886", "params": {"iters": "\"1000\"", "alpha": "\"0.05\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7171", "id": "adba32ec9811aba7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_anosim.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "3f322b493a2c6407"}, "otu": {"src": "hda", "id": "616a01dfb111aa65"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "3f322b493a2c6407", "uuid": "a4414c4a-10ad-49a7-898b-ea5e812efe13"}, "otu": {"src": "hda", "id": "616a01dfb111aa65", "uuid": "7434bb32-62f4-4bf8-9c54-e7dd572a2c96"}}, "update_time": "2018-02-08T16:52:08.320737", "tool_id": "mothur_bin_seqs", "outputs": {"__new_primary_file_unique\|0.10__": {"src": "hda", "id": "48f3e8809447c25a", "uuid": "82255b24-0f88-412b-ac83-4169df892ddb"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "bcb334d054d0b7ff", "uuid": "07f9a0b2-3558-490b-a4be-3666561874d5"}, "__new_primary_file_unique\|0.17__": {"src": "hda", "id": "087a78e08fef416e", "uuid": "c09649da-75d2-42fb-87eb-f84b3d976439"}, "__new_primary_file_unique\|0.02__": {"src": "hda", "id": "a6b9cabbe61f73ca", "uuid": "b3af742b-d000-4a66-b58b-40ba1aa441e6"}, "__new_primary_file_unique\|0.21__": {"src": "hda", "id": "288a67f7f32bb2fd", "uuid": "05d8f777-6439-45d3-8728-8bb62ce73dd5"}, "__new_primary_file_unique\|0.16__": {"src": "hda", "id": "9649d2d367737693", "uuid": "b7db14ef-f926-478c-9efc-c902c834a38f"}, "__new_primary_file_unique\|0.45__": {"src": "hda", "id": "945d4aa2c8920004", "uuid": "e7446bee-fbb5-41fc-ad27-5022478132c7"}, "__new_primary_file_unique\|0.03__": {"src": "hda", "id": "bab99c776d4b9391", "uuid": "514147bf-71da-4aa2-9cf5-749b73813977"}, "__new_primary_file_unique\|0.15__": {"src": "hda", "id": "9268a0f969417b28", "uuid": "4af76395-320c-4f71-897d-101bcbe66a89"}, "__new_primary_file_unique\|0.08__": {"src": "hda", "id": "0e797101c95aea67", "uuid": "ae90e95f-c5d9-40a9-bb67-808f3781b410"}, "__new_primary_file_unique\|0.14__": {"src": "hda", "id": "4ec7f8db939dbc03", "uuid": "41e9763e-8502-4f82-987c-6bcadeac8c99"}, "__new_primary_file_unique\|0.13__": {"src": "hda", "id": "b908d9d86f8a3d36", "uuid": "85c4005f-926f-45f4-aed6-5a1761fdc78d"}, "__new_primary_file_unique\|0.09__": {"src": "hda", "id": "baa1080356b320b7", "uuid": "1d245aaa-593e-4858-bb72-99a06bd16a2b"}, "__new_primary_file_unique\|0.12__": {"src": "hda", "id": "f8cc3c3467afd773", "uuid": "ef61051b-92ef-4e4f-8072-f73c13337b44"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "03229f6bce6358e8", "uuid": "034876ff-b15d-4736-b637-e0b2651498ce"}, "__new_primary_file_unique\|0.11__": {"src": "hda", "id": "85f590476b78f8ed", "uuid": "6dddc8da-c256-41c4-8e09-5e54a864ce97"}, "__new_primary_file_unique\|0.41__": {"src": "hda", "id": "315992a54eac5ecc", "uuid": "46af4cfc-722a-4cfb-9e82-4b7b21b4d650"}, "__new_primary_file_unique\|0.06__": {"src": "hda", "id": "5e6ad6ca0afeaf24", "uuid": "f997f7fc-426f-4878-a3da-82263f0d56cf"}, "__new_primary_file_unique\|0.25__": {"src": "hda", "id": "ca4ebafec84c6506", "uuid": "443e82af-ee52-4570-aba4-6f6c70b2cf24"}, "__new_primary_file_unique\|0.22__": {"src": "hda", "id": "fed9b1622ba4118e", "uuid": "e9e9f881-f8fb-4895-ba58-3a6d576e9652"}, "__new_primary_file_unique\|0.36__": {"src": "hda", "id": "a94ebc130565c5b1", "uuid": "d7181b5c-5b42-4dc7-95e2-90aa2c31a4b0"}, "__new_primary_file_unique\|0.04__": {"src": "hda", "id": "dccb60510b24da2f", "uuid": "44a715ff-3bbe-42fb-aefa-bc39b6edb766"}, "__new_primary_file_unique\|0.23__": {"src": "hda", "id": "b323ca264f40001e", "uuid": "55b4447a-958d-4da0-8729-16c09d97e464"}, "__new_primary_file_unique\|0.33__": {"src": "hda", "id": "0ed16744ccfa2592", "uuid": "a9523881-2f20-46a2-8562-6286e628bea3"}, "logfile": {"src": "hda", "id": "25cc0305829779de", "uuid": "7d161dc7-876c-4537-9422-0f6dbbcce3b2"}, "__new_primary_file_unique\|0.20__": {"src": "hda", "id": "5617b66919498d02", "uuid": "7eca21fd-952c-48e9-b065-ad8faf6890f7"}, "__new_primary_file_unique\|0.29__": {"src": "hda", "id": "4163d05c3cc243fc", "uuid": "601b3468-2d3a-42fb-94ec-5ec4d44c5ba0"}, "__new_primary_file_unique\|0.38__": {"src": "hda", "id": "c57c922a3f91222f", "uuid": "210756e0-0676-4ffe-9552-6254ac608881"}, "__new_primary_file_unique\|0.55__": {"src": "hda", "id": "f276a8cc85beb7f0", "uuid": "e8840d4f-f1b7-4d78-ad58-d78d06ab1a97"}, "__new_primary_file_unique\|0.07__": {"src": "hda", "id": "0ff3854aee1a95dd", "uuid": "0e733526-2d9b-47ce-8226-86822da0cfed"}, "__new_primary_file_unique\|0.26__": {"src": "hda", "id": "b31f4d82ada5e956", "uuid": "efe00c7e-df09-4162-a39e-7e3ad6b6992b"}, "__new_primary_file_unique\|0.32__": {"src": "hda", "id": "87dca8aa4ee9d3de", "uuid": "6523651c-1ec4-4bd0-b61c-43cff9a14b35"}, "__new_primary_file_unique\|0.27__": {"src": "hda", "id": "a96f5ebdac2d8d75", "uuid": "276db109-89f3-4bc8-95bb-f5ed726886fc"}, "__new_primary_file_unique\|0.19__": {"src": "hda", "id": "fb9b740929ea3f54", "uuid": "8f1f88dd-1218-4481-922a-a4d0407edc75"}, "__new_primary_file_unique\|0.01__": {"src": "hda", "id": "1c6e228e19b11e1b", "uuid": "79e53fa2-5eca-41cb-94b5-6294a1de4784"}, "__new_primary_file_unique\|0.24__": {"src": "hda", "id": "08fbf3fbfe908f7c", "uuid": "afa5db0d-aef3-48f8-8272-f62179616e19"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "2987a55ca6380b3a", "uuid": "9ed42128-8ed0-4fb0-8899-f3675ff10a2c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > bin.seqs(fasta=fasta.dat,list=otu.dat)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.unique.fasta\notu.0.01.fasta\notu.0.02.fasta\notu.0.03.fasta\notu.0.04.fasta\notu.0.05.fasta\notu.0.06.fasta\notu.0.07.fasta\notu.0.08.fasta\notu.0.09.fasta\notu.0.10.fasta\notu.0.11.fasta\notu.0.12.fasta\notu.0.13.fasta\notu.0.14.fasta\notu.0.15.fasta\notu.0.16.fasta\notu.0.17.fasta\notu.0.18.fasta\notu.0.19.fasta\notu.0.20.fasta\notu.0.21.fasta\notu.0.22.fasta\notu.0.23.fasta\notu.0.24.fasta\notu.0.25.fasta\notu.0.26.fasta\notu.0.27.fasta\notu.0.29.fasta\notu.0.32.fasta\notu.0.33.fasta\notu.0.36.fasta\notu.0.38.fasta\notu.0.41.fasta\notu.0.45.fasta\notu.0.55.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s 'None' name.dat && ln -s 'None' group.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_45.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_46.dat' otu.dat && ln -s 'None' count.dat && echo 'bin.seqs( fasta=fasta.dat, list=otu.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:52:03.131907", "params": {"count": "null", "group": "null", "name": "null", "dbkey": "\"hg17\"", "label": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7287", "id": "27a22803849b1486", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_bin_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "f1e243926043ec87"}, "label": ["0.03", "0.05", "0.22"], "group": {"src": "hda", "id": "19ec6936a7590160"}, "otu": {"src": "hda", "id": "73de4610aed2490c"}, "name": {"src": "hda", "id": "df545be7ad5cd764"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "f1e243926043ec87", "uuid": "c435f069-2cb4-401d-b4b6-f13dc04e0f48"}, "group": {"src": "hda", "id": "19ec6936a7590160", "uuid": "d4862a29-d42f-4c4c-8200-bb560e04e0fc"}, "name": {"src": "hda", "id": "df545be7ad5cd764", "uuid": "cf3ab84b-8a5c-46d0-b016-c567300ff9bd"}, "otu": {"src": "hda", "id": "73de4610aed2490c", "uuid": "630b9f6c-7e41-453f-a3a1-1e61ce6cbf73"}}, "update_time": "2018-02-08T16:52:37.247581", "tool_id": "mothur_bin_seqs", "outputs": {"__new_primary_file_0.22\|0.22__": {"src": "hda", "id": "97f8596e58df898c", "uuid": "76baa1ae-3604-4d9c-b169-ccc567946ec3"}, "logfile": {"src": "hda", "id": "330fe5822b24a25f", "uuid": "5acd7d94-805c-4499-a898-0b4846b38603"}, "__new_primary_file_0.22\|0.05__": {"src": "hda", "id": "adcc13f516c5d573", "uuid": "d5c89c69-11b2-4bc4-a480-785f8f546e38"}, "__new_primary_file_0.22\|0.03__": {"src": "hda", "id": "3d556e8e35b754dc", "uuid": "1fe58d24-effc-454d-b5f8-aec9adaed90d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > bin.seqs(name=name.dat,group=group.dat,label=0.03-0.05-0.22,fasta=fasta \r.dat,list=otu.dat)\n0.03\n0.05\n0.22\n\nOutput File Names: \notu.0.03.fasta\notu.0.05.fasta\notu.0.22.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_86.dat' name.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_87.dat' group.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_84.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_85.dat' otu.dat && ln -s 'None' count.dat && echo 'bin.seqs( name=name.dat, group=group.dat, label=0.03-0.05-0.22, fasta=fasta.dat, list=otu.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:52:34.180038", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\", \"0.22\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7458", "id": "95a5ac7e4618a243", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_bin_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"biom": {"src": "hda", "id": "e5cd870596a22f3d"}}, "job": {"inputs": {"biom": {"src": "hda", "id": "e5cd870596a22f3d", "uuid": "67321c4f-07f3-4496-a259-7d117cea03f2"}}, "update_time": "2018-02-08T16:52:54.726633", "tool_id": "mothur_biom_info", "outputs": {"shared": {"src": "hda", "id": "8e7a170d28bd3e46", "uuid": "4f910a6e-fda9-42b8-a952-3a560dba90af"}, "logfile": {"src": "hda", "id": "4923f2d7e29ffb4f", "uuid": "8176bc7a-5017-4c4b-9111-1e9c7ffb0df8"}, "tax.summary": {"src": "hda", "id": "facf9cd8e60ad8cf", "uuid": "97fe1137-5c9b-460b-8428-ac899fa45989"}, "taxonomy": {"src": "hda", "id": "2fd653ff8fe916b4", "uuid": "827a2b58-7246-42d2-b94f-3b732d61fefb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > biom.info(biom=input.biom,label=userLabel,basis=otu,output=simple,relab \rund=F,printlevel=-1)\n\nuserLabel\n\nIt took 0 create mothur files from your biom file.\n\n\nOutput File Names: \ninput.userLabel.shared\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_92.dat' input.biom && echo 'biom.info( biom=input.biom, label=userLabel, basis=otu, output=simple, relabund=F, printlevel=-1 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:52:51.473940", "params": {"relabund": "\"false\"", "basis": "\"otu\"", "dbkey": "\"hg17\"", "label": "\"userLabel\"", "printlevel": "\"-1\"", "output": "\"simple\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7557", "id": "a068cbb083194156", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_biom_info.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"biom": {"src": "hda", "id": "27a98c5f1b1968ef"}}, "job": {"inputs": {"biom": {"src": "hda", "id": "27a98c5f1b1968ef", "uuid": "b908b050-c74b-4347-9782-3755018efab3"}}, "update_time": "2018-02-08T16:53:12.209875", "tool_id": "mothur_biom_info", "outputs": {"shared": {"src": "hda", "id": "c0ae89d2a79fffb2", "uuid": "f4472a81-c659-4978-8fd9-e91063d57521"}, "logfile": {"src": "hda", "id": "4f5573cc87ed03c8", "uuid": "49be22ce-821c-47e7-9b1a-0a27db8b435f"}, "tax.summary": {"src": "hda", "id": "b028110e32789f9f", "uuid": "29e87425-3e47-45a2-82d6-ec9b97531e8d"}, "taxonomy": {"src": "hda", "id": "7e4191b982566cec", "uuid": "01441a21-25e1-4649-a372-5bc7e9f9732f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > biom.info(biom=input.biom,label=userLabel,basis=otu,output=simple,relab \rund=F,printlevel=-1)\n\nuserLabel\n\nIt took 0 create mothur files from your biom file.\n\n\nOutput File Names: \ninput.userLabel.shared\ninput.userLabel.cons.taxonomy\ninput.userLabel.cons.tax.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_97.dat' input.biom && echo 'biom.info( biom=input.biom, label=userLabel, basis=otu, output=simple, relabund=F, printlevel=-1 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:53:09.050031", "params": {"relabund": "\"false\"", "basis": "\"otu\"", "dbkey": "\"hg17\"", "label": "\"userLabel\"", "printlevel": "\"-1\"", "output": "\"simple\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7642", "id": "f16a54a3ef316466", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_biom_info.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"basis": "sequence", "output": "detail", "printlevel": "4", "label": "0.03", "biom": {"src": "hda", "id": "2aec3223e9c2f754"}}, "job": {"inputs": {"biom": {"src": "hda", "id": "2aec3223e9c2f754", "uuid": "ceb35272-ae07-460b-9c0f-c4287106f26d"}}, "update_time": "2018-02-08T16:53:39.840477", "tool_id": "mothur_biom_info", "outputs": {"shared": {"src": "hda", "id": "0a3452e55f15c193", "uuid": "88445107-8ce0-4cdf-9706-fbaa9b955b00"}, "logfile": {"src": "hda", "id": "20de7af3d288c35f", "uuid": "2c3d7d5f-12eb-4fe3-96f6-aed61451fdbd"}, "tax.summary": {"src": "hda", "id": "bd73887c155f3ede", "uuid": "b29a8bcb-c556-4272-8253-f2be5dcca19d"}, "taxonomy": {"src": "hda", "id": "7f39b8b663207ef1", "uuid": "6b18fa32-dd9f-4bcb-9063-7deafdd5c733"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > biom.info(biom=input.biom,label=0.03,basis=sequence,output=detail,relab \rund=F,printlevel=4)\n\n0.03\n\nIt took 0 create mothur files from your biom file.\n\n\nOutput File Names: \ninput.0.03.shared\ninput.0.03.cons.taxonomy\ninput.0.03.cons.tax.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_102.dat' input.biom && echo 'biom.info( biom=input.biom, label=0.03, basis=sequence, output=detail, relabund=F, printlevel=4 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:53:36.530476", "params": {"relabund": "\"false\"", "basis": "\"sequence\"", "dbkey": "\"hg17\"", "label": "\"0.03\"", "printlevel": "\"4\"", "output": "\"detail\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7734", "id": "25f486d5fc93a1ce", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_biom_info.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "69ce05044577833e"}, "window": "-1"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "69ce05044577833e", "uuid": "4a4ca0f1-a747-4892-9e90-04b34813c88f"}}, "update_time": "2018-02-08T16:54:07.782597", "tool_id": "mothur_chimera_bellerophon", "outputs": {"bellerophon.chimeras": {"src": "hda", "id": "3654d500199ce491", "uuid": "b675145d-c6c4-42df-a6e9-e4f20f2707e6"}, "logfile": {"src": "hda", "id": "4942bca139ae755c", "uuid": "b79f6a27-827d-490c-bd89-c79da2102d71"}, "bellerophon.accnos": {"src": "hda", "id": "a46b181036e98e92", "uuid": "ebae94f6-1fe2-4c17-baa8-2a033cd00057"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.bellerophon(fasta=fasta.dat,filter=False,correction=True,increm \rent=25,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\nReading sequences from fasta.dat...Done.\nProcessing sliding window: 5\nM00967_43_000000000-A3JHG_1_1101_10073_7632 is a suspected chimera at breakpoint 88\nIt's score is 1.6254 with suspected left parent M00967_43_000000000-A3JHG_1_1101_8480_7498 and right parent M00967_43_000000000-A3JHG_1_1101_8480_7498\nM00967_43_000000000-A3JHG_1_1101_8480_7498 is a suspected chimera at breakpoint 88\nIt's score is 1.6254 with suspected left parent M00967_43_000000000-A3JHG_1_1101_10073_7632 and right parent M00967_43_000000000-A3JHG_1_1101_10073_7632\nM00967_43_000000000-A3JHG_1_1101_23552_5194 is a suspected chimera at breakpoint 138\nIt's score is 1.16994 with suspected left parent M00967_43_000000000-A3JHG_1_1101_7079_6722 and right parent M00967_43_000000000-A3JHG_1_1101_7079_6722\nM00967_43_000000000-A3JHG_1_1101_5170_7771 is a suspected chimera at breakpoint 138\nIt's score is 1.11972 with suspected left parent M00967_43_000000000-A3JHG_1_1101_13293_4703 and right parent M00967_43_000000000-A3JHG_1_1101_13293_4703\nM00967_43_000000000-A3JHG_1_1101_13293_4703 is a suspected chimera at breakpoint 138\nIt's score is 1.11972 with suspected left parent M00967_43_000000000-A3JHG_1_1101_11148_6457 and right parent M00967_43_000000000-A3JHG_1_1101_11148_6457\nM00967_43_000000000-A3JHG_1_1101_11148_6457 is a suspected chimera at breakpoint 138\nIt's score is 1.11972 with suspected left parent M00967_43_000000000-A3JHG_1_1101_13293_4703 and right parent M00967_43_000000000-A3JHG_1_1101_13293_4703\nM00967_43_000000000-A3JHG_1_1101_24357_4866 is a suspected chimera at breakpoint 138\nIt's score is 1.02604 with suspected left parent M00967_43_000000000-A3JHG_1_1101_11790_7581 and right parent M00967_43_000000000-A3JHG_1_1101_11790_7581\nM00967_43_000000000-A3JHG_1_1101_11790_7581 is a suspected chimera at breakpoint 138\nIt's score is 1.02604 with suspected left parent M00967_43_000000000-A3JHG_1_1101_24357_4866 and right parent M00967_43_000000000-A3JHG_1_1101_24357_4866\nM00967_43_000000000-A3JHG_1_1101_15923_3823 is a suspected chimera at breakpoint 138\nIt's score is 1.0226 with suspected left parent M00967_43_000000000-A3JHG_1_1101_7326_5417 and right parent M00967_43_000000000-A3JHG_1_1101_7326_5417\nM00967_43_000000000-A3JHG_1_1101_7326_5417 is a suspected chimera at breakpoint 138\nIt's score is 1.0226 with suspected left parent M00967_43_000000000-A3JHG_1_1101_15923_3823 and right parent M00967_43_000000000-A3JHG_1_1101_15923_3823\nM00967_43_000000000-A3JHG_1_1101_15208_7185 is a suspected chimera at breakpoint 138\nIt's score is 1.0226 with suspected left parent M00967_43_000000000-A3JHG_1_1101_15923_3823 and right parent M00967_43_000000000-A3JHG_1_1101_15923_3823\nM00967_43_000000000-A3JHG_1_1101_7079_6722 is a suspected chimera at breakpoint 138\nIt's score is 1.01583 with suspected left parent M00967_43_000000000-A3JHG_1_1101_23552_5194 and right parent M00967_43_000000000-A3JHG_1_1101_23552_5194\n\nSequence with preference score above 1.0: 12\nMinimum:\t0.682701\n2.5%-tile:\t0.682701\n25%-tile:\t0.837302\nMedian: \t1.01583\n75%-tile:\t1.11972\n97.5%-tile:\t1.6254\nMaximum:\t1.6254\n\nIt took 0 secs to check 22 sequences.\n\n\nOutput File Names: \nfasta.bellerophon.chimeras\nfasta.bellerophon.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_107.dat' fasta.dat && echo 'chimera.bellerophon( fasta=fasta.dat, filter=False, correction=True, increment=25, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:54:04.495851", "params": {"correction": "\"true\"", "dbkey": "\"hg17\"", "filter": "\"false\"", "window": "\"-1\"", "increment": "\"25\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7832", "id": "8c9b639396181d1e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_bellerophon.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "00c35829965cb81b"}, "alignment\|reference": {"src": "hda", "id": "566489874e32c504"}, "alignment\|source": "hist"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "00c35829965cb81b", "uuid": "67503ee2-ad54-4780-bde6-14f9662c2d6d"}, "reference": {"src": "hda", "id": "566489874e32c504", "uuid": "fe96ace6-a92a-47c6-b67d-573970b930d0"}}, "update_time": "2018-02-08T16:54:39.839013", "tool_id": "mothur_chimera_ccode", "outputs": {"ccode.chimeras": {"src": "hda", "id": "1fb9c7b21f94ef77", "uuid": "bc86b0c8-6d13-47d9-a386-f39638719b24"}, "logfile": {"src": "hda", "id": "e7d42a199e1d2420", "uuid": "b942c08b-5e97-4757-bb2c-3a4a440024ff"}, "ccode.accnos": {"src": "hda", "id": "c299b389e85e4513", "uuid": "4c11cc11-c934-41ef-887e-f3590ea4f715"}, "mapinfo": {"src": "hda", "id": "cf18f77993464b22", "uuid": "be0c8b32-7ab5-4dca-985b-17129a55606c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.ccode(fasta=fasta.dat,reference=alignment.template.dat,filter=F \ralse,numwanted=20,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\nReading sequences from alignment.template.dat...Done.\nM00967_43_000000000-A3JHG_1_1101_7326_5417 was found have at least one chimeric window.\nProcessing sequence: 10\n\nIt took 1 secs to check 10 sequences.\n\nOutput File Names: \nfasta.ccode.chimeras\nfasta.mapinfo\nfasta.ccode.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_111.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_112.dat' alignment.template.dat && echo 'chimera.ccode( fasta=fasta.dat, reference=alignment.template.dat, filter=False, numwanted=20, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:54:35.274166", "params": {"numwanted": "\"20\"", "dbkey": "\"hg17\"", "filter": "\"false\"", "window": "\"0\"", "mask_cond": "{\"source2\": \"\", \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 112}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7952", "id": "25cc0305829779de", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_ccode.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "7ea23f5e4ed72fcd"}, "alignment\|reference": {"src": "hda", "id": "161ef5576377f4a0"}, "window": "100", "alignment\|source": "hist", "mask_cond\|source2": "default"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "7ea23f5e4ed72fcd", "uuid": "a7f568a1-096d-4715-a052-f419660e59b2"}, "reference": {"src": "hda", "id": "161ef5576377f4a0", "uuid": "871b1483-4128-403f-b26a-080be516b889"}}, "update_time": "2018-02-08T16:55:13.593399", "tool_id": "mothur_chimera_ccode", "outputs": {"ccode.chimeras": {"src": "hda", "id": "f21e60058e4146e2", "uuid": "9e3f3299-f941-4c90-854e-f0c9c1e461e6"}, "logfile": {"src": "hda", "id": "ba60dc8fe2d987d5", "uuid": "d2c0e7c6-bcc6-4632-a668-37944112eef9"}, "ccode.accnos": {"src": "hda", "id": "4826aef2afaebe4b", "uuid": "5b78ccd6-a9c6-4fff-b063-175f0412a1e5"}, "mapinfo": {"src": "hda", "id": "c95281174db2641a", "uuid": "92ac37ff-50a5-4ad1-b132-a261727351bf"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.ccode(fasta=fasta.dat,reference=alignment.template.dat,filter=F \ralse,mask=default,window=100,numwanted=20,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\nI am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013.\nReading sequences from alignment.template.dat...Done.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_19936_3208 does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity. I will continue, but please check.\nM00967_43_000000000-A3JHG_1_1101_19936_3208 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_15923_3823 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_14010_4122 does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity. I will continue, but please check.\nM00967_43_000000000-A3JHG_1_1101_14010_4122 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_13293_4703 does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity. I will continue, but please check.\nM00967_43_000000000-A3JHG_1_1101_13293_4703 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_24357_4866 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_23552_5194 does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity. I will continue, but please check.\nM00967_43_000000000-A3JHG_1_1101_23552_5194 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_7326_5417 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_11148_6457 does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity. I will continue, but please check.\nM00967_43_000000000-A3JHG_1_1101_11148_6457 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_7079_6722 does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity. I will continue, but please check.\nM00967_43_000000000-A3JHG_1_1101_7079_6722 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_8607_6805 does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity. I will continue, but please check.\nM00967_43_000000000-A3JHG_1_1101_8607_6805 was found have at least one chimeric window.\nProcessing sequence: 10\n\nIt took 1 secs to check 10 sequences.\n\nOutput File Names: \nfasta.default.ccode.chimeras\nfasta.mapinfo\nfasta.default.ccode.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_117.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_118.dat' alignment.template.dat && echo 'chimera.ccode( fasta=fasta.dat, reference=alignment.template.dat, filter=False, mask=default, window=100, numwanted=20, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:55:09.142586", "params": {"numwanted": "\"20\"", "dbkey": "\"hg17\"", "filter": "\"false\"", "window": "\"100\"", "mask_cond": "{\"source2\": \"default\", \"__current_case__\": 2}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 118}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8064", "id": "bab99c776d4b9391", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_ccode.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "bd8ef6624a47d26f"}, "alignment\|reference": {"src": "hda", "id": "39209c3a4b0cef4c"}, "alignment\|source": "hist"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "bd8ef6624a47d26f", "uuid": "afb976b9-ef60-4b12-a931-c027c8cef9a2"}, "reference": {"src": "hda", "id": "39209c3a4b0cef4c", "uuid": "9e147cf5-6480-4227-b024-e04e1e4ef7e2"}}, "update_time": "2018-02-08T16:55:49.157744", "tool_id": "mothur_chimera_check", "outputs": {"logfile": {"src": "hda", "id": "26b7e36460fca86e", "uuid": "a2a768ac-9391-4632-9810-2d0d9c806298"}, "chimeracheck.chimeras": {"src": "hda", "id": "eb21622d9b6e26b4", "uuid": "d6031a8a-cb57-41e2-98e2-ed5829d4972d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.check(fasta=fasta.dat,reference=alignment.reference.dat,increme \rnt=10,ksize=7,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\n\nReading in the alignment.reference.dat template sequences...\tDONE.\nIt took 0 to read 32 sequences.\n\nProcessing: M00967_43_000000000-A3JHG_1_1101_19936_3208\nProcessing: M00967_43_000000000-A3JHG_1_1101_15923_3823\nProcessing: M00967_43_000000000-A3JHG_1_1101_14010_4122\nProcessing: M00967_43_000000000-A3JHG_1_1101_13293_4703\nProcessing: M00967_43_000000000-A3JHG_1_1101_24357_4866\nProcessing: M00967_43_000000000-A3JHG_1_1101_23552_5194\nProcessing: M00967_43_000000000-A3JHG_1_1101_7326_5417\nProcessing: M00967_43_000000000-A3JHG_1_1101_11148_6457\nProcessing: M00967_43_000000000-A3JHG_1_1101_7079_6722\nProcessing: M00967_43_000000000-A3JHG_1_1101_8607_6805\nProcessing sequence: 10\n\nThis method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values.\n\nIt took 3 secs to check 10 sequences.\n\n\nOutput File Names: \nfasta.chimeracheck.chimeras\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_123.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_124.dat' alignment.reference.dat && echo 'chimera.check( fasta=fasta.dat, reference=alignment.reference.dat, increment=10, ksize=7, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:55:43.089163", "params": {"svg_cond": "{\"svg\": \"no\", \"__current_case__\": 0}", "dbkey": "\"hg17\"", "ksize": "\"7\"", "increment": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 124}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8186", "id": "5e6ad6ca0afeaf24", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_check.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "598efe8f302ea8ae"}, "svg_cond\|name": {"src": "hda", "id": "e9cf7d8d4867436b"}, "svg_cond\|svg": "yes", "alignment\|source": "hist", "alignment\|reference": {"src": "hda", "id": "5c14fa19c3fe9aa2"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "598efe8f302ea8ae", "uuid": "9ddbdf54-67b8-4edd-a6e9-bb7604e31dc4"}, "name": {"src": "hda", "id": "e9cf7d8d4867436b", "uuid": "75ab04f2-b35c-467b-88d1-a899fa003606"}, "reference": {"src": "hda", "id": "5c14fa19c3fe9aa2", "uuid": "9a079bc8-ceb1-4c5e-82df-a59c14e77494"}}, "update_time": "2018-02-08T16:56:16.969800", "tool_id": "mothur_chimera_check", "outputs": {"logfile": {"src": "hda", "id": "fc5c2ad70cbb4f9f", "uuid": "ac4cefa6-bfaa-4401-be90-336ca98d7b8f"}, "__new_primary_file_M00967_43_000000000-A3JHG_1_1101_14010_4122\|M00967_43_000000000-A3JHG_1_1101_14010_4122__": {"src": "hda", "id": "83e248eabb1b3d31", "uuid": "9000d45e-4973-4578-99f2-617d128cb499"}, "chimeracheck.chimeras": {"src": "hda", "id": "5e985d59d5900484", "uuid": "e280ac0c-fac1-4b3c-a13d-b7885916062b"}, "__new_primary_file_M00967_43_000000000-A3JHG_1_1101_14010_4122\|M00967_43_000000000-A3JHG_1_1101_13293_4703__": {"src": "hda", "id": "2f2abd7e16b39826", "uuid": "bbdec5e0-e4dc-448a-9007-43d0b3a0f8d0"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.check(fasta=fasta.dat,reference=alignment.reference.dat,svg=yes \r,name=svg.name.dat,increment=10,ksize=7,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\n\nReading in the alignment.reference.dat template sequences...\tDONE.\nIt took 0 to read 32 sequences.\n\nProcessing: M00967_43_000000000-A3JHG_1_1101_19936_3208\nProcessing: M00967_43_000000000-A3JHG_1_1101_15923_3823\nProcessing: M00967_43_000000000-A3JHG_1_1101_14010_4122\nProcessing: M00967_43_000000000-A3JHG_1_1101_13293_4703\nProcessing: M00967_43_000000000-A3JHG_1_1101_24357_4866\nProcessing: M00967_43_000000000-A3JHG_1_1101_23552_5194\nProcessing: M00967_43_000000000-A3JHG_1_1101_7326_5417\nProcessing: M00967_43_000000000-A3JHG_1_1101_11148_6457\nProcessing: M00967_43_000000000-A3JHG_1_1101_7079_6722\nProcessing: M00967_43_000000000-A3JHG_1_1101_8607_6805\nProcessing sequence: 10\n\nThis method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values.\n\nIt took 3 secs to check 10 sequences.\n\n\nOutput File Names: \nfasta.chimeracheck.chimeras\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_127.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_128.dat' alignment.reference.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_129.dat' svg.name.dat && echo 'chimera.check( fasta=fasta.dat, reference=alignment.reference.dat, svg=yes, name=svg.name.dat, increment=10, ksize=7, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:56:10.148586", "params": {"svg_cond": "{\"svg\": \"yes\", \"name\": {\"values\": [{\"src\": \"hda\", \"id\": 129}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\"", "ksize": "\"7\"", "increment": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 128}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8324", "id": "48f3e8809447c25a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_check.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "a01e20e32f0965d9"}, "name": {"src": "hda", "id": "4e27b888e0f89616"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "a01e20e32f0965d9", "uuid": "8521e069-b6cd-4c45-b6e5-8f7e69e73bba"}, "name": {"src": "hda", "id": "4e27b888e0f89616", "uuid": "491e5558-aa9e-46c8-846f-1bbb96a90abb"}}, "update_time": "2018-02-08T16:56:43.817915", "tool_id": "mothur_chimera_perseus", "outputs": {"out_chimeras": {"src": "hda", "id": "d760e1d92679b730", "uuid": "b722e5b1-053c-44cf-a2f8-7286ea3d18e4"}, "logfile": {"src": "hda", "id": "15839f6e830b1abe", "uuid": "420f680c-4cb1-4cdf-8752-30f636784f1e"}, "out_accnos": {"src": "hda", "id": "237cecdf0f984d5b", "uuid": "ea9ffc98-afb0-4985-86d3-80850d6525a1"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.perseus(fasta=fasta.dat,name=name.dat,alpha=-5.54,beta=0.33,cut \roff=0.5,dereplicate=false,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\nProcessing sequence: 98\n\nIt took 0 secs to check 98 sequences. 0 chimeras were found.\n\nOutput File Names: \nfasta.perseus.chimeras\nfasta.perseus.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_134.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_135.dat' name.dat && ln -s 'None' group.dat && echo 'chimera.perseus( fasta=fasta.dat, name=name.dat, alpha=-5.54, beta=0.33, cutoff=0.5, dereplicate=false, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:56:40.622188", "params": {"dereplicate": "\"false\"", "group": "null", "cutoff": "\"0.5\"", "dbkey": "\"hg17\"", "beta": "\"0.33\"", "alpha": "\"-5.54\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8441", "id": "b908d9d86f8a3d36", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_perseus.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"alignment\|source": "hist", "quantile": {"src": "hda", "id": "449eb427f528cea7"}, "window": "200", "fasta": {"src": "hda", "id": "3995f2aeb4b1e9b8"}, "alignment\|reference": {"src": "hda", "id": "43c20e86f8351b08"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "3995f2aeb4b1e9b8", "uuid": "1b6d12bd-53eb-4adf-a8c9-2d517a1a06c2"}, "quantile": {"src": "hda", "id": "449eb427f528cea7", "uuid": "0dac3ed3-c5b1-4c88-a6cd-a09f73785ecb"}, "reference": {"src": "hda", "id": "43c20e86f8351b08", "uuid": "88a5d249-7780-4cc3-905d-5a78e67947c0"}}, "update_time": "2018-02-08T16:57:10.496322", "tool_id": "mothur_chimera_pintail", "outputs": {"out_freq": {"src": "hda", "id": "8bfda5654e551614", "uuid": "ea730516-89b4-498e-ba79-cba6bea15f91"}, "logfile": {"src": "hda", "id": "05698cd4bb850c59", "uuid": "2f32594b-954f-4c6e-bb7f-10246c03305d"}, "out_accnos": {"src": "hda", "id": "4674f339b90935da", "uuid": "bbe2d533-8860-40b9-8ce5-7fe8ea944655"}, "pintail.chimeras": {"src": "hda", "id": "bfa55a0374b9a6bf", "uuid": "d9543da6-6d05-4a3f-9017-9b3eb6fa0d4f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.pintail(fasta=fasta.dat,reference=alignment.reference.dat,filte \rr=false,quantile=quantile.dat,window=200,increment=25,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\nReading sequences from alignment.reference.dat...Done.\nGetting conservation... Calculating probability of conservation for your template sequences. This can take a while... I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command. Providing the .freq file will improve speed. Done.\n\nM00967_43_000000000-A3JHG_1_1101_15923_3823\tdiv: 26.9841\tstDev: 1.41584\tchimera flag: Yes\nM00967_43_000000000-A3JHG_1_1101_13293_4703\tdiv: 29.3651\tstDev: 1.59916\tchimera flag: Yes\nM00967_43_000000000-A3JHG_1_1101_24357_4866\tdiv: 26.5873\tstDev: 1.39697\tchimera flag: Yes\nM00967_43_000000000-A3JHG_1_1101_11148_6457\tdiv: 29.3651\tstDev: 1.59916\tchimera flag: Yes\nProcessing sequence: 10\n\n\nIt took 2 secs to check 10 sequences.\n\nOutput File Names: \nfasta.pintail.chimeras\nfasta.pintail.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_139.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_140.dat' alignment.reference.dat && ln -s 'None' conservation.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_141.dat' quantile.dat && echo 'chimera.pintail( fasta=fasta.dat, reference=alignment.reference.dat, filter=false, quantile=quantile.dat, window=200, increment=25, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:57:04.307339", "params": {"increment": "\"25\"", "dbkey": "\"hg17\"", "filter": "\"false\"", "window": "\"200\"", "conservation": "null", "mask_cond": "{\"source2\": \"\", \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 140}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8577", "id": "087a78e08fef416e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_pintail.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "7959e4ab20d6a14d"}, "alignment\|reference": {"src": "hda", "id": "54ea706d2daa88f1"}, "window": "200", "alignment\|source": "hist", "mask_cond\|source2": "default"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "7959e4ab20d6a14d", "uuid": "6839dbc1-616a-4882-96ea-ce6b374044f0"}, "reference": {"src": "hda", "id": "54ea706d2daa88f1", "uuid": "a32c495f-3e9b-4732-8ec6-129955955c3b"}}, "update_time": "2018-02-08T16:57:38.924061", "tool_id": "mothur_chimera_pintail", "outputs": {"out_freq": {"src": "hda", "id": "2567f547ea0518b1", "uuid": "d49dd2af-548c-4371-838d-2da9e7ca1379"}, "logfile": {"src": "hda", "id": "0b8510c6952c9474", "uuid": "e114c580-5d03-48e9-81c5-8cdccff4565a"}, "out_accnos": {"src": "hda", "id": "db1aec3269b07642", "uuid": "07a38fd5-d854-4740-bf6b-281d87ca512b"}, "pintail.chimeras": {"src": "hda", "id": "c48fc7b200585e1b", "uuid": "457f3666-d072-481c-a032-41dc8ed38044"}, "out_quantile": {"src": "hda", "id": "ac2ea1acb48016aa", "uuid": "eb5bca93-0ccf-4b62-a247-6ddd34b86c46"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.pintail(fasta=fasta.dat,reference=alignment.reference.dat,filte \rr=false,mask=default,window=200,increment=25,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\nI am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013.\nReading sequences from alignment.reference.dat...Done.\nGetting conservation... Calculating probability of conservation for your template sequences. This can take a while... I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command. Providing the .freq file will improve speed. Done.\n\nCalculating quantiles for your template. This can take a while... I will output the quantiles to a .quan file that you can input them using the quantiles parameter next time you run this command. Providing the .quan file will dramatically improve speed. Processing sequence 0\nProcessing sequence 1\nYou have selected too large a window size for sequence A.odontolyticus.1. I will choose an appropriate window size.\nProcessing sequence 2\nYou have selected too large a window size for sequence B.cereus.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.cereus.1. I will choose an appropriate window size.\nProcessing sequence 3\nYou have selected too large a window size for sequence B.vulgatus.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.1. I will choose an appropriate window size.\nProcessing sequence 4\nYou have selected too large a window size for sequence B.vulgatus.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.2. I will choose an appropriate window size.\nProcessing sequence 5\nYou have selected too large a window size for sequence B.vulgatus.4. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.4. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.4. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.4. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.4. I will choose an appropriate window size.\nProcessing sequence 6\nYou have selected too large a window size for sequence B.vulgatus.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.5. I will choose an appropriate window size.\nProcessing sequence 7\nYou have selected too large a window size for sequence B.vulgatus.7. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.7. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.7. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.7. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.7. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.7. I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.7. I will choose an appropriate window size.\nProcessing sequence 8\nYou have selected too large a window size for sequence C.beijerinckii.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.1. I will choose an appropriate window size.\nProcessing sequence 9\nYou have selected too large a window size for sequence C.beijerinckii.3. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.3. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.3. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.3. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.3. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.3. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.3. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.3. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.3. I will choose an appropriate window size.\nProcessing sequence 10\nYou have selected too large a window size for sequence C.beijerinckii.4. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4. I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4. I will choose an appropriate window size.\nProcessing sequence 11\nYou have selected too large a window size for sequence D.radiodurans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1. I will choose an appropriate window size.\nProcessing sequence 12\nYou have selected too large a window size for sequence E.faecalis.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1. I will choose an appropriate window size.\nProcessing sequence 13\nYou have selected too large a window size for sequence E.faecalis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2. I will choose an appropriate window size.\nProcessing sequence 14\nYou have selected too large a window size for sequence E.coli.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1. I will choose an appropriate window size.\nProcessing sequence 15\nYou have selected too large a window size for sequence H.pylori.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1. I will choose an appropriate window size.\nProcessing sequence 16\nYou have selected too large a window size for sequence L.gasseri.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence L.gasseri.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence L.gasseri.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence L.gasseri.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence L.gasseri.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence L.gasseri.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence L.gasseri.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence L.gasseri.1. I will choose an appropriate window size.\nYou have selected too large a window size f\n..\nte window size.\nYou have selected too large a window size for sequence S.epidermidis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2. I will choose an appropriate window size.\nProcessing sequence 28\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5. I will choose an appropriate window size.\nProcessing sequence 29\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1. I will choose an appropriate window size.\nProcessing sequence 30\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1. I will choose an appropriate window size.\nProcessing sequence 31\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1. I will choose an appropriate window size.\nDone.\nReading sequences from alignment.reference.dat...Done.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_19936_3208. I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_15923_3823. I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_14010_4122. I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_13293_4703. I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_24357_4866. I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_23552_5194. I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_7326_5417. I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_11148_6457. I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_7079_6722. I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_8607_6805. I will choose an appropriate window size.\nProcessing sequence: 10\n\n\nIt took 3 secs to check 10 sequences.\n\nOutput File Names: \nfasta.default.pintail.chimeras\nfasta.default.pintail.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_146.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_147.dat' alignment.reference.dat && ln -s 'None' conservation.dat && ln -s 'None' quantile.dat && echo 'chimera.pintail( fasta=fasta.dat, reference=alignment.reference.dat, filter=false, mask=default, window=200, increment=25, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:57:32.943369", "params": {"increment": "\"25\"", "quantile": "null", "dbkey": "\"hg17\"", "filter": "\"false\"", "window": "\"200\"", "conservation": "null", "mask_cond": "{\"source2\": \"default\", \"__current_case__\": 2}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 147}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8698", "id": "5617b66919498d02", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_pintail.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "3af8c7b9f683116f"}, "alignment\|reference": {"src": "hda", "id": "d7d0eb8e9bed0c39"}, "alignment\|source": "hist"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "3af8c7b9f683116f", "uuid": "0c3c0bcd-0458-4195-af6b-c079b4996632"}, "reference": {"src": "hda", "id": "d7d0eb8e9bed0c39", "uuid": "96ffc55e-61f9-4e01-b8b1-5d270f2f9d1a"}}, "update_time": "2018-02-08T16:58:10.044025", "tool_id": "mothur_chimera_slayer", "outputs": {"slayer.chimeras": {"src": "hda", "id": "3f47e446edb5d442", "uuid": "f920d4ae-4e8c-4f4e-b1c9-386711a26402"}, "logfile": {"src": "hda", "id": "b7d4a98a7bb9e1bc", "uuid": "ba043b24-a39a-41e6-bffc-0e07740ed585"}, "out_accnos": {"src": "hda", "id": "8984b162f62c6c24", "uuid": "19589feb-b856-43dd-a3ee-1441b657ddea"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.slayer(fasta=fasta.dat,reference=/tmp/saskia/tmpKSDp0p/files/00 \r0/dataset_154.dat,dereplicate=false,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\nReading sequences from /tmp/saskia/tmpKSDp0p/files/000/dataset_154.dat...Done.\n\nOnly reporting sequence supported by 90% of bootstrapped results.\nProcessing sequence: 10\nIt took 0 secs to check 10 sequences.\n\nOutput File Names: \nfasta.slayer.chimeras\nfasta.slayer.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s ln -s `dirname $(which mothur)`/* . && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_153.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_154.dat' alignment.reference.dat && echo 'chimera.slayer( fasta=fasta.dat, reference=/tmp/saskia/tmpKSDp0p/files/000/dataset_154.dat, dereplicate=false, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| ./mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:58:06.756216", "params": {"dereplicate": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 154}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\"", "options": "{\"setby\": \"default\", \"__current_case__\": 0}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8814", "id": "b323ca264f40001e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_slayer.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"options\|setby": "user", "fasta": {"src": "hda", "id": "50c648a3603e917e"}, "options\|search": "kmer", "alignment\|source": "self", "alignment\|name": {"src": "hda", "id": "71db30c33f7a1d97"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "50c648a3603e917e", "uuid": "b5946a78-cf06-49cd-baed-908c4ba5a099"}, "name": {"src": "hda", "id": "71db30c33f7a1d97", "uuid": "e5af7032-d15c-490d-8f99-315bab985aaa"}}, "update_time": "2018-02-08T16:58:30.636077", "tool_id": "mothur_chimera_slayer", "outputs": {"slayer.chimeras": {"src": "hda", "id": "c6239e5379f31f0f", "uuid": "bbdfd559-4c07-4742-adbe-c98f6e5d5f3e"}, "logfile": {"src": "hda", "id": "9c12fd6a3ba76792", "uuid": "c3deba55-280e-4a02-bc5c-7777f998fa52"}, "out_accnos": {"src": "hda", "id": "4d003f3f8bfebf53", "uuid": "8dde0258-7d7d-4cee-9ee3-4d5f186b4acb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.slayer(fasta=fasta.dat,reference=self,name=/tmp/saskia/tmpKSDp0 \rp/files/000/dataset_159.dat,search=kmer,window=50,increment=5,match=5,mismatch=- \r4,numwanted=15,parents=3,minsim=90,mincov=70,iters=1000,minbs=90,minsnp=10,diver \rgence=1.007,trim=false,split=false,dereplicate=false,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\nSorting fastafile according to abundance...Done.\nReading sequences from fasta.dat...Done.\n\nOnly reporting sequence supported by 90% of bootstrapped results.\nProcessing sequence: 32\nIt took 0 secs to check 32 sequences.\n\nOutput File Names: \nfasta.slayer.chimeras\nfasta.slayer.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s ln -s `dirname $(which mothur)`/* . && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_158.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_159.dat' alignment.name.dat && ln -s 'None' alignment.group.dat && ln -s 'None' alignment.count.dat && echo 'chimera.slayer( fasta=fasta.dat, reference=self, name=/tmp/saskia/tmpKSDp0p/files/000/dataset_159.dat, search=kmer, window=50, increment=5, match=5, mismatch=-4, numwanted=15, parents=3, minsim=90, mincov=70, iters=1000, minbs=90, minsnp=10, divergence=1.007, trim=false, split=false, dereplicate=false, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| ./mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:58:27.298736", "params": {"dereplicate": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"count\": null, \"source\": \"self\", \"group\": null, \"name\": {\"values\": [{\"src\": \"hda\", \"id\": 159}]}, \"__current_case__\": 2}", "dbkey": "\"hg17\"", "options": "{\"trim\": \"false\", \"mincov\": \"70\", \"search\": \"kmer\", \"numwanted\": \"15\", \"increment\": \"5\", \"iters\": \"1000\", \"divergence\": \"1.007\", \"mismatch\": \"-4\", \"minsnp\": \"10\", \"window\": \"50\", \"parents\": \"3\", \"split\": \"false\", \"__current_case__\": 1, \"minsim\": \"90\", \"setby\": \"user\", \"minbs\": \"90\", \"match\": \"5\"}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8976", "id": "b31f4d82ada5e956", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_slayer.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "cd5f25030bbf4788"}, "template\|source": "hist", "template\|reference": {"src": "hda", "id": "c32d13cb5f20eb1c"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "cd5f25030bbf4788", "uuid": "1e26bb54-6b57-4320-9a90-ff58a5d3684d"}, "reference": {"src": "hda", "id": "c32d13cb5f20eb1c", "uuid": "c08ca8ce-f149-457f-b640-d65b8ffd0a69"}}, "update_time": "2018-02-08T16:58:51.128610", "tool_id": "mothur_chimera_uchime", "outputs": {"out_count": {"src": "hda", "id": "c011a4b8aa5812a2", "uuid": "34e4372e-3ac7-4a13-8dce-eed7ac1cc51a"}, "logfile": {"src": "hda", "id": "33d716567e7a5529", "uuid": "266a88bd-2fe5-4e91-a8f8-92b3dbfd7eb3"}, "out_accnos": {"src": "hda", "id": "b0fc776b5139d032", "uuid": "7c5c28ae-4502-404e-828e-9c8d3d2949b0"}, "uchime.chimeras": {"src": "hda", "id": "c9cd75d91880a01c", "uuid": "69d3f258-8abc-47ba-a723-57a96bdeea7c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.uchime(fasta=fasta.dat,reference=template.reference.dat,minh=0. \r3,mindiv=0.5,xn=8.0,dn=1.4,xa=1.0,chunks=4,minchunk=64,idsmoothwindow=32,maxp=2, \rminlen=10,maxlen=10000,skipgaps=true,skipgaps2=true,dereplicate=false,chimealns= \rfalse,processors=1)\n\nUsing 1 processors.\n/home/saskia/miniconda3/envs/__mothur@1.39.5/bin/mothuruchime file does not exist. Checking path... \nFound uchime in your path, using /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/uchime\n\nuchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\n\nChecking sequences from fasta.dat ...\nuchime v4.2.40\nby Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\n\n\nIt took 0 secs to check 3 sequences. 1 chimeras were found.\n\nOutput File Names: \nfasta.ref.uchime.chimeras\nfasta.ref.uchime.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_163.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_164.dat' template.reference.dat && echo 'chimera.uchime( fasta=fasta.dat, reference=template.reference.dat, minh=0.3, mindiv=0.5, xn=8.0, dn=1.4, xa=1.0, chunks=4, minchunk=64, idsmoothwindow=32, maxp=2, minlen=10, maxlen=10000, skipgaps=true, skipgaps2=true, dereplicate=false, chimealns=false, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log 2>&1", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:58:47.885084", "params": {"dn": "\"1.4\"", "dereplicate": "\"false\"", "minh": "\"0.3\"", "minchunk": "\"64\"", "xn": "\"8.0\"", "skipgaps2": "\"true\"", "minlen": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "maxp": "\"2\"", "xa": "\"1.0\"", "skipgaps": "\"true\"", "dbkey": "\"hg17\"", "maxlen": "\"10000\"", "mindiv": "\"0.5\"", "template": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 164}]}, \"__current_case__\": 1}", "chunks": "\"4\"", "idsmoothwindow": "\"32\"", "alignment": "{\"ucl\": \"global\", \"__current_case__\": 0}", "chimealns": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n00:00 31Mb 0.1% Reading fasta.dat.uchime_formatted\r00:00 31Mb 0.1% Reading fasta.dat.uchime_formatted\r\nWARNING: Ignoring gaps in FASTA file 'fasta.dat.uchime_formatted'\n00:00 31Mb 100.0% Reading fasta.dat.uchime_formatted\r\n00:00 31Mb 3 sequences \n00:00 32Mb 0.1% Reading template.reference.dat\r00:00 32Mb 0.1% Reading template.reference.dat\r00:00 32Mb 100.0% Reading template.reference.dat\r\n00:00 32Mb 32 sequences \n00:00 32Mb 33.3% 0/0 chimeras found (0.0%)\r00:00 32Mb 100.0% 1/2 chimeras found (33.3%)\r\n", "job_metrics": [], "model_class": "Job", "external_id": "9098", "id": "87dca8aa4ee9d3de", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_uchime.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "89c96313ae93d0a8"}, "template\|source": "self"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "89c96313ae93d0a8", "uuid": "5fd9ba22-20a6-490e-8491-5b27dc07ab63"}}, "update_time": "2018-02-08T16:59:13.498829", "tool_id": "mothur_chimera_uchime", "outputs": {"logfile": {"src": "hda", "id": "e78965a26b62ba53", "uuid": "b2eaa7cc-4350-4ca0-b3bf-3078bd04e439"}, "out_accnos": {"src": "hda", "id": "6fbaeb4019cd0c5e", "uuid": "68914b1b-7095-49ba-b798-c947f7d0315c"}, "uchime.chimeras": {"src": "hda", "id": "8b9818d7842d6e75", "uuid": "377b8759-870f-4f64-ac84-5c8c55c7be7a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.uchime(fasta=fasta.dat,reference=self,abskew=1.9,minh=0.3,mindi \rv=0.5,xn=8.0,dn=1.4,xa=1.0,chunks=4,minchunk=64,idsmoothwindow=32,maxp=2,minlen= \r10,maxlen=10000,skipgaps=true,skipgaps2=true,dereplicate=false,chimealns=false,p \rrocessors=1)\n\nUsing 1 processors.\n/home/saskia/miniconda3/envs/__mothur@1.39.5/bin/mothuruchime file does not exist. Checking path... \nFound uchime in your path, using /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/uchime\n\nuchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\n\nChecking sequences from fasta.dat ...\n\nNo namesfile given, running unique.seqs command to generate one.\n\n/****************************************/\nRunning command: unique.seqs(fasta=fasta.dat)\n10\t9\n\nOutput File Names: \nfasta.names\nfasta.unique.dat\n\n/***************************************/\nuchime v4.2.40\nby Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\n\n\nIt took 0 secs to check 9 sequences. 0 chimeras were found.\n\nOutput File Names: \nfasta.denovo.uchime.chimeras\nfasta.denovo.uchime.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_169.dat' fasta.dat && ln -s 'None' template.count.dat && ln -s 'None' template.group.dat && echo 'chimera.uchime( fasta=fasta.dat, reference=self, abskew=1.9, minh=0.3, mindiv=0.5, xn=8.0, dn=1.4, xa=1.0, chunks=4, minchunk=64, idsmoothwindow=32, maxp=2, minlen=10, maxlen=10000, skipgaps=true, skipgaps2=true, dereplicate=false, chimealns=false, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log 2>&1", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:59:10.293294", "params": {"dn": "\"1.4\"", "dereplicate": "\"false\"", "minh": "\"0.3\"", "minchunk": "\"64\"", "xn": "\"8.0\"", "skipgaps2": "\"true\"", "minlen": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "maxp": "\"2\"", "xa": "\"1.0\"", "skipgaps": "\"true\"", "dbkey": "\"hg17\"", "maxlen": "\"10000\"", "mindiv": "\"0.5\"", "template": "{\"count\": null, \"source\": \"self\", \"group\": null, \"abskew\": \"1.9\", \"__current_case__\": 2}", "chunks": "\"4\"", "idsmoothwindow": "\"32\"", "alignment": "{\"ucl\": \"global\", \"__current_case__\": 0}", "chimealns": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n00:00 31Mb 0.1% Reading fasta.temp\r00:00 31Mb 0.1% Reading fasta.temp\r\nWARNING: Ignoring gaps in FASTA file 'fasta.temp'\n00:00 31Mb 100.0% Reading fasta.temp\r\n00:00 31Mb 9 sequences \n00:00 15Mb 11.1% 0/0 chimeras found (0.0%)\r00:00 15Mb 100.0% 0/8 chimeras found (0.0%)\r\n", "job_metrics": [], "model_class": "Job", "external_id": "9189", "id": "a94ebc130565c5b1", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_uchime.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "b3dbb33ff37f6ca1"}, "chimealns": true, "template\|source": "hist", "template\|reference": {"src": "hda", "id": "2ff97a24d56d906f"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "b3dbb33ff37f6ca1", "uuid": "b5bcf445-3dac-4b1d-a8c4-9aad3d469bf9"}, "reference": {"src": "hda", "id": "2ff97a24d56d906f", "uuid": "cfd51060-1f31-447d-a1ea-948717638e70"}}, "update_time": "2018-02-08T16:59:39.670466", "tool_id": "mothur_chimera_uchime", "outputs": {"out_count": {"src": "hda", "id": "e8a2248405ed0640", "uuid": "be2c0c51-cce2-4283-880c-db5b089e59fa"}, "logfile": {"src": "hda", "id": "7de538ea4ff833f8", "uuid": "30ca70fd-4cf8-423b-9ccc-d868063ad1de"}, "out_accnos": {"src": "hda", "id": "3917f5d5eeab2729", "uuid": "a351d373-127a-4808-a5ba-58cf7e7fd433"}, "out_alns": {"src": "hda", "id": "1be3f70673e658a4", "uuid": "1c5ceafc-ee74-4abe-8743-5423286b75b8"}, "uchime.chimeras": {"src": "hda", "id": "a6edf8654f66f4d6", "uuid": "7a10a59e-a7d3-4093-b364-5d92e7978df3"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.uchime(fasta=fasta.dat,reference=template.reference.dat,minh=0. \r3,mindiv=0.5,xn=8.0,dn=1.4,xa=1.0,chunks=4,minchunk=64,idsmoothwindow=32,maxp=2, \rminlen=10,maxlen=10000,skipgaps=true,skipgaps2=true,dereplicate=false,chimealns= \rtrue,processors=1)\n\nUsing 1 processors.\n/home/saskia/miniconda3/envs/__mothur@1.39.5/bin/mothuruchime file does not exist. Checking path... \nFound uchime in your path, using /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/uchime\n\nuchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\n\nChecking sequences from fasta.dat ...\nuchime v4.2.40\nby Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\n\n\nIt took 0 secs to check 3 sequences. 1 chimeras were found.\n\nOutput File Names: \nfasta.ref.uchime.chimeras\nfasta.ref.uchime.accnos\nfasta.ref.uchime.alns\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_173.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_174.dat' template.reference.dat && echo 'chimera.uchime( fasta=fasta.dat, reference=template.reference.dat, minh=0.3, mindiv=0.5, xn=8.0, dn=1.4, xa=1.0, chunks=4, minchunk=64, idsmoothwindow=32, maxp=2, minlen=10, maxlen=10000, skipgaps=true, skipgaps2=true, dereplicate=false, chimealns=true, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log 2>&1", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:59:36.186909", "params": {"dn": "\"1.4\"", "dereplicate": "\"false\"", "minh": "\"0.3\"", "minchunk": "\"64\"", "xn": "\"8.0\"", "skipgaps2": "\"true\"", "minlen": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "maxp": "\"2\"", "xa": "\"1.0\"", "skipgaps": "\"true\"", "dbkey": "\"hg17\"", "maxlen": "\"10000\"", "mindiv": "\"0.5\"", "template": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 174}]}, \"__current_case__\": 1}", "chunks": "\"4\"", "idsmoothwindow": "\"32\"", "alignment": "{\"ucl\": \"global\", \"__current_case__\": 0}", "chimealns": "\"true\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n00:00 31Mb 0.1% Reading fasta.dat.uchime_formatted\r00:00 31Mb 0.1% Reading fasta.dat.uchime_formatted\r\nWARNING: Ignoring gaps in FASTA file 'fasta.dat.uchime_formatted'\n00:00 31Mb 100.0% Reading fasta.dat.uchime_formatted\r\n00:00 31Mb 3 sequences \n00:00 32Mb 0.1% Reading template.reference.dat\r00:00 32Mb 0.1% Reading template.reference.dat\r00:00 32Mb 100.0% Reading template.reference.dat\r\n00:00 32Mb 32 sequences \n00:00 32Mb 33.3% 0/0 chimeras found (0.0%)\r00:00 32Mb 100.0% 1/2 chimeras found (33.3%)\r\n", "job_metrics": [], "model_class": "Job", "external_id": "9321", "id": "945d4aa2c8920004", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_uchime.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "df2cbca38520d0f1"}, "name": {"src": "hda", "id": "26f324d382d6d8c1"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "df2cbca38520d0f1", "uuid": "1f74f4c9-d4fc-46cd-a4ad-6fb3730b4472"}, "name": {"src": "hda", "id": "26f324d382d6d8c1", "uuid": "0944afd4-1adc-40bc-abf9-65e7952db00c"}}, "update_time": "2018-02-08T17:00:13.194061", "tool_id": "mothur_chop_seqs", "outputs": {"logfile": {"src": "hda", "id": "168b8fc92b5c87b9", "uuid": "98e386fc-76dc-4d81-a1ff-9c56fd20b90a"}, "out_fasta": {"src": "hda", "id": "8877579cefa7ba1d", "uuid": "97deef1f-9c02-4dde-86cc-b5a06a207a90"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chop.seqs(fasta=fasta.dat,numbases=10,keep=front,countgaps=false,short= \rfalse,name=name.dat,processors=1)\n\nUsing 1 processors.\n10\n\nOutput File Names: \nfasta.chop.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_180.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_181.dat' name.dat && ln -s 'None' group.dat && ln -s 'None' count.dat && echo 'chop.seqs( fasta=fasta.dat, numbases=10, keep=front, countgaps=false, short=false, name=name.dat, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:00:10.059551", "params": {"count": "null", "short": "\"false\"", "group": "null", "countgaps": "\"false\"", "dbkey": "\"hg17\"", "keep": "\"front\"", "numbases": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "9437", "id": "f1e243926043ec87", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chop_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"tax\|source": "hist", "tax\|taxonomy": {"src": "hda", "id": "6f4bdab7a73c92f2"}, "otu": {"src": "hda", "id": "f28875befd5fbf72"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "6f4bdab7a73c92f2", "uuid": "697b7231-c675-4892-8fd9-b834494f696b"}, "otu": {"src": "hda", "id": "f28875befd5fbf72", "uuid": "b964b877-996d-4a03-b9aa-4e1d117702b1"}}, "update_time": "2018-02-08T17:00:32.931798", "tool_id": "mothur_classify_otu", "outputs": {"__new_primary_file_unique\|0.10__": {"src": "hda", "id": "3b3b4832b2563c85", "uuid": "bda53660-3c27-4d8d-8b4b-d247ef5b7118"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "c786be9a5c4573e3", "uuid": "e16c1b48-9ead-4458-99e3-31f258779006"}, "__new_primary_file_unique\|0.17__": {"src": "hda", "id": "2d6c63bdf033511b", "uuid": "39b45b1d-7ebb-4a80-b5ab-742caf969874"}, "__new_primary_file_unique\|0.02__": {"src": "hda", "id": "f2fbab8d8d8f0547", "uuid": "7c56cf9b-045c-47a3-b98a-0aa0c93b7acb"}, "__new_primary_file_unique\|0.21__": {"src": "hda", "id": "da62383fb67fc13a", "uuid": "6e6df4ea-9ce0-4f4c-b107-4d9386add82c"}, "__new_primary_file_unique\|0.16__": {"src": "hda", "id": "10a6a0683c3e243b", "uuid": "80b036be-5867-48cb-88f4-40ce7344bb63"}, "__new_primary_file_unique\|0.45__": {"src": "hda", "id": "6fb508dbe1736155", "uuid": "2e569b9d-2044-4a05-8838-6ea41802ff58"}, "__new_primary_file_unique\|0.03__": {"src": "hda", "id": "ce239e512e8f2197", "uuid": "40ba3095-2425-4eff-89ea-6374a45740b9"}, "__new_primary_file_unique\|0.15__": {"src": "hda", "id": "c6c2b27cd5eb370b", "uuid": "77e71211-c70f-4457-8d94-a4ed4aa5482e"}, "__new_primary_file_unique\|0.08__": {"src": "hda", "id": "6fccc2792c7809ba", "uuid": "18655ff0-6f1c-4fbd-a36c-914bc55f2f3e"}, "__new_primary_file_unique\|0.14__": {"src": "hda", "id": "2c1f3fe730d02717", "uuid": "146c2dda-42f7-4c98-82ce-9c9648eaaac7"}, "__new_primary_file_unique\|0.13__": {"src": "hda", "id": "01949e60fe484dc7", "uuid": "8a9200bb-0cdf-4781-93c3-f4a7d0ff0dcc"}, "__new_primary_file_unique\|0.09__": {"src": "hda", "id": "06bb318fcaf8f1eb", "uuid": "d5735185-f59a-467a-8c8f-fc0acf2a2038"}, "__new_primary_file_unique\|0.12__": 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"3b3bdb52-fc24-419e-9e43-5c548056c18f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > classify.otu(list=otu.dat,taxonomy=tax.taxonomy.dat,basis=otu,probs=tru \re,persample=false,cutoff=60)\nunique\t96\n[WARNING]: U68667 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68688 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68686 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68637 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68635 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68634 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68630 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68629 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68628 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68626 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68623 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68619 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68617 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68616 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68614 is not in your taxonomy file. I will not include it in the consensus.\n0.01\t93\n[WARNING]: U68688 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68667 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68686 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy f\n..\n.\n[WARNING]: U68641 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file. I will not include it in the consensus.\n0.55\t1\n[WARNING]: U68688 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68626 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68623 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68630 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68634 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68628 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68629 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68617 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68614 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68616 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68686 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68635 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68637 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68619 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68667 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file. I will not include it in the consensus.\n\nOutput File Names: \notu.unique.cons.taxonomy\notu.unique.cons.tax.summary\notu.0.01.cons.taxonomy\notu.0.01.cons.tax.summary\notu.0.02.cons.taxonomy\notu.0.02.cons.tax.summary\notu.0.03.cons.taxonomy\notu.0.03.cons.tax.summary\notu.0.04.cons.taxonomy\notu.0.04.cons.tax.summary\notu.0.05.cons.taxonomy\notu.0.05.cons.tax.summary\notu.0.06.cons.taxonomy\notu.0.06.cons.tax.summary\notu.0.07.cons.taxonomy\notu.0.07.cons.tax.summary\notu.0.08.cons.taxonomy\notu.0.08.cons.tax.summary\notu.0.09.cons.taxonomy\notu.0.09.cons.tax.summary\notu.0.10.cons.taxonomy\notu.0.10.cons.tax.summary\notu.0.11.cons.taxonomy\notu.0.11.cons.tax.summary\notu.0.12.cons.taxonomy\notu.0.12.cons.tax.summary\notu.0.13.cons.taxonomy\notu.0.13.cons.tax.summary\notu.0.14.cons.taxonomy\notu.0.14.cons.tax.summary\notu.0.15.cons.taxonomy\notu.0.15.cons.tax.summary\notu.0.16.cons.taxonomy\notu.0.16.cons.tax.summary\notu.0.17.cons.taxonomy\notu.0.17.cons.tax.summary\notu.0.18.cons.taxonomy\notu.0.18.cons.tax.summary\notu.0.19.cons.taxonomy\notu.0.19.cons.tax.summary\notu.0.20.cons.taxonomy\notu.0.20.cons.tax.summary\notu.0.21.cons.taxonomy\notu.0.21.cons.tax.summary\notu.0.22.cons.taxonomy\notu.0.22.cons.tax.summary\notu.0.23.cons.taxonomy\notu.0.23.cons.tax.summary\notu.0.24.cons.taxonomy\notu.0.24.cons.tax.summary\notu.0.25.cons.taxonomy\notu.0.25.cons.tax.summary\notu.0.26.cons.taxonomy\notu.0.26.cons.tax.summary\notu.0.27.cons.taxonomy\notu.0.27.cons.tax.summary\notu.0.29.cons.taxonomy\notu.0.29.cons.tax.summary\notu.0.32.cons.taxonomy\notu.0.32.cons.tax.summary\notu.0.33.cons.taxonomy\notu.0.33.cons.tax.summary\notu.0.36.cons.taxonomy\notu.0.36.cons.tax.summary\notu.0.38.cons.taxonomy\notu.0.38.cons.tax.summary\notu.0.41.cons.taxonomy\notu.0.41.cons.tax.summary\notu.0.45.cons.taxonomy\notu.0.45.cons.tax.summary\notu.0.55.cons.taxonomy\notu.0.55.cons.tax.summary\n\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 3528 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_184.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_185.dat' tax.taxonomy.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && ln -s 'None' group.dat && echo 'classify.otu( list=otu.dat, taxonomy=tax.taxonomy.dat, basis=otu, probs=true, persample=false, cutoff=60 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:00:25.557457", "params": {"count": "null", "cutoff": "\"60\"", "group": "null", "name": "null", "basis": "\"otu\"", "tax": "{\"source\": \"hist\", \"__current_case__\": 1, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 185}]}}", "dbkey": "\"hg17\"", "label": "null", "persample": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "probs": "\"true\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "9552", "id": "19ec6936a7590160", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_classify_otu.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"tax\|source": "hist", "label": ["unique", "0.05", "0.18"], "tax\|taxonomy": {"src": "hda", "id": "3ecde483422ba55d"}, "otu": {"src": "hda", "id": "14e20f44bf5d2d72"}, "name": {"src": "hda", "id": "41b140d702d99e07"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "3ecde483422ba55d", "uuid": "33feb10f-4177-4489-b970-66fc6003bfe6"}, "name": {"src": "hda", "id": "41b140d702d99e07", "uuid": "f1f2dffb-4746-4ada-874b-c73b5608005d"}, "otu": {"src": "hda", "id": "14e20f44bf5d2d72", "uuid": "bfd08ef0-ab87-4f1b-b5a8-ff566db8e822"}}, "update_time": "2018-02-08T17:01:08.949778", "tool_id": "mothur_classify_otu", "outputs": {"__new_primary_file_unique\|unique__": {"src": "hda", "id": "daf78d18ceb29125", "uuid": "b556847d-9014-4648-8be2-855a3334b841"}, "logfile": {"src": "hda", "id": "0e8c18395d13c78f", "uuid": "06734564-dbf7-41b7-a2ea-8bc0c717029d"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "5e8952dd122908bb", "uuid": "b5ed355a-7e41-4d91-a152-ba11da766200"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "7cd46ccec257d13d", "uuid": "4b444b6f-7a24-4cb6-8fb2-02221aecf0a9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > classify.otu(list=otu.dat,taxonomy=tax.taxonomy.dat,name=name.dat,label \r=unique-0.05-0.18,basis=otu,probs=true,persample=false,cutoff=60)\nunique\t96\nU68667 is not in your taxonomy file. I will not include it in the consensus.\nU68641 is not in your taxonomy file. I will not include it in the consensus.\nU68620 is not in your taxonomy file. I will not include it in the consensus.\nU68618 is not in your taxonomy file. I will not include it in the consensus.\nU68663 is not in your taxonomy file. I will not include it in the consensus.\nU68662 is not in your taxonomy file. I will not include it in the consensus.\nU68661 is not in your taxonomy file. I will not include it in the consensus.\nU68660 is not in your taxonomy file. I will not include it in the consensus.\nU68659 is not in your taxonomy file. I will not include it in the consensus.\nU68658 is not in your taxonomy file. I will not include it in the consensus.\nU68657 is not in your taxonomy file. I will not include it in the consensus.\nU68656 is not in your taxonomy file. I will not include it in the consensus.\nU68655 is not in your taxonomy file. I will not include it in the consensus.\nU68654 is not in your taxonomy file. I will not include it in the consensus.\nU68653 is not in your taxonomy file. I will not include it in the consensus.\nU68652 is not in your taxonomy file. I will not include it in the consensus.\nU68651 is not in your taxonomy file. I will not include it in the consensus.\nU68649 is not in your taxonomy file. I will not include it in the consensus.\nU68648 is not in your taxonomy file. I will not include it in the consensus.\nU68647 is not in your taxonomy file. I will not include it in the consensus.\nU68646 is not in your taxonomy file. I will not include it in the consensus.\nU68645 is not in your taxonomy file. I will not include it in the consensus.\nU68644 is not in your taxonomy file. I will not include it in the consensus.\nU68643 is not in your taxonomy file. I will not include it in the consensus.\nU68642 is not in your taxonomy file. I will not include it in the consensus.\nU68640 is not in your taxonomy file. I will not include it in the consensus.\nU68639 is not in your taxonomy file. I will not include it in the consensus.\nU68688 is not in your taxonomy file. I will not include it in the consensus.\nU68687 is not in your taxonomy file. I will not include it in the consensus.\nU68686 is not in your taxonomy file. I will not include it in the consensus.\nU68685 is not in your taxonomy file. I will not include it in the consensus.\nU68684 is not in your taxonomy file. I will not include it in the consensus.\nU68683 is not in your taxonomy file. I will not include it in the consensus.\nU68682 is not in your taxonomy file. I will not include it in the consensus.\nU68681 is not in your taxonomy file. I will not include it in the consensus.\nU68680 is not in your taxonomy file. I will not include it in the consensus.\nU68679 is not in your taxonomy file. I will not include it in the consensus.\nU68678 is not in your taxonomy file. I will not include it in the consensus.\nU68677 is not in your taxonomy file. I will not include it in the consensus.\nU68676 is not in your taxonomy file. I will not include it in the consensus.\nU68675 is not in your taxonomy file. I will not include it in the consensus.\nU68674 is not in your taxonomy file. I will not include it in the consensus.\nU68673 is not in your taxonomy file. I will not include it in the consensus.\nU68672 is not in your taxonomy file. I will not include it in the consensus.\nU68671 is not in your taxonomy file. I will not include it in the consensus.\nU68670 is not in your taxonomy file. I will not include it in the consensus.\nU68669 is not in your taxonomy file. I will not include it in the consensus.\nU68668 is not in your taxonomy file. I will not include it in the consensus.\nU68666 is not in your taxonomy file. I will not include it in the consensus.\nU68665 is not in your taxonomy file. I will not include it in the consensus.\nU68664 is not in your taxonomy file. I will not include it in the consensus.\nU68613 is not in your taxonomy file. I will not include it in the consensus.\nU68612 is not in your taxonomy file. I will not include it in the consensus.\nU68611 is not in your taxonomy file. I will not include it in the consensus.\nU68610 is not in your taxonomy file. I will not include it in the consensus.\nU68609 is not in your taxonomy file. I will not include it in the consensus.\nU68608 is not in your taxonomy file. I will not include it in the consensus.\nU68607 is not in your taxonomy file. I will not include it in the consensus.\nU68606 is not in your taxonomy file. I will not include it in the consensus.\nU68605 is not in your taxonomy file. I will not include it in the consensus.\nU68603 is not in your taxonomy file. I will not include it in the consensus.\nU68602 is not in your taxonomy file. I will not include it in the consensus.\nU68601 is not in your taxonomy file. I will not include it in the consensus.\nU68600 is not in your taxonomy file. I will not include it in the consensus.\nU68599 is not in your taxonomy file. I will not include it in the consensus.\nU68598 is not in your taxonomy file. I will not include it in the consensus.\nU68597 is not in your taxonomy file. I will not include it in the consensus.\nU68596 is not in your taxonomy file. I will not include it in the consensus.\nU68595 is not in your taxonomy file. I will not include it in the consensus.\nU68594 is not in your taxonomy file. I will not include it in the consensus.\nU68593 is not in your taxonomy file. I will not include it in the consensus.\nU68592 is not in your taxonomy file. I will not include it in the consensus.\nU68591 is not in your taxonomy file. I will not include it in the consensus.\nU68590 is not in your taxonomy file. I will not include it in the consensus.\nU68589 is not in your taxonomy file. I will not include it in the consensus.\nU68638 is not in your taxonomy file. I will not include it in the consensus.\nU68637 is not in your taxonomy file. I will not include it in the consensus.\nU68636 is not in your taxonomy file. I will not include it in the consensus.\nU68635 is not in your taxonomy file. I will not include it in the consensus.\nU68634 is not in your taxonomy file. I will not include it in the consensus.\nU68633 is not in your taxonomy file. I will not include it in the consensus.\nU68632 is not in your taxonomy file. I will not include it in the consensus.\nU68631 is not in your taxonomy file. I will not include it in the consensus.\nU68630 is not in your taxonomy file. I will not include it in the consensus.\nU68629 is not in your taxonomy file. I will not include it in the consensus.\nU68628 is not in your taxonomy file. I will not include it in the consensus.\nU68627 is not in your taxonomy file. I will not include it in the consensus.\nU68626 is not in your taxonomy file. I will not include it in the consensus.\nU68625 is not in your taxonomy file. I will not include it in the consensus.\nU68624 is not in your taxonomy file. I will not include it in the consensus.\nU68623 is not in your taxonomy file. I will not include it in the consensus.\nU68622 is not in your taxonomy file. I will not include it in the consensus.\nU68621 is not in your taxonomy file. I will not include it in the consensus.\nU68619 is not in your taxonomy file. I will not include it in the consensus.\nU68617 is not in your taxonomy file. I will not include it in the consensus.\nU68616 is not in your taxonomy file. I will not include it in the consensus.\nU68615 is not in your taxonomy file. I will not include it in the consensus.\nU68614 is not in your taxonomy file. I will not include it in the consensus.\n0.05\t78\nU68688 is not in your taxonomy file. I will not include it in the consensus.\nU68665 is not in your taxonomy file. I will not include it in the consensus.\nU68679 is not in your taxonomy file. I will not include it in the consensus.\nU68663 is not in your taxonomy file. I will not include it in the consensus.\nU68658 is not in your taxonomy file. I will not include it in the consensus.\nU68638 is not in your taxonomy file. I will not include it in the consensus.\nU68620 is not in your taxonomy file. I will not include it in the consensus.\nU68618 is not in your taxonomy file. I will not include it in the consensus.\nU68683 is not in your taxonomy file. I will not include it in the consensus.\nU68652 is not in your taxonomy file. I will not include it in the consensus.\nU68610 is not in your taxonomy file. I will not include it in the consensus.\nU68673 is not in your taxonomy file. I will not include it in the consensus.\nU68667 is not in your taxonomy file. I will not include it in the consensus.\nU68641 is not in your taxonomy file. I will not include it in the consensus.\nU68636 is not in your taxonomy file. I will not include it in the consensus.\nU68631 is not in your taxonomy file. I will not include it in the consensus.\nU68637 is not in your taxonomy file. I will not include it in the consensus.\nU68602 is not in your taxonomy file. I will not include it in the consensus.\nU68628 is not in your taxonomy file. I will not include it in the consensus.\nU68601 is not in your taxonomy file. I will not include it in the consensus.\nU68614 is not in your taxonomy file. I will not include it in the consensus.\nU68596 is not in your taxonomy file. I will not include it in the consensus.\nU68666 is not in your taxonomy file. I will not include it in the consensus.\nU68595 is not in your taxonomy file. I will not include it in the consensus.\nU68672 is not in your taxonomy file. I will not include it in the consensus.\nU68621 is not in your taxonomy file. I will not include it in the consensus.\nU68686 is not in your taxonomy file. I will not include it in the consensus.\nU68635 is not in your taxonomy file. I will not include it in the consensus.\nU68678 is not in your taxonomy file. I will not include it in the consensus.\nU68619 is not in your taxonomy file. I will not include it in the consensus.\nU68680 is not in your taxonomy file. I will not include it in the consensus.\nU68615 is not in your taxonomy file. I will not include it in the consensus.\nU68681 is not in your taxonomy file. I will not include it in the consensus.\nU68677 is not in your taxonomy file. I will not include it in the consensus.\nU68654 is not in your taxonomy file. I will not include it in the consensus.\nU68653 is not in your taxonomy file. I will not include it in the consensus.\nU68651 is not in your taxonomy file. I will not include it in the consensus.\nU68649 is not in your taxonomy file. I will not include it in the consensus.\nU68648 is not in your taxonomy file. I will not include it in the consensus.\nU68647 is not in your taxonomy file. I will not include it in the consensus.\nU68646 is not in your taxonomy file. I will not include it in the consensus.\nU68645 is not in your taxonomy file. I will not include it in the consensus.\nU68685 is not in your taxonomy file. I will not include it in the consensus.\nU68644 is not in your taxonomy file. I will not include it in the consensus.\nU68643 is not in your taxonomy file. I will not include it in the consensus.\nU68642 is not in your taxonomy file. I will not include it in the consensus.\nU68640 is not in your taxonomy file. I will not include it in the consensus.\nU68639 is not in your taxonomy file. I will not include it in the consensus.\nU68687 is not in your taxonomy file. I will not include it in the consensus.\nU68676 is not in your taxonomy file. I will not include it in the consensus.\nU68675 is not in your taxonomy file. I will not include it in the consensus.\nU68674 is not in your taxonomy file. I will not include it in the consensus.\nU68671 is not in your taxonomy file. I will not include it in the consensus.\nU68670 is not in your taxonomy file. I will not include it in the consensus.\nU68669 is not in your taxonomy file. I will not include it in the consensus.\nU68668 is not in your taxonomy file. I will not include it in the consensus.\nU68664 is not in your taxonomy file. I will not include it in the consensus.\nU68662 is not in your taxonomy file. I will not include it in the consensus.\nU68661 is not in your taxonomy file. I will not include it in the consensus.\nU68660 is not in your taxonomy file. I will not include it in the consensus.\nU68682 is not in your taxonomy file. I will not include it in the consensus.\nU68659 is not in your taxonomy file. I will not include it in the consensus.\nU68684 is not in your taxonomy file. I will not include it in the consensus.\nU68657 is not in your taxonomy file. I will not include it in the consensus.\nU68656 is not in your taxonomy file. I will not include it in the consensus.\nU68655 is not in your taxonomy file. I will not include it in the consensus.\nU68607 is not in your taxonomy file. I will not include it in the consensus.\nU68608 is not in your taxonomy file. I will not include it in the consensus.\nU68600 is not in your taxonomy file. I will not include it in the consensus.\nU68609 is not in your taxonomy file. I will not include it in the consensus.\nU68599 is not in your taxonomy file. I will not include it in the consensus.\nU68606 is not in your taxonomy file. I will not include it in the consensus.\nU68598 is not in your taxonomy file. I will not include it in the consensus.\nU68611 is not in your taxonomy file. I will not include it in the consensus.\nU68612 is not in your taxonomy file. I will not include it in the consensus.\nU68613 is not in your taxonomy file. I will not include it in the consensus.\nU68605 is not in your taxonomy file. I will not include it in the consensus.\nU68616 is not in your taxonomy file. I will not include it in the consensus.\nU68617 is not in your taxonomy file. I will not include it in the consensus.\nU68597 is not in your taxonomy file. I will not include it in the consensus.\nU68603 is not in your taxonomy file. I will not include it in the consensus.\nU68594 is not in your taxonomy file. I will not include it in the consensus.\nU68589 is not in your taxonomy file. I will not include it in the consensus.\nU68634 is not in your taxonomy file. I will not include it in the consensus.\nU68590 is not in your taxonomy file. I will not include it in the consensus.\nU68633 is not in your taxonomy file. I will not include it in the consensus.\nU68632 is not in your taxonomy file. I will not include it in the consensus.\nU68591 is not in your taxonomy file. I will not include it in the consensus.\nU68592 is not in your taxonomy file. I will not include it in the consensus.\nU68630 is not in your taxonomy file. I will not include it in the consensus.\nU68629 is not in your taxonomy file. I will not include it in the consensus.\nU68627 is not in your taxonomy file. I will not include it in the consensus.\nU68626 is not in your taxonomy file. I will not include it in the consensus.\nU68625 is not in your taxonomy file. I will not include it in the consensus.\nU68624 is not in your taxonomy file. I will not include it in the consensus.\nU68623 is not in your taxonomy file. I will not include it in the consensus.\nU68622 is not in your taxonomy file. I will not include it in the consensus.\nU68593 is not in your taxonomy file. I will not include it in the consensus.\n0.18\t31\nU68686 is not in your taxonomy file. I will not include it in the consensus.\nU68635 is not in your taxonomy file. I will not include it in the consensus.\nU68613 is not in your taxonomy file. I will not include it in the consensus.\nU68637 is not in your taxonomy file. I will not include it in the consensus.\nU68602 is not in your taxonomy file. I will not include it in the consensus.\nU68678 is not in your taxonomy file. I will not include it in the consensus.\nU68619 is not in your taxonomy file. I will not include it in the consensus.\nU68645 is not in your taxonomy file. I will not include it in the consensus.\nU68673 is not in your taxonomy file. I will not include it in the consensus.\nU68667 is not in your taxonomy file. I will not include it in the consensus.\nU68641 is not in your taxonomy file. I will not include it in the consensus.\nU68598 is not in your taxonomy file. I will not include it in the consensus.\nU68658 is not in your taxonomy file. I will not include it in the consensus.\nU68638 is not in your taxonomy file. I will not include it in the consensus.\nU68620 is not in your taxonomy file. I will not include it in the consensus.\nU68618 is not in your taxonomy file. I will not include it in the consensus.\nU68659 is not in your taxonomy file. I will not include it in the consensus.\nU68624 is not in your taxonomy file. I will not include it in the consensus.\nU68655 is not in your taxonomy file. I will not include it in the consensus.\nU68651 is not in your taxonomy file. I will not include it in the consensus.\nU68640 is not in your taxonomy file. I will not include it in the consensus.\nU68688 is not in your taxonomy file. I will not include it in the consensus.\nU68665 is not in your taxonomy file. I will not include it in the consensus.\nU68679 is not in your taxonomy file. I will not include it in the consensus.\nU68663 is not in your taxonomy file. I will not include it in the consensus.\nU68653 is not in your taxonomy file. I will not include it in the consensus.\nU68676 is not in your taxonomy file. I will not include it in the consensus.\nU68660 is not in your taxonomy file. I will not include it in the consensus.\nU68647 is not in your taxonomy file. I will not include it in the consensus.\nU68626 is not in your taxonomy file. I will not include it in the consensus.\nU68623 is not in your taxonomy file. I will not include it in the consensus.\nU68683 is not in your taxonomy file. I will not include it in the consensus.\nU68652 is not in your taxonomy file. I will not include it in the consensus.\nU68610 is not in your taxonomy file. I will not include it in the consensus.\nU68671 is not in your taxonomy file. I will not include it in the consensus.\nU68666 is not in your taxonomy file. I will not include it in the consensus.\nU68595 is not in your taxonomy file. I will not include it in the consensus.\nU68636 is not in your taxonomy file. I will not include it in the consensus.\nU68631 is not in your taxonomy file. I will not include it in the consensus.\nU68634 is not in your taxonomy file. I will not include it in the consensus.\nU68628 is not in your taxonomy file. I will not include it in the consensus.\nU68601 is not in your taxonomy file. I will not include it in the consensus.\nU68607 is not in your taxonomy file. I will not include it in the consensus.\nU68629 is not in your taxonomy file. I will not include it in the consensus.\nU68617 is not in your taxonomy file. I will not include it in the consensus.\nU68614 is not in your taxonomy file. I will not include it in the consensus.\nU68596 is not in your taxonomy file. I will not include it in the consensus.\nU68684 is not in your taxonomy file. I will not include it in the consensus.\nU68654 is not in your taxonomy file. I will not include it in the consensus.\nU68593 is not in your taxonomy file. I will not include it in the consensus.\nU68649 is not in your taxonomy file. I will not include it in the consensus.\nU68639 is not in your taxonomy file. I will not include it in the consensus.\nU68606 is not in your taxonomy file. I will not include it in the consensus.\nU68682 is not in your taxonomy file. I will not include it in the consensus.\nU68657 is not in your taxonomy file. I will not include it in the consensus.\nU68675 is not in your taxonomy file. I will not include it in the consensus.\nU68627 is not in your taxonomy file. I will not include it in the consensus.\nU68609 is not in your taxonomy file. I will not include it in the consensus.\nU68680 is not in your taxonomy file. I will not include it in the consensus.\nU68615 is not in your taxonomy file. I will not include it in the consensus.\nU68670 is not in your taxonomy file. I will not include it in the consensus.\nU68611 is not in your taxonomy file. I will not include it in the consensus.\nU68648 is not in your taxonomy file. I will not include it in the consensus.\nU68632 is not in your taxonomy file. I will not include it in the consensus.\nU68605 is not in your taxonomy file. I will not include it in the consensus.\nU68597 is not in your taxonomy file. I will not include it in the consensus.\nU68687 is not in your taxonomy file. I will not include it in the consensus.\nU68592 is not in your taxonomy file. I will not include it in the consensus.\nU68685 is not in your taxonomy file. I will not include it in the consensus.\nU68681 is not in your taxonomy file. I will not include it in the consensus.\nU68677 is not in your taxonomy file. I will not include it in the consensus.\nU68669 is not in your taxonomy file. I will not include it in the consensus.\nU68646 is not in your taxonomy file. I will not include it in the consensus.\nU68590 is not in your taxonomy file. I will not include it in the consensus.\nU68644 is not in your taxonomy file. I will not include it in the consensus.\nU68633 is not in your taxonomy file. I will not include it in the consensus.\nU68612 is not in your taxonomy file. I will not include it in the consensus.\nU68600 is not in your taxonomy file. I will not include it in the consensus.\nU68591 is not in your taxonomy file. I will not include it in the consensus.\nU68672 is not in your taxonomy file. I will not include it in the consensus.\nU68621 is not in your taxonomy file. I will not include it in the consensus.\nU68625 is not in your taxonomy file. I will not include it in the consensus.\nU68630 is not in your taxonomy file. I will not include it in the consensus.\nU68622 is not in your taxonomy file. I will not include it in the consensus.\nU68616 is not in your taxonomy file. I will not include it in the consensus.\nU68642 is not in your taxonomy file. I will not include it in the consensus.\nU68643 is not in your taxonomy file. I will not include it in the consensus.\nU68656 is not in your taxonomy file. I will not include it in the consensus.\nU68661 is not in your taxonomy file. I will not include it in the consensus.\nU68662 is not in your taxonomy file. I will not include it in the consensus.\nU68664 is not in your taxonomy file. I will not include it in the consensus.\nU68668 is not in your taxonomy file. I will not include it in the consensus.\nU68674 is not in your taxonomy file. I will not include it in the consensus.\nU68599 is not in your taxonomy file. I will not include it in the consensus.\nU68608 is not in your taxonomy file. I will not include it in the consensus.\nU68603 is not in your taxonomy file. I will not include it in the consensus.\nU68594 is not in your taxonomy file. I will not include it in the consensus.\nU68589 is not in your taxonomy file. I will not include it in the consensus.\n\nOutput File Names: \notu.unique.cons.taxonomy\notu.unique.cons.tax.summary\notu.0.05.cons.taxonomy\notu.0.05.cons.tax.summary\notu.0.18.cons.taxonomy\notu.0.18.cons.tax.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_259.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_261.dat' tax.taxonomy.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_260.dat' name.dat && ln -s 'None' count.dat && ln -s 'None' group.dat && echo 'classify.otu( list=otu.dat, taxonomy=tax.taxonomy.dat, name=name.dat, label=unique-0.05-0.18, basis=otu, probs=true, persample=false, cutoff=60 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:01:05.437469", "params": {"count": "null", "cutoff": "\"60\"", "group": "null", "basis": "\"otu\"", "tax": "{\"source\": \"hist\", \"__current_case__\": 1, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 261}]}}", "dbkey": "\"hg17\"", "label": "[\"unique\", \"0.05\", \"0.18\"]", "persample": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "probs": "\"true\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "9694", "id": "97f8596e58df898c", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_classify_otu.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"count": {"src": "hda", "id": "a658f0c7b599f85a"}, "tax\|source": "hist", "tax\|taxonomy": {"src": "hda", "id": "5d952db0f0e41e99"}, "otu": {"src": "hda", "id": "1d5ca124ec943537"}, "label": ["unique", "0.05", "0.18"]}, "job": {"inputs": {"count": {"src": "hda", "id": "a658f0c7b599f85a", "uuid": "7051ce7a-a5d0-4ed9-a13e-7882ad5f7bed"}, "taxonomy": {"src": "hda", "id": "5d952db0f0e41e99", "uuid": "20a3ee2a-4eb1-4153-babd-2de585f13f8e"}, "otu": {"src": "hda", "id": "1d5ca124ec943537", "uuid": "9e4d3e13-6fd2-4c20-acfc-6891473c8bb8"}}, "update_time": "2018-02-08T17:01:41.985823", "tool_id": "mothur_classify_otu", "outputs": {"__new_primary_file_unique\|unique__": {"src": "hda", "id": "648ee5580acb394c", "uuid": "968165ec-5a61-489b-9f5a-1c4a44d8209b"}, "logfile": {"src": "hda", "id": "a419613b7d66b4dd", "uuid": "22b5cf38-8021-4ac3-b82a-b3775dc54efc"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "e038b12fcc34712c", "uuid": "46b94bc7-fc22-413a-b0d9-e9fcc3140e56"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "846dc31143592f08", "uuid": "1777501a-5552-444e-b5f1-b8817295f9ea"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > classify.otu(list=otu.dat,taxonomy=tax.taxonomy.dat,count=count.dat,lab \rel=unique-0.05-0.18,basis=otu,probs=true,persample=false,cutoff=60)\nunique\t96\n[WARNING]: U68667 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68688 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68686 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68637 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68635 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68634 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68630 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68629 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68628 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68626 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68623 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68619 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68617 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68616 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68614 is not in your taxonomy file. I will not include it in the consensus.\n0.05\t78\n[WARNING]: U68688 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68667 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68637 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68628 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68614 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68686 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68635 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68619 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68616 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68617 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68634 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68630 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68629 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68626 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68623 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file. I will not include it in the consensus.\n0.18\t31\n[WARNING]: U68686 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68635 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68637 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68619 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68667 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68688 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68626 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68623 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68634 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68628 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68629 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68617 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68614 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68630 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68616 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy file. I will not include it in the consensus.\n\nOutput File Names: \notu.unique.cons.taxonomy\notu.unique.cons.tax.summary\notu.0.05.cons.taxonomy\notu.0.05.cons.tax.summary\notu.0.18.cons.taxonomy\notu.0.18.cons.tax.summary\n\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 294 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_269.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_271.dat' tax.taxonomy.dat && ln -s 'None' name.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_270.dat' count.dat && ln -s 'None' group.dat && echo 'classify.otu( list=otu.dat, taxonomy=tax.taxonomy.dat, count=count.dat, label=unique-0.05-0.18, basis=otu, probs=true, persample=false, cutoff=60 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:01:37.698586", "params": {"cutoff": "\"60\"", "group": "null", "name": "null", "basis": "\"otu\"", "tax": "{\"source\": \"hist\", \"__current_case__\": 1, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 271}]}}", "dbkey": "\"hg17\"", "label": "[\"unique\", \"0.05\", \"0.18\"]", "persample": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "probs": "\"true\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "9833", "id": "2fd653ff8fe916b4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_classify_otu.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"tax\|source": "hist", "group": {"src": "hda", "id": "b76e2c1d909ec95b"}, "tax\|taxonomy": {"src": "hda", "id": "813e726c1c531093"}, "otu": {"src": "hda", "id": "57d21b82f66bdde1"}, "label": ["unique", "0.05", "0.18"]}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "813e726c1c531093", "uuid": "8f98eaf9-8d3f-4b95-8d5c-2827160af834"}, "group": {"src": "hda", "id": "b76e2c1d909ec95b", "uuid": "b108d363-b53b-4ba9-a5ab-5514370b9031"}, "otu": {"src": "hda", "id": "57d21b82f66bdde1", "uuid": "4b4c9c08-0b9e-4c76-8c65-1bf75ba8a076"}}, "update_time": "2018-02-08T17:02:13.958072", "tool_id": "mothur_classify_otu", "outputs": {"__new_primary_file_unique\|unique__": {"src": "hda", "id": "3eabac299c8a6493", "uuid": "9fce3e7c-3d6c-489a-afd1-0157a5edb910"}, "logfile": {"src": "hda", "id": "694613cce11a624b", "uuid": "d6b6fbb4-5321-4709-af2f-e7c17755f3ea"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "4b73dece6b8202b2", "uuid": "8ee4e725-22ba-4778-a6ac-2a0f9b10b8e0"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "8960b7e82c319407", "uuid": "010aef81-9c17-4c7f-9413-ac98a3b10a6c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > classify.otu(list=otu.dat,taxonomy=tax.taxonomy.dat,label=unique-0.05-0 \r.18,group=group.dat,basis=otu,probs=true,persample=false,cutoff=60)\nunique\t96\n[WARNING]: U68667 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68688 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68686 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68637 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68635 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68634 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68630 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68629 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68628 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68626 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68623 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68619 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68617 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68616 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68614 is not in your taxonomy file. I will not include it in the consensus.\n0.05\t78\n[WARNING]: U68688 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68667 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68637 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68628 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68614 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68686 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68635 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68619 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68616 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68617 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68634 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68630 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68629 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68626 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68623 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file. I will not include it in the consensus.\n0.18\t31\n[WARNING]: U68686 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68635 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68637 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68619 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68667 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68688 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68626 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68623 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68634 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68628 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68629 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68617 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68614 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68630 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68616 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file. I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy file. I will not include it in the consensus.\n\nOutput File Names: \notu.unique.cons.taxonomy\notu.unique.cons.tax.summary\notu.0.05.cons.taxonomy\notu.0.05.cons.tax.summary\notu.0.18.cons.taxonomy\notu.0.18.cons.tax.summary\n\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 294 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_279.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_280.dat' tax.taxonomy.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_281.dat' group.dat && echo 'classify.otu( list=otu.dat, taxonomy=tax.taxonomy.dat, label=unique-0.05-0.18, group=group.dat, basis=otu, probs=true, persample=false, cutoff=60 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:02:10.308889", "params": {"count": "null", "cutoff": "\"60\"", "name": "null", "basis": "\"otu\"", "tax": "{\"source\": \"hist\", \"__current_case__\": 1, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 280}]}}", "dbkey": "\"hg17\"", "label": "[\"unique\", \"0.05\", \"0.18\"]", "persample": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "probs": "\"true\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "9963", "id": "c0ae89d2a79fffb2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_classify_otu.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"alignment\|template": {"src": "hda", "id": "349f287fcb778b99"}, "fasta": {"src": "hda", "id": "0407161672f94bd4"}, "tax\|taxonomy": {"src": "hda", "id": "4b1441c8dda2d2fe"}, "alignment\|source": "hist", "tax\|source2": "hist"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "4b1441c8dda2d2fe", "uuid": "381f807d-770b-42d4-b24a-32d31669b6b9"}, "fasta": {"src": "hda", "id": "0407161672f94bd4", "uuid": "be23beec-f064-475f-b29d-ad87f64cc62f"}, "template": {"src": "hda", "id": "349f287fcb778b99", "uuid": "391175a3-7a7e-4fd8-804a-bcc27d515553"}}, "update_time": "2018-02-08T17:02:47.091134", "tool_id": "mothur_classify_seqs", "outputs": {"tree_sum": {"src": "hda", "id": "377e6a8287fa8b6a", "uuid": "fe77ae40-a1fd-44c7-9b99-30842ebd72aa"}, "logfile": {"src": "hda", "id": "f66e4e467d639b46", "uuid": "0e7a3aee-7e4d-42fe-b662-09330ca5f7db"}, "taxonomy_out": {"src": "hda", "id": "d60bc3c056ce6d02", "uuid": "6376f71e-8f69-4634-8b4a-de2fd2b243b8"}, "tax_summary": {"src": "hda", "id": "513510c2b856e80e", "uuid": "a49b76f5-5eac-4dfb-a188-bafce159c86e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > classify.seqs(fasta=fasta.dat,reference=alignment.template.dat,taxonomy \r=tax.taxonomy.dat,method=wang,ksize=8,iters=100,cutoff=80,probs=true,relabund=fa \rlse,printlevel=-1,processors=1)\n\nUsing 1 processors.\nGenerating search database... DONE.\nIt took 0 seconds generate search database. \n\nReading in the tax.taxonomy.dat taxonomy...\tDONE.\nCalculating template taxonomy tree... DONE.\nCalculating template probabilities... DONE.\nIt took 1 seconds get probabilities. \nClassifying sequences from fasta.dat ...\n[WARNING]: U68596 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68609 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68611 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68614 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68617 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68618 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68627 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68634 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68638 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68640 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68642 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68643 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68651 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68653 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68656 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68657 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68658 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68668 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68669 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68670 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68675 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68677 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68681 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68682 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\nProcessing sequence: 98\n\n[WARNING]: mothur reversed some your sequences for a better classification. If you would like to take a closer look, please check fasta.taxonomy.wang.flip.accnos for the list of the sequences.\n\nIt took 0 secs to classify 98 sequences.\n\n\nIt took 0 secs to create the summary file for 98 sequences.\n\n\nOutput File Names: \nfasta.taxonomy.wang.taxonomy\nfasta.taxonomy.wang.tax.summary\nfasta.taxonomy.wang.flip.accnos\n\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 25 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s `dirname $(which mothur)`/ . && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_289.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_290.dat' alignment.template.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_291.dat' tax.taxonomy.dat && ln -s 'None' count.dat && ln -s 'None' name.dat && echo 'classify.seqs( fasta=fasta.dat, reference=alignment.template.dat, taxonomy=tax.taxonomy.dat, method=wang, ksize=8, iters=100, cutoff=80, probs=true, relabund=false, printlevel=-1, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| ./mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:02:43.203871", "params": {"count": "null", "name": "null", "relabund": "\"false\"", "tax": "{\"source2\": \"hist\", \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 291}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\"", "classify": "{\"cutoff\": \"80\", \"iters\": \"100\", \"method\": \"wang\", \"ksize\": \"8\", \"__current_case__\": 0, \"probs\": \"true\"}", "printlevel": "\"-1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"template\": {\"values\": [{\"src\": \"hda\", \"id\": 290}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "10110", "id": "20de7af3d288c35f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_classify_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"alignment\|source": "hist", "alignment\|template": {"src": "hda", "id": "b09dd54432ee600c"}, "classify\|method": "knn", "fasta": {"src": "hda", "id": "25de304670fe7732"}, "tax\|taxonomy": {"src": "hda", "id": "d57022ef22692475"}, "tax\|source2": "hist"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "d57022ef22692475", "uuid": "c5a22f6a-70ff-4be6-9ba1-539f6d461dc9"}, "fasta": {"src": "hda", "id": "25de304670fe7732", "uuid": "831ee786-6fba-4803-b0ec-193c971e80e0"}, "template": {"src": "hda", "id": "b09dd54432ee600c", "uuid": "d6d8be3f-1709-46c3-a983-664e37ff6a50"}}, "update_time": "2018-02-08T17:03:25.633396", "tool_id": "mothur_classify_seqs", "outputs": {"tree_sum": {"src": "hda", "id": "c64bfc8445bed47e", "uuid": "678f639a-1732-4d98-8d91-e026ba091ebb"}, "logfile": {"src": "hda", "id": "7528831c3de506aa", "uuid": "9da71a0b-5901-4861-b9af-a7d50b40fd6d"}, "taxonomy_out": {"src": "hda", "id": "9b36a3aa47b79bf2", "uuid": "d0682327-05f1-48b6-8135-0888ec93e2ea"}, "tax_summary": {"src": "hda", "id": "14f44a11533277c1", "uuid": "754d8fee-d74e-402b-a9bd-e38b3c9b05d9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > classify.seqs(fasta=fasta.dat,reference=alignment.template.dat,taxonomy \r=tax.taxonomy.dat,method=knn,numwanted=10,search=kmer,ksize=8,relabund=false,pri \rntlevel=-1,processors=1)\n\nUsing 1 processors.\nGenerating search database... DONE.\nIt took 0 seconds generate search database. \n\nReading in the tax.taxonomy.dat taxonomy...\tDONE.\nClassifying sequences from fasta.dat ...\nProcessing sequence: 98\n\nIt took 0 secs to classify 98 sequences.\n\n\nIt took 0 secs to create the summary file for 98 sequences.\n\n\nOutput File Names: \nfasta.taxonomy.knn.taxonomy\nfasta.taxonomy.knn.tax.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s `dirname $(which mothur)`/* . && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_296.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_297.dat' alignment.template.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_298.dat' tax.taxonomy.dat && ln -s 'None' count.dat && ln -s 'None' name.dat && echo 'classify.seqs( fasta=fasta.dat, reference=alignment.template.dat, taxonomy=tax.taxonomy.dat, method=knn, numwanted=10, search=kmer, ksize=8, relabund=false, printlevel=-1, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| ./mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:03:21.352750", "params": {"count": "null", "name": "null", "relabund": "\"false\"", "tax": "{\"source2\": \"hist\", \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 298}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\"", "classify": "{\"search\": {\"__current_case__\": 0, \"algorithm\": \"kmer\", \"ksize\": \"8\"}, \"numwanted\": \"10\", \"method\": \"knn\", \"__current_case__\": 1}", "printlevel": "\"-1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"template\": {\"values\": [{\"src\": \"hda\", \"id\": 297}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "10262", "id": "69ce05044577833e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_classify_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"alignment\|source": "hist", "alignment\|template": {"src": "hda", "id": "266b4c416078dc76"}, "classify\|method": "knn", "classify\|search\|algorithm": "blast", "fasta": {"src": "hda", "id": "266b4c416078dc76"}, "tax\|taxonomy": {"src": "hda", "id": "0b62b0b7271d572a"}, "tax\|source2": "hist"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "0b62b0b7271d572a", "uuid": "40100a80-787e-42c4-9675-299ce099136f"}, "fasta": {"src": "hda", "id": "266b4c416078dc76", "uuid": "b7c393c3-fcd3-4602-8d08-19c7b41c1c11"}, "template": {"src": "hda", "id": "266b4c416078dc76", "uuid": "b7c393c3-fcd3-4602-8d08-19c7b41c1c11"}}, "update_time": "2018-02-08T17:04:00.015489", "tool_id": "mothur_classify_seqs", "outputs": {"tree_sum": {"src": "hda", "id": "044df8528177c496", "uuid": "0f333d2b-e98f-4c1d-9885-b9442a00d0ad"}, "logfile": {"src": "hda", "id": "8543024575f6f30b", "uuid": "94d5ad8d-bac4-4263-9369-41a64e40fb91"}, "taxonomy_out": {"src": "hda", "id": "74219090cb2d0112", "uuid": "10a61d0e-97a8-4051-8e84-49992c7ef157"}, "tax_summary": {"src": "hda", "id": "c8288be11b30d2bc", "uuid": "336d67d8-5c97-4c99-852b-a60d956a0402"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > classify.seqs(fasta=fasta.dat,reference=alignment.template.dat,taxonomy \r=tax.taxonomy.dat,method=knn,numwanted=10,search=blast,match=1,mismatch=-1,gapop \ren=-2,gapextend=-1,relabund=false,printlevel=-1,processors=1)\n\nUsing 1 processors.\nGenerating search database... DONE.\nIt took 0 seconds generate search database. \n\nReading in the tax.taxonomy.dat taxonomy...\tDONE.\nClassifying sequences from fasta.dat ...\nProcessing sequence: 100\nProcessing sequence: 200\nProcessing sequence: 242\n\nIt took 2 secs to classify 242 sequences.\n\n\nIt took 0 secs to create the summary file for 242 sequences.\n\n\nOutput File Names: \nfasta.taxonomy.knn.taxonomy\nfasta.taxonomy.knn.tax.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s `dirname $(which mothur)`/* . && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_304.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_304.dat' alignment.template.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_305.dat' tax.taxonomy.dat && ln -s 'None' count.dat && ln -s 'None' name.dat && echo 'classify.seqs( fasta=fasta.dat, reference=alignment.template.dat, taxonomy=tax.taxonomy.dat, method=knn, numwanted=10, search=blast, match=1, mismatch=-1, gapopen=-2, gapextend=-1, relabund=false, printlevel=-1, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| ./mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:03:54.993513", "params": {"count": "null", "name": "null", "relabund": "\"false\"", "tax": "{\"source2\": \"hist\", \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 305}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\"", "classify": "{\"search\": {\"algorithm\": \"blast\", \"gapopen\": \"-2\", \"mismatch\": \"-1\", \"__current_case__\": 1, \"gapextend\": \"-1\", \"match\": \"1\"}, \"numwanted\": \"10\", \"method\": \"knn\", \"__current_case__\": 1}", "printlevel": "\"-1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"template\": {\"values\": [{\"src\": \"hda\", \"id\": 304}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "10403", "id": "00c35829965cb81b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_classify_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"taxonomy": {"src": "hda", "id": "466b5293998bb5d6"}, "tree": {"src": "hda", "id": "906904e43ca63ecd"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "466b5293998bb5d6", "uuid": "f20e3c76-1740-4eff-8630-3d567e7839be"}, "tree": {"src": "hda", "id": "906904e43ca63ecd", "uuid": "4af15274-31d4-47f9-8d4c-b4e4f9a9adcf"}}, "update_time": "2018-02-08T17:04:27.158188", "tool_id": "mothur_classify_tree", "outputs": {"out_tree": {"src": "hda", "id": "1eb4a85cdfd1d969", "uuid": "104fa8be-7644-42c1-ac6a-5d57cf6fbe19"}, "logfile": {"src": "hda", "id": "59d26e2d28c3eb74", "uuid": "4320b983-e868-4c16-87da-966b2e111b80"}, "summary": {"src": "hda", "id": "8078f99fccaa607a", "uuid": "6b82ae77-a2de-422f-9cc5-652ce31296b1"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > classify.tree(tree=tree.dat,taxonomy=taxonomy.dat)\na is not in your taxonomy file. I will not include it in the consensus.\nd is not in your taxonomy file. I will not include it in the consensus.\na is not in your taxonomy file. I will not include it in the consensus.\nd is not in your taxonomy file. I will not include it in the consensus.\nf is not in your taxonomy file. I will not include it in the consensus.\n\n\nIt took 0 secs to find the concensus taxonomies.\n\nOutput File Names: \ntree.taxonomy.summary\ntree.taxonomy.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_311.dat' tree.dat && ln -s 'None' name.dat && ln -s 'None' group.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_310.dat' taxonomy.dat && echo 'classify.tree( tree=tree.dat, taxonomy=taxonomy.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:04:23.889464", "params": {"cutoff": "\"51\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name": "null", "dbkey": "\"hg17\"", "group": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "11070", "id": "1fb9c7b21f94ef77", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_classify_tree.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|source": "phylip", "input\|infile": {"src": "hda", "id": "e71a1c7a27ae6506"}}, "job": {"inputs": {"infile": {"src": "hda", "id": "e71a1c7a27ae6506", "uuid": "eb16f0aa-2f7d-4385-a0d9-8893849c19bc"}}, "update_time": "2018-02-08T17:04:49.595673", "tool_id": "mothur_clearcut", "outputs": {"logfile": {"src": "hda", "id": "b41e07faea40178d", "uuid": "17ef5d40-149c-43ad-a520-f7546721c4cf"}, "tree": {"src": "hda", "id": "0ea0054cb0d7ae96", "uuid": "ab2586c0-c483-47ff-98ce-5c92766ad47b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > clearcut(phylip=input.infile.dat,ntrees=1,norandom=false,shuffle=false, \rexpblen=OFF,expdist=OFF,neighbor=true)\n\nOutput File Names: \ninput.infile.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_315.dat' input.infile.dat && echo 'clearcut( phylip=input.infile.dat, ntrees=1, norandom=false, shuffle=false, expblen=OFF, expdist=OFF, neighbor=true )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:04:46.486175", "params": {"expdist": "\"false\"", "ntrees": "\"1\"", "shuffle": "\"false\"", "matrixout": "\"false\"", "dbkey": "\"hg17\"", "norandom": "\"false\"", "seed": "\"\"", "expblen": "\"false\"", "neighbor": "\"true\"", "input": "{\"source\": \"phylip\", \"infile\": {\"values\": [{\"src\": \"hda\", \"id\": 315}]}, \"__current_case__\": 2}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "11169", "id": "cf18f77993464b22", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_clearcut.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"expdist": true, "ntrees": "3", "shuffle": true, "norandom": true, "input\|infile": {"src": "hda", "id": "aa70baf734620bdc"}, "matrixout": true, "input\|source": "phylip", "expblen": true, "neighbor": false}, "job": {"inputs": {"infile": {"src": "hda", "id": "aa70baf734620bdc", "uuid": "c5ef22fd-857f-4977-a690-b821788054f9"}}, "update_time": "2018-02-08T17:05:03.113363", "tool_id": "mothur_clearcut", "outputs": {"logfile": {"src": "hda", "id": "2b0e2d16a6440935", "uuid": "c487b0c3-d332-43b8-be67-8ac767c93ab2"}, "tree": {"src": "hda", "id": "a81292b81d01663f", "uuid": "e5ce56a6-79c4-47d5-83b8-6cc4a6f68013"}, "matrix": {"src": "hda", "id": "e6bde25d0e72014d", "uuid": "09b640a1-dc3a-4ce9-ba5e-451e328abf99"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > clearcut(phylip=input.infile.dat,matrixout=matrixout.dist,ntrees=3,nora \rndom=true,shuffle=true,expblen=ON,expdist=ON,neighbor=false)\n\nOutput File Names: \ninput.infile.tre\nmatrixout.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_318.dat' input.infile.dat && echo 'clearcut( phylip=input.infile.dat, matrixout=matrixout.dist, ntrees=3, norandom=true, shuffle=true, expblen=ON, expdist=ON, neighbor=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:04:59.020694", "params": {"expdist": "\"true\"", "ntrees": "\"3\"", "shuffle": "\"true\"", "matrixout": "\"true\"", "dbkey": "\"hg17\"", "norandom": "\"true\"", "seed": "\"\"", "expblen": "\"true\"", "neighbor": "\"false\"", "input": "{\"source\": \"phylip\", \"infile\": {\"values\": [{\"src\": \"hda\", \"id\": 318}]}, \"__current_case__\": 2}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "11257", "id": "161ef5576377f4a0", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_clearcut.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"matrixout": true, "input\|source": "dna", "input\|infile": {"src": "hda", "id": "3b972a2e0d2ad508"}}, "job": {"inputs": {"infile": {"src": "hda", "id": "3b972a2e0d2ad508", "uuid": "42b137e8-ee9a-4fcd-9125-f44f25e16653"}}, "update_time": "2018-02-08T17:05:23.706458", "tool_id": "mothur_clearcut", "outputs": {"logfile": {"src": "hda", "id": "bf269ecfb1e2517b", "uuid": "f08be317-84d0-40a3-9e7f-71c6f8c47ebf"}, "tree": {"src": "hda", "id": "b756dc95aa3bca1d", "uuid": "29b63329-68d2-466e-8cbc-4f2bb9822b12"}, "matrix": {"src": "hda", "id": "72392165690065e0", "uuid": "94005b9d-5213-43f1-8ed6-624f86aa72d1"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > clearcut(fasta=input.infile.dat,DNA=true,matrixout=matrixout.dist,ntree \rs=1,norandom=false,shuffle=false,expblen=OFF,expdist=OFF,neighbor=true)\n\nOutput File Names: \ninput.infile.tre\nmatrixout.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_322.dat' input.infile.dat && echo 'clearcut( fasta=input.infile.dat, DNA=true, matrixout=matrixout.dist, ntrees=1, norandom=false, shuffle=false, expblen=OFF, expdist=OFF, neighbor=true )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:05:20.414063", "params": {"expdist": "\"false\"", "ntrees": "\"1\"", "shuffle": "\"false\"", "matrixout": "\"true\"", "dbkey": "\"hg17\"", "norandom": "\"false\"", "seed": "\"\"", "expblen": "\"false\"", "neighbor": "\"true\"", "input": "{\"source\": \"dna\", \"infile\": {\"values\": [{\"src\": \"hda\", \"id\": 322}]}, \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "11345", "id": "f21e60058e4146e2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_clearcut.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"matrix\|format": "phylip", "matrix\|dist": {"src": "hda", "id": "94bd5fbd2d4dc748"}}, "job": {"inputs": {"dist": {"src": "hda", "id": "94bd5fbd2d4dc748", "uuid": "ad044749-8a81-439a-9fc9-cef9c22d1dcc"}}, "update_time": "2018-02-08T17:05:42.437919", "tool_id": "mothur_cluster", "outputs": {"rabund": {"src": "hda", "id": "35e639f464fb8f4d", "uuid": "1d4871ed-9f54-483f-95fd-5ec6e68af090"}, "logfile": {"src": "hda", "id": "ffc368cd972b6cba", "uuid": "309c09e9-25e7-4587-aa9b-610dbfed4648"}, "otulist": {"src": "hda", "id": "3c43ce8ab3a9cd20", "uuid": "a2c686bc-bc70-4ece-af0b-387a4e03ba6d"}, "sabund": {"src": "hda", "id": "475e4ad0b99b0c18", "uuid": "53f99ebc-3088-43cc-9403-64b6b285ba67"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster(phylip=matrix.dist.dat,metric=mcc,initialize=singleton,delta=0. \r0001,iters=100,precision=100,sim=false,method=opti)\n\nUsing 1 processors.\n\nYou did not set a cutoff, using 0.03.\n******************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering matrix.dist.dat\n\n\niter\ttime\tlabel\tnum_otus\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0\t0\t0.03\t98\t0.03\t0\t4736\t0\t17\t0\t1\t0\t0.996423\t0\t0.996423\t0\t0\t\n1\t0\t0.03\t88\t0.03\t17\t4736\t0\t0\t1\t1\t1\t1\t0\t1\t1\t1\t\n2\t0\t0.03\t88\t0.03\t17\t4736\t0\t0\t1\t1\t1\t1\t0\t1\t1\t1\t\n\n\nIt took 0 seconds to cluster\n\nOutput File Names: \nmatrix.dist.opti_mcc.list\nmatrix.dist.opti_mcc.steps\nmatrix.dist.opti_mcc.sabund\nmatrix.dist.opti_mcc.rabund\nmatrix.dist.opti_mcc.sensspec\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_326.dat' matrix.dist.dat && ln -s 'None' matrix.name.dat && ln -s 'None' count.dat && echo 'cluster( phylip=matrix.dist.dat, metric=mcc, initialize=singleton, delta=0.0001, iters=100, precision=100, sim=false, method=opti )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:05:37.908897", "params": {"count": "null", "cutoff": "\"0.0\"", "matrix": "{\"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 326}]}, \"name\": null, \"__current_case__\": 1, \"format\": \"phylip\"}", "select_method": "{\"iters\": \"100\", \"metric\": \"mcc\", \"__current_case__\": 5, \"delta\": \"0.0001\", \"initialize\": \"singleton\", \"method\": \"opti\"}", "dbkey": "\"hg17\"", "precision": "\"100\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "sim": "\"false\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "11445", "id": "c95281174db2641a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"matrix\|format": "column", "matrix\|dist": {"src": "hda", "id": "555065f5aff402d2"}, "matrix\|name": {"src": "hda", "id": "597e4b92c7768991"}}, "job": {"inputs": {"dist": {"src": "hda", "id": "555065f5aff402d2", "uuid": "a8c89c54-a556-4e5a-bffc-3a38dd6130d8"}, "name": {"src": "hda", "id": "597e4b92c7768991", "uuid": "5f592839-3c46-4865-9ccc-734ebdc5e415"}}, "update_time": "2018-02-08T17:06:18.213444", "tool_id": "mothur_cluster", "outputs": {"rabund": {"src": "hda", "id": "ea74846895a98ad3", "uuid": "aa327386-1426-45e7-9f55-12e85d15b4ec"}, "logfile": {"src": "hda", "id": "6a9009e6b944272b", "uuid": "bfad486b-574e-4864-9770-3aadc0bf5a3f"}, "otulist": {"src": "hda", "id": "90fd946e89881eaf", "uuid": "d1317f90-e5ab-4c75-8679-28965c9824ae"}, "sabund": {"src": "hda", "id": "2df305d2bcf63841", "uuid": "b0c4d1d2-56c8-47cc-a5a0-cb68bca73f8b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster(column=matrix.dist.dat,name=matrix.name.dat,metric=mcc,initiali \rze=singleton,delta=0.0001,iters=100,precision=100,sim=false,method=opti)\n\nUsing 1 processors.\n\nYou did not set a cutoff, using 0.03.\n\nClustering matrix.dist.dat\n\n\niter\ttime\tlabel\tnum_otus\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0\t0\t0.03\t96\t0.03\t0\t4560\t0\t0\t0\t1\t0\t1\t0\t1\t0\t0\t\n1\t0\t0.03\t96\t0.03\t0\t4560\t0\t0\t0\t1\t0\t1\t0\t1\t0\t0\t\n\n\nIt took 0 seconds to cluster\n\nOutput File Names: \nmatrix.dist.opti_mcc.list\nmatrix.dist.opti_mcc.steps\nmatrix.dist.opti_mcc.sabund\nmatrix.dist.opti_mcc.rabund\nmatrix.dist.opti_mcc.sensspec\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_331.dat' matrix.dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_332.dat' matrix.name.dat && ln -s 'None' count.dat && echo 'cluster( column=matrix.dist.dat, name=matrix.name.dat, metric=mcc, initialize=singleton, delta=0.0001, iters=100, precision=100, sim=false, method=opti )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:06:12.756285", "params": {"count": "null", "cutoff": "\"0.0\"", "matrix": "{\"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 331}]}, \"name\": {\"values\": [{\"src\": \"hda\", \"id\": 332}]}, \"__current_case__\": 0, \"format\": \"column\"}", "select_method": "{\"iters\": \"100\", \"metric\": \"mcc\", \"__current_case__\": 5, \"delta\": \"0.0001\", \"initialize\": \"singleton\", \"method\": \"opti\"}", "dbkey": "\"hg17\"", "precision": "\"100\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "sim": "\"false\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "11596", "id": "26b7e36460fca86e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"matrix\|format": "column", "matrix\|dist": {"src": "hda", "id": "8ea35917f4649fec"}, "matrix\|name": {"src": "hda", "id": "48c17343dcb0fe59"}}, "job": {"inputs": {"dist": {"src": "hda", "id": "8ea35917f4649fec", "uuid": "c9f7d113-9030-4115-82ee-9d65edd27e3a"}, "name": {"src": "hda", "id": "48c17343dcb0fe59", "uuid": "4174a4bd-d31b-42e3-9a07-b5858c5b925a"}}, "update_time": "2018-02-08T17:06:51.168891", "tool_id": "mothur_cluster", "outputs": {"rabund": {"src": "hda", "id": "459ebd1d4b9be0d2", "uuid": "c8f134ea-eb5e-4118-9fbb-57397b54ef29"}, "logfile": {"src": "hda", "id": "940151f28ccfd679", "uuid": "3ce4b4ef-c34d-43af-8595-156fea1810ec"}, "otulist": {"src": "hda", "id": "acb5efb55c8f2fca", "uuid": "b9eed437-fa24-4763-9798-48ebc331434d"}, "sabund": {"src": "hda", "id": "86fc1a32b14d4612", "uuid": "97a259d7-58c2-4e3e-9301-9f6b4eaf1012"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster(column=matrix.dist.dat,name=matrix.name.dat,metric=mcc,initiali \rze=singleton,delta=0.0001,iters=100,precision=100,sim=false,method=opti)\n\nUsing 1 processors.\n\nYou did not set a cutoff, using 0.03.\n\nClustering matrix.dist.dat\n\n\niter\ttime\tlabel\tnum_otus\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0\t0\t0.03\t96\t0.03\t0\t4560\t0\t0\t0\t1\t0\t1\t0\t1\t0\t0\t\n1\t0\t0.03\t96\t0.03\t0\t4560\t0\t0\t0\t1\t0\t1\t0\t1\t0\t0\t\n\n\nIt took 0 seconds to cluster\n\nOutput File Names: \nmatrix.dist.opti_mcc.list\nmatrix.dist.opti_mcc.steps\nmatrix.dist.opti_mcc.sabund\nmatrix.dist.opti_mcc.rabund\nmatrix.dist.opti_mcc.sensspec\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_337.dat' matrix.dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_338.dat' matrix.name.dat && ln -s 'None' count.dat && echo 'cluster( column=matrix.dist.dat, name=matrix.name.dat, metric=mcc, initialize=singleton, delta=0.0001, iters=100, precision=100, sim=false, method=opti )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:06:46.589877", "params": {"count": "null", "cutoff": "\"0.0\"", "matrix": "{\"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 337}]}, \"name\": {\"values\": [{\"src\": \"hda\", \"id\": 338}]}, \"__current_case__\": 0, \"format\": \"column\"}", "select_method": "{\"iters\": \"100\", \"metric\": \"mcc\", \"__current_case__\": 5, \"delta\": \"0.0001\", \"initialize\": \"singleton\", \"method\": \"opti\"}", "dbkey": "\"hg17\"", "precision": "\"100\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "sim": "\"false\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "11767", "id": "5c14fa19c3fe9aa2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"dist": {"src": "hda", "id": "c2096fa94981c9cc"}}, "job": {"inputs": {"dist": {"src": "hda", "id": "c2096fa94981c9cc", "uuid": "457e36fb-13ec-40ee-9969-e08fefad8496"}}, "update_time": "2018-02-08T17:07:21.690682", "tool_id": "mothur_cluster_classic", "outputs": {"rabund": {"src": "hda", "id": "aa6cc630da5109fb", "uuid": "564a1502-1ffc-414c-91dd-bb7b7a442616"}, "logfile": {"src": "hda", "id": "37f9ab3378d23774", "uuid": "69ef929f-cc25-41b2-86a0-2d58b70bf44e"}, "otulist": {"src": "hda", "id": "4c469a959b869c08", "uuid": "8e7894e4-13ae-4ba0-a182-db5048ef9f4d"}, "sabund": {"src": "hda", "id": "8c559fb88d75a36b", "uuid": "e2b7d2e7-d821-4291-8384-da431189328d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > cluster.classic(phylip=dist.dat,method=average,precision=100,sim=false) \r\u001b[A\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[K)\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\nunique\t1\t24\n1.75\t2\t22\t1\n2.01\t2\t20\t2\n2.10\t2\t18\t3\n2.13\t2\t16\t4\n2.22\t2\t14\t5\n2.26\t3\t11\t5\t1\n2.42\t5\t11\t4\t0\t0\t1\n2.93\t6\t10\t4\t0\t0\t0\t1\n3.07\t6\t10\t2\t0\t1\t0\t1\n3.27\t6\t9\t1\t1\t1\t0\t1\n3.34\t6\t7\t2\t1\t1\t0\t1\n3.44\t6\t6\t1\t2\t1\t0\t1\n3.53\t7\t6\t1\t1\t0\t0\t1\t1\n3.56\t7\t4\t2\t1\t0\t0\t1\t1\n4.07\t7\t3\t2\t0\t1\t0\t1\t1\n4.15\t13\t3\t2\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t1\n4.58\t13\t2\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t1\n4.72\t13\t1\t1\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t1\n5.18\t16\t1\t1\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\n5.76\t21\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\n5.91\t23\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\n6.67\t24\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\n\nOutput File Names: \ndist.an.sabund\ndist.an.rabund\ndist.an.list\n\nIt took 0 seconds to cluster\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_343.dat' dist.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && echo 'cluster.classic( phylip=dist.dat, method=average, precision=100, sim=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:07:18.320079", "params": {"count": "null", "cutoff": "\"\"", "name": "null", "precision": "\"100\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"average\"", "sim": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "11897", "id": "fc5c2ad70cbb4f9f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_classic.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "82ea1c58d22fbeef"}, "names": {"src": "hda", "id": "3d5f803521123c6e"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "82ea1c58d22fbeef", "uuid": "4b29d8b2-b22d-4643-a7f1-7bdb8254276e"}, "names": {"src": "hda", "id": "3d5f803521123c6e", "uuid": "342207f4-9855-4fa3-ab02-b062f576deb6"}}, "update_time": "2018-02-08T17:07:53.344919", "tool_id": "mothur_cluster_fragments", "outputs": {"out_names": {"src": "hda", "id": "0c1eec7a0b69039e", "uuid": "397fead2-7a43-4716-8db4-a1f09b18b77a"}, "logfile": {"src": "hda", "id": "d5273cf5fa0c242d", "uuid": "a5fa27a5-b40b-4bcb-8cd9-e909b56c9370"}, "out_fasta": {"src": "hda", "id": "ec0fb831200675f4", "uuid": "db083fe2-064f-4445-837c-2584ba3c2999"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > cluster.fragments(fasta=fasta.dat,diffs=0,percent=0,name=names.dat)\n0\t98\t0\n98\t96\t2\n\nTotal number of sequences before cluster.fragments was 98.\ncluster.fragments removed 2 sequences.\n\nIt took 0 secs to cluster 98 sequences.\n\nOutput File Names: \nfasta.fragclust.fasta\nfasta.fragclust.names\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_348.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_349.dat' names.dat && ln -s 'None' count.dat && echo 'cluster.fragments( fasta=fasta.dat, diffs=0, percent=0, name=names.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:07:49.188733", "params": {"count": "null", "diffs": "\"0\"", "percent": "\"0\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "12010", "id": "83e248eabb1b3d31", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_fragments.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"splitby\|condmethod\|method": "average", "splitby\|matrix\|format": "phylip", "splitby\|matrix\|dist": {"src": "hda", "id": "f1f75462f416e186"}, "splitby\|splitmethod": "distance"}, "job": {"inputs": {"splitby\|dist": {"src": "hda", "id": "f1f75462f416e186", "uuid": "74f96c23-ef2d-4632-abaa-2b2a0d763fab"}}, "update_time": "2018-02-08T17:08:20.393794", "tool_id": "mothur_cluster_split", "outputs": {"rabund": {"src": "hda", "id": "f283e96027016ec6", "uuid": "d18af698-5952-4a8f-aae0-9daddd004626"}, "logfile": {"src": "hda", "id": "0ab9f8045882e86f", "uuid": "a832c53d-dbd3-4455-85f3-1bf23af63e6e"}, "otulist": {"src": "hda", "id": "2c72ab2ea314d830", "uuid": "c2874287-ffa4-4064-b4bb-e682011a03b9"}, "sabund": {"src": "hda", "id": "f3e7443ed4070d7c", "uuid": "b1621de1-03a0-4536-81db-30c4948b7a8f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster.split(splitmethod=distance,phylip=splitby.matrix.dist.dat,metho \rd=average,precision=100,large=false,cluster=true,runsensspec=true,processors=1)\n\nUsing 1 processors.\nConverting to column format...\nIt took 0 seconds to convert the distance file.\nSplitting the file...\nIt took 0 seconds to split the distance file.\n\nReading splitby.matrix.dist.column.dist.2.temp\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering splitby.matrix.dist.column.dist.2.temp\nCutoff was 0.15 changed cutoff to 0.11\n\nReading splitby.matrix.dist.column.dist.5.temp\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering splitby.matrix.dist.column.dist.5.temp\nCutoff was 0.15 changed cutoff to 0.14\n\nReading splitby.matrix.dist.column.dist.1.temp\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering splitby.matrix.dist.column.dist.1.temp\n\nReading splitby.matrix.dist.column.dist.7.temp\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering splitby.matrix.dist.column.dist.7.temp\nCutoff was 0.15 changed cutoff to 0.12\n\nReading splitby.matrix.dist.column.dist.4.temp\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering splitby.matrix.dist.column.dist.4.temp\nCutoff was 0.15 changed cutoff to 0.13\n\nReading splitby.matrix.dist.column.dist.6.temp\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering splitby.matrix.dist.column.dist.6.temp\n\nReading splitby.matrix.dist.column.dist.3.temp\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering splitby.matrix.dist.column.dist.3.temp\n\nReading splitby.matrix.dist.column.dist.10.temp\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering splitby.matrix.dist.column.dist.10.temp\n\nReading splitby.matrix.dist.column.dist.13.temp\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering splitby.matrix.dist.column.dist.13.temp\n\nReading splitby.matrix.dist.column.dist.0.temp\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering splitby.matrix.dist.column.dist.0.temp\n\nReading splitby.matrix.dist.column.dist.9.temp\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering splitby.matrix.dist.column.dist.9.temp\n\nReading splitby.matrix.dist.column.dist.11.temp\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering splitby.matrix.dist.column.dist.11.temp\n\nReading splitby.matrix.dist.column.dist.12.temp\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering splitby.matrix.dist.column.dist.12.temp\n\nCutoff was 0.15 changed cutoff to 0.11\nIt took 0 seconds to cluster\nMerging the clustered files...\nIt took 0 seconds to merge.\n\nOutput File Names: \nsplitby.matrix.dist.column.an.sabund\nsplitby.matrix.dist.column.an.rabund\nsplitby.matrix.dist.column.an.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_353.dat' splitby.matrix.dist.dat && ln -s 'None' splitby.matrix.nameOrCount.dat && echo 'cluster.split( splitmethod=distance, phylip=splitby.matrix.dist.dat, method=average, precision=100, large=false, cluster=true, runsensspec=true, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:08:15.820483", "params": {"runsensspec": "\"true\"", "cutoff": "\"0.0\"", "splitby": "{\"splitmethod\": \"distance\", \"condmethod\": {\"method\": \"average\", \"__current_case__\": 2}, \"matrix\": {\"nameOrCount\": null, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 353}]}, \"__current_case__\": 1, \"format\": \"phylip\"}, \"__current_case__\": 0}", "precision": "\"100\"", "dbkey": "\"hg17\"", "large": "\"false\"", "cluster": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "12104", "id": "4e27b888e0f89616", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_split.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"splitby\|condmethod\|method": "average", "cluster": false, "splitby\|matrix\|format": "phylip", "splitby\|matrix\|dist": {"src": "hda", "id": "22ac87488bc814b9"}, "splitby\|splitmethod": "distance"}, "job": {"inputs": {"splitby\|dist": {"src": "hda", "id": "22ac87488bc814b9", "uuid": "c5ddd9c1-e9b1-4dc8-b471-62e1cbe7a970"}}, "update_time": "2018-02-08T17:08:54.553537", "tool_id": "mothur_cluster_split", "outputs": {"__new_primary_file_9\|7__": {"src": "hda", "id": "6cc323ea174af743", "uuid": "8d26ad52-9bce-4d0f-a128-b83232d63c1f"}, "__new_primary_file_9\|13__": {"src": "hda", "id": "09f8fd3b2e41755d", "uuid": "9dfe2404-8d7d-4c8f-9a12-e4ab0f96348f"}, "__new_primary_file_extra\|9__": {"src": "hda", "id": "4b964545b41f57a8", "uuid": "9c3fb19a-ae9a-483d-ae59-748b4fbba575"}, "__new_primary_file_extra\|13__": {"src": "hda", "id": "f85178165ba80947", "uuid": "d9eb5cc4-dc67-4594-b6de-f1124b2fd87a"}, "splitfile": {"src": "hda", "id": "2b49763c55874680", "uuid": "a2e63b7f-b705-4c61-b529-35a803f011b6"}, "__new_primary_file_9\|6__": {"src": "hda", "id": "158be0d01c91f0d3", "uuid": "bbffb137-e152-482f-9ace-f67324722714"}, "__new_primary_file_extra\|12__": {"src": "hda", "id": "721a73f13e9921b7", "uuid": "f81f533a-0778-4f91-9207-e4c6d719af46"}, "__new_primary_file_9\|4__": {"src": "hda", "id": "709f4e85f6d2c262", "uuid": "becf4ab3-c26a-486c-ab10-33b3825c8df7"}, "__new_primary_file_9\|9__": {"src": "hda", "id": "64b146a0a237cf0e", "uuid": "febc9484-9717-44ff-af5d-45b9754a6fc1"}, "__new_primary_file_extra\|1__": {"src": "hda", "id": "0aed0175215b082a", "uuid": "ea0c11c9-c633-4875-949c-f09c41bc174e"}, "__new_primary_file_9\|10__": {"src": "hda", "id": "a5b8d21ac8fc30ea", "uuid": "68d1b13a-2f52-448c-a2e9-c2afce62a48e"}, "otulist": {"src": "hda", "id": "9b8f9fbdb2c6dd2c", "uuid": "c14e1520-e196-4f6c-8ba7-e7aeeeb304bf"}, "rabund": {"src": "hda", "id": "25296282d079fac6", "uuid": "a86dcd47-c38c-459d-931f-ae8bcc85f6f4"}, "__new_primary_file_9\|1__": {"src": "hda", "id": "18d19b643e7062cc", "uuid": "54c1d879-b21a-4847-aed7-99baa3d0dd33"}, "__new_primary_file_extra\|2__": {"src": "hda", "id": "943b175492f370d8", "uuid": "492e9178-cdd8-4980-a515-c5b5893c190d"}, "__new_primary_file_extra\|4__": {"src": "hda", "id": "4b36d8f744e89cdc", "uuid": "2b557902-ec34-4d1e-9ffd-6684b6cb6aaa"}, "__new_primary_file_extra\|3__": {"src": "hda", "id": "f2c720655bd71813", "uuid": "aa9544d9-d154-4660-91d1-2e1148f4d3d8"}, "__new_primary_file_9\|3__": {"src": "hda", "id": "ec3c9d08d9062ead", "uuid": "9011b542-a9ce-4969-a7db-03335616cc9f"}, "logfile": {"src": "hda", "id": "a5170ff908b4401b", "uuid": "a2151d9c-8c36-4d47-9aad-6de7c3cc8c28"}, "__new_primary_file_extra\|5__": {"src": "hda", "id": "3b057c0454a7c801", "uuid": "a3af2bdb-7aa7-41a3-be3b-2fe53ea22060"}, "__new_primary_file_9\|2__": {"src": "hda", "id": "759c19e61550929d", "uuid": "ba70dc4a-4d0f-4520-b7d6-fb30b0537e73"}, "__new_primary_file_9\|11__": {"src": "hda", "id": "43766c028675eda0", "uuid": "89a4c048-b087-4bdd-b710-824f099129b2"}, "__new_primary_file_extra\|6__": {"src": "hda", "id": "07fd1c8ec8f13176", "uuid": "664abf4a-5daa-4332-a09f-e855aa50d616"}, "sabund": {"src": "hda", "id": "c1fc90e177f46aff", "uuid": "03d7e66e-b2d6-44ec-a951-085714c44993"}, "__new_primary_file_extra\|7__": {"src": "hda", "id": "5adbd2172c54d7c8", "uuid": "edba9c0a-9a76-4763-ad86-9e5dce81155c"}, "__new_primary_file_9\|5__": {"src": "hda", "id": "802ffc5c50268813", "uuid": "5e40989a-9e9d-4a19-86f7-817b94d331da"}, "__new_primary_file_extra\|11__": {"src": "hda", "id": "20b89408decf8a23", "uuid": "ef137ee7-ea8d-4b59-85f1-dd5e2dc31c27"}, "__new_primary_file_9\|0__": {"src": "hda", "id": "d49ecd190d765ffa", "uuid": "19c3dc84-9217-4b1e-89c7-a39d84bcaa66"}, "__new_primary_file_extra\|extra__": {"src": "hda", "id": "2915b60ef025819a", "uuid": "ed8f847c-6e65-4458-9167-55265ad85dbb"}, "__new_primary_file_extra\|0__": {"src": "hda", "id": "af2b33d2c4a65f6c", "uuid": "623ad805-121d-4e8d-ae7d-5a5cd9dddb10"}, "__new_primary_file_extra\|10__": {"src": "hda", "id": "3c8273a46e218a3f", "uuid": "2a5dbc9d-f71c-411b-bb5f-7f403f708199"}, "__new_primary_file_9\|12__": {"src": "hda", "id": "84069f8e0a4c5a8e", "uuid": "5a41226d-54e2-41f6-9058-be37cfb62bd5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster.split(splitmethod=distance,phylip=splitby.matrix.dist.dat,metho \rd=average,precision=100,large=false,cluster=false,runsensspec=true,processors=1) \r\u001b[A\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[K)\n\nUsing 1 processors.\nConverting to column format...\nIt took 0 seconds to convert the distance file.\nSplitting the file...\nIt took 0 seconds to split the distance file.\n\nOutput File Names: \n\nsplitby.matrix.dist.column.file\nsplitby.matrix.dist.column.dist.2.temp\nsplitby.matrix.dist.dat.names.2.temp\nsplitby.matrix.dist.column.dist.5.temp\nsplitby.matrix.dist.dat.names.5.temp\nsplitby.matrix.dist.column.dist.1.temp\nsplitby.matrix.dist.dat.names.1.temp\nsplitby.matrix.dist.column.dist.7.temp\nsplitby.matrix.dist.dat.names.7.temp\nsplitby.matrix.dist.column.dist.4.temp\nsplitby.matrix.dist.dat.names.4.temp\nsplitby.matrix.dist.column.dist.6.temp\nsplitby.matrix.dist.dat.names.6.temp\nsplitby.matrix.dist.column.dist.3.temp\nsplitby.matrix.dist.dat.names.3.temp\nsplitby.matrix.dist.column.dist.10.temp\nsplitby.matrix.dist.dat.names.10.temp\nsplitby.matrix.dist.column.dist.13.temp\nsplitby.matrix.dist.dat.names.13.temp\nsplitby.matrix.dist.column.dist.0.temp\nsplitby.matrix.dist.dat.names.0.temp\nsplitby.matrix.dist.column.dist.9.temp\nsplitby.matrix.dist.dat.names.9.temp\nsplitby.matrix.dist.column.dist.11.temp\nsplitby.matrix.dist.dat.names.11.temp\nsplitby.matrix.dist.column.dist.12.temp\nsplitby.matrix.dist.dat.names.12.temp\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_358.dat' splitby.matrix.dist.dat && ln -s 'None' splitby.matrix.nameOrCount.dat && echo 'cluster.split( splitmethod=distance, phylip=splitby.matrix.dist.dat, method=average, precision=100, large=false, cluster=false, runsensspec=true, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:08:47.634172", "params": {"runsensspec": "\"true\"", "cutoff": "\"0.0\"", "splitby": "{\"splitmethod\": \"distance\", \"condmethod\": {\"method\": \"average\", \"__current_case__\": 2}, \"matrix\": {\"nameOrCount\": null, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 358}]}, \"__current_case__\": 1, \"format\": \"phylip\"}, \"__current_case__\": 0}", "precision": "\"100\"", "dbkey": "\"hg17\"", "large": "\"false\"", "cluster": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "12239", "id": "d760e1d92679b730", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_split.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"splitby\|taxonomy": {"src": "hda", "id": "0af7797da2f1a1c7"}, "splitby\|condmethod\|method": "average", "splitby\|splitmethod": "classify", "splitby\|dist": {"src": "hda", "id": "732b43bd12cd060f"}, "splitby\|nameOrCount": {"src": "hda", "id": "b7d5085eacaa6509"}}, "job": {"inputs": {"nameOrCount": {"src": "hda", "id": "b7d5085eacaa6509", "uuid": "f3ee5a09-1ec0-4b77-b0ef-9a3dafda896d"}, "taxonomy": {"src": "hda", "id": "0af7797da2f1a1c7", "uuid": "61860e61-15bb-4d6a-9de7-b1c9df4cf18e"}, "dist": {"src": "hda", "id": "732b43bd12cd060f", "uuid": "f4a7c395-0387-4a9b-8653-dc3131dc8eb0"}}, "update_time": "2018-02-08T17:09:37.257438", "tool_id": "mothur_cluster_split", "outputs": {"rabund": {"src": "hda", "id": "fde5d0b73a42236a", "uuid": "8732d6da-19a3-40bd-86a8-9500089d5048"}, "logfile": {"src": "hda", "id": "de19e90a144e923c", "uuid": "45df5879-94af-48ac-b35e-df3cd6caafc9"}, "otulist": {"src": "hda", "id": "6ed393d03ba7fd0e", "uuid": "846f0381-4cbb-4aa2-bd67-1c2482726beb"}, "sabund": {"src": "hda", "id": "7535296d23a37c60", "uuid": "2baef149-c8d7-455d-9460-07edf376752b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster.split(splitmethod=classify,column=splitby.dist.dat,taxonomy=spl \ritby.taxonomy.dat,name=splitby.nameOrCount.dat,taxlevel=1,method=average,precisi \ron=100,large=false,cluster=true,runsensspec=true,processors=1)\n\nUsing 1 processors.\nSplitting the file...\nIt took 0 seconds to split the distance file.\n\nReading splitby.dist.dat.0.temp\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering splitby.dist.dat.0.temp\nIt took 0 seconds to cluster\nMerging the clustered files...\nIt took 0 seconds to merge.\n\nOutput File Names: \nsplitby.dist.an.sabund\nsplitby.dist.an.rabund\nsplitby.dist.an.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_391.dat' splitby.dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_393.dat' splitby.nameOrCount.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_392.dat' splitby.taxonomy.dat && echo 'cluster.split( splitmethod=classify, column=splitby.dist.dat, taxonomy=splitby.taxonomy.dat, name=splitby.nameOrCount.dat, taxlevel=1, method=average, precision=100, large=false, cluster=true, runsensspec=true, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:09:31.700719", "params": {"runsensspec": "\"true\"", "cutoff": "\"0.0\"", "splitby": "{\"splitmethod\": \"classify\", \"condmethod\": {\"method\": \"average\", \"__current_case__\": 2}, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 391}]}, \"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 393}]}, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 392}]}, \"__current_case__\": 1, \"taxlevel\": \"1\"}", "precision": "\"100\"", "dbkey": "\"hg17\"", "large": "\"false\"", "cluster": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "12408", "id": "449eb427f528cea7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_split.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"splitby\|taxonomy": {"src": "hda", "id": "957dec9f2200cbe4"}, "splitby\|condmethod\|method": "average", "splitby\|splitmethod": "classify", "splitby\|dist": {"src": "hda", "id": "fcbedabdda23c338"}, "splitby\|nameOrCount": {"src": "hda", "id": "7f45e41d747c3b22"}}, "job": {"inputs": {"nameOrCount": {"src": "hda", "id": "7f45e41d747c3b22", "uuid": "495ee28e-4f96-447e-9d34-8388522ce56d"}, "taxonomy": {"src": "hda", "id": "957dec9f2200cbe4", "uuid": "0e1582f5-cba2-44fc-9afd-a6a6a68bcf12"}, "dist": {"src": "hda", "id": "fcbedabdda23c338", "uuid": "16c9486e-d67a-4e27-a72f-8f18dfd26971"}}, "update_time": "2018-02-08T17:10:13.687017", "tool_id": "mothur_cluster_split", "outputs": {"logfile": {"src": "hda", "id": "a6780727682706fd", "uuid": "ebe106d6-2ee0-47b6-9d24-4fd6e52e36fb"}, "otulist": {"src": "hda", "id": "c809b2abaed97358", "uuid": "f5f10b68-5385-4a18-97b8-7bd03cd541d8"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster.split(splitmethod=classify,column=splitby.dist.dat,taxonomy=spl \ritby.taxonomy.dat,count=splitby.nameOrCount.dat,taxlevel=1,method=average,precis \rion=100,large=false,cluster=true,runsensspec=true,processors=1)\n\nUsing 1 processors.\nSplitting the file...\nIt took 0 seconds to split the distance file.\n\nReading splitby.dist.dat.0.temp\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering splitby.dist.dat.0.temp\nIt took 0 seconds to cluster\nMerging the clustered files...\nIt took 0 seconds to merge.\n\nOutput File Names: \nsplitby.dist.an.unique_list.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_398.dat' splitby.dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_400.dat' splitby.nameOrCount.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_399.dat' splitby.taxonomy.dat && echo 'cluster.split( splitmethod=classify, column=splitby.dist.dat, taxonomy=splitby.taxonomy.dat, count=splitby.nameOrCount.dat, taxlevel=1, method=average, precision=100, large=false, cluster=true, runsensspec=true, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:10:09.362326", "params": {"runsensspec": "\"true\"", "cutoff": "\"0.0\"", "splitby": "{\"splitmethod\": \"classify\", \"condmethod\": {\"method\": \"average\", \"__current_case__\": 2}, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 398}]}, \"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 400}]}, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 399}]}, \"__current_case__\": 1, \"taxlevel\": \"1\"}", "precision": "\"100\"", "dbkey": "\"hg17\"", "large": "\"false\"", "cluster": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "12591", "id": "8bfda5654e551614", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_split.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"splitby\|taxonomy": {"src": "hda", "id": "6fb516af7370ea7a"}, "splitby\|fasta": {"src": "hda", "id": "71bc98c5ef351f59"}, "splitby\|condmethod\|method": "average", "cutoff": "9999", "splitby\|splitmethod": "fasta", "splitby\|nameOrCount": {"src": "hda", "id": "63f8201b30d2cadd"}}, "job": {"inputs": {"nameOrCount": {"src": "hda", "id": "63f8201b30d2cadd", "uuid": "ced19938-b32a-477b-9b2f-7f97faff871f"}, "taxonomy": {"src": "hda", "id": "6fb516af7370ea7a", "uuid": "cea8d185-870c-488d-84eb-544d8084b763"}, "fasta": {"src": "hda", "id": "71bc98c5ef351f59", "uuid": "107d7fcb-2c10-4ee1-91ca-285b91ceafe6"}}, "update_time": "2018-02-08T17:10:41.676918", "tool_id": "mothur_cluster_split", "outputs": {"rabund": {"src": "hda", "id": "41a728572c331a9d", "uuid": "91789c46-7cc2-46b9-b081-8a8330db86b1"}, "logfile": {"src": "hda", "id": "dfb58ec7c7cde5ba", "uuid": "709949a8-e538-4f95-b9fd-3cfdcb6aeca9"}, "otulist": {"src": "hda", "id": "598476a21fa893cd", "uuid": "bc4b64e8-3ad1-4287-9e78-6ea4bad03d30"}, "sabund": {"src": "hda", "id": "9c8aa3de76c5f0c4", "uuid": "8cc44192-61ab-4e70-a827-b3f559379040"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster.split(splitmethod=fasta,fasta=splitby.fasta.dat,taxonomy=splitb \ry.taxonomy.dat,name=splitby.nameOrCount.dat,taxlevel=3,classic=false,method=aver \rage,cutoff=9999.0,precision=100,large=false,cluster=true,runsensspec=true,proces \rsors=1)\n\nUsing 1 processors.\nSplitting the file...\n/**************************************/\nRunning command: dist.seqs(fasta=splitby.fasta.dat.0.temp, processors=1, cutoff=9999)\n\nUsing 1 processors.\n/**************************************/\n0\t0\n1\t0\n\nOutput File Names: \nsplitby.fasta.dat.0.dist\n\nIt took 0 seconds to calculate the distances for 2 sequences.\nIt took 0 seconds to split the distance file.\n\nReading splitby.fasta.dat.0.dist\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nClustering splitby.fasta.dat.0.dist\nIt took 0 seconds to cluster\nMerging the clustered files...\nIt took 0 seconds to merge.\n\nOutput File Names: \nsplitby.fasta.an.sabund\nsplitby.fasta.an.rabund\nsplitby.fasta.an.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_403.dat' splitby.fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_405.dat' splitby.nameOrCount.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_404.dat' splitby.taxonomy.dat && echo 'cluster.split( splitmethod=fasta, fasta=splitby.fasta.dat, taxonomy=splitby.taxonomy.dat, name=splitby.nameOrCount.dat, taxlevel=3, classic=false, method=average, cutoff=9999.0, precision=100, large=false, cluster=true, runsensspec=true, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:10:36.383791", "params": {"runsensspec": "\"true\"", "cutoff": "\"9999.0\"", "splitby": "{\"splitmethod\": \"fasta\", \"condmethod\": {\"method\": \"average\", \"__current_case__\": 2}, \"classic\": \"false\", \"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 405}]}, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 404}]}, \"__current_case__\": 2, \"fasta\": {\"values\": [{\"src\": \"hda\", \"id\": 403}]}, \"taxlevel\": \"3\"}", "precision": "\"100\"", "dbkey": "\"hg17\"", "large": "\"false\"", "cluster": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "12771", "id": "c48fc7b200585e1b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_split.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"splitby\|taxonomy": {"src": "hda", "id": "3529226cbbc41f8d"}, "splitby\|fasta": {"src": "hda", "id": "f8fb2d243923edf0"}, "splitby\|condmethod\|method": "agc", "splitby\|splitmethod": "fasta", "splitby\|nameOrCount": {"src": "hda", "id": "77d4412f77f6b180"}}, "job": {"inputs": {"nameOrCount": {"src": "hda", "id": "77d4412f77f6b180", "uuid": "e91d0fcc-18a6-4a8a-8a57-d58f08d5d4af"}, "taxonomy": {"src": "hda", "id": "3529226cbbc41f8d", "uuid": "07076206-9095-48f8-9629-8ad06d34a2f9"}, "fasta": {"src": "hda", "id": "f8fb2d243923edf0", "uuid": "73a485b3-aa97-46b3-aba3-2badac802195"}}, "update_time": "2018-02-08T17:11:20.597824", "tool_id": "mothur_cluster_split", "outputs": {"rabund": {"src": "hda", "id": "c397987c596ee46a", "uuid": "6f652e8d-9dbb-4c3b-9c9b-95182510e58d"}, "logfile": {"src": "hda", "id": "7196b214b6870b7e", "uuid": "0ae1803c-9339-41a6-91f4-53e28da0bb6d"}, "otulist": {"src": "hda", "id": "94d7eab7ff1b5670", "uuid": "90d83bd3-0e54-4b4b-9d24-3c0e6339bf4c"}, "sabund": {"src": "hda", "id": "d5962eb1211503b9", "uuid": "b6587fd2-8292-457a-9b9a-e4f8b659d078"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster.split(splitmethod=fasta,fasta=splitby.fasta.dat,taxonomy=splitb \ry.taxonomy.dat,name=splitby.nameOrCount.dat,taxlevel=3,classic=false,method=agc, \rprecision=100,large=false,cluster=true,runsensspec=true,processors=1)\n\nUsing 1 processors.\nSplitting the file...\n\nYou did not set a cutoff, using 0.03.\n/home/saskia/miniconda3/envs/mulled-v1-736475004b65901caa33ce32368de7bd390f9f20eaf8369d7ccbbf0be4fb73c4/bin/mothurvsearch file does not exist. Checking path... \nFound vsearch in your path, using /home/saskia/miniconda3/envs/mulled-v1-736475004b65901caa33ce32368de7bd390f9f20eaf8369d7ccbbf0be4fb73c4/bin/vsearch\nIt took 0 seconds to split the distance file.\n\nClustering splitby.fasta.dat.0.temp\nIt took 0 seconds to cluster\nMerging the clustered files...\nIt took 0 seconds to merge.\n\nOutput File Names: \nsplitby.fasta.agc.sabund\nsplitby.fasta.agc.rabund\nsplitby.fasta.agc.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_410.dat' splitby.fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_412.dat' splitby.nameOrCount.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_411.dat' splitby.taxonomy.dat && echo 'cluster.split( splitmethod=fasta, fasta=splitby.fasta.dat, taxonomy=splitby.taxonomy.dat, name=splitby.nameOrCount.dat, taxlevel=3, classic=false, method=agc, precision=100, large=false, cluster=true, runsensspec=true, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:11:15.331832", "params": {"runsensspec": "\"true\"", "cutoff": "\"0.0\"", "splitby": "{\"splitmethod\": \"fasta\", \"condmethod\": {\"method\": \"agc\", \"__current_case__\": 3}, \"classic\": \"false\", \"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 412}]}, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 411}]}, \"__current_case__\": 2, \"fasta\": {\"values\": [{\"src\": \"hda\", \"id\": 410}]}, \"taxlevel\": \"3\"}", "precision": "\"100\"", "dbkey": "\"hg17\"", "large": "\"false\"", "cluster": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "vsearch v2.6.0_linux_x86_64, 62.8GB RAM, 8 cores\nhttps://github.com/torognes/vsearch\n\nReading file splitby.fasta.dat.0.temp.sorted.fasta.temp 100%\n1873 nt in 2 seqs, min 930, max 943, avg 936\nMasking 100%\nCounting k-mers 100%\nClustering 100%\nSorting clusters 100%\nWriting clusters 100%\nClusters: 2 Size min 1, max 1, avg 1.0\nSingletons: 2, 100.0% of seqs, 100.0% of clusters\n", "job_metrics": [], "model_class": "Job", "external_id": "12940", "id": "3af8c7b9f683116f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_split.test_tool_000005", "has_data": true}, {"data": {"status": "success", "inputs": {"splitby\|condmethod\|method": "opti", "splitby\|matrix\|format": "phylip", "splitby\|matrix\|dist": {"src": "hda", "id": "f5edea7d52e42cd6"}, "splitby\|splitmethod": "distance"}, "job": {"inputs": {"splitby\|dist": {"src": "hda", "id": "f5edea7d52e42cd6", "uuid": "59e654f0-8e3f-40f2-a48d-7cb6cc2360f3"}}, "update_time": "2018-02-08T17:11:50.352932", "tool_id": "mothur_cluster_split", "outputs": {"rabund": {"src": "hda", "id": "69ae44680e47ff1d", "uuid": "90e27f2b-c64d-41c8-b138-04ab9781c74f"}, "sensspec": {"src": "hda", "id": "9fa13b46d25f1a47", "uuid": "ee1e6cc4-52ab-418d-aa6e-d5338c6319f3"}, "logfile": {"src": "hda", "id": "2be21af3e0b30a72", "uuid": "a41387cc-7003-4dc9-9946-85e75f38884b"}, "otulist": {"src": "hda", "id": "8f5442c8ae200d3a", "uuid": "3c429842-3285-4b6e-9296-2ed6722d7f27"}, "sabund": {"src": "hda", "id": "e6b222c9649e44d2", "uuid": "8c096a41-2fd1-4857-af5f-7d4ce21cef45"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster.split(splitmethod=distance,phylip=splitby.matrix.dist.dat,metho \rd=opti,metric=mcc,initialize=singleton,delta=0.0001,iters=100,precision=100,larg \re=false,cluster=true,runsensspec=true,processors=1)\n\nUsing 1 processors.\nConverting to column format...\nIt took 0 seconds to convert the distance file.\nSplitting the file...\nIt took 0 seconds to split the distance file.\n\nYou did not set a cutoff, using 0.03.\n\nClustering splitby.matrix.dist.column.dist.2.temp\n\ntp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0\t3735\t0\t6\t0\t1\t0\t0.998396\t0\t0.998396\t0\t0\t\n\n\nYou did not set a cutoff, using 0.03.\n\nClustering splitby.matrix.dist.column.dist.0.temp\n\ntp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0\t3735\t0\t6\t0\t1\t0\t0.998396\t0\t0.998396\t0\t0\t\n\n\nYou did not set a cutoff, using 0.03.\n\nClustering splitby.matrix.dist.column.dist.3.temp\n\ntp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0\t3652\t0\t3\t0\t1\t0\t0.999179\t0\t0.999179\t0\t0\t\n\n\nYou did not set a cutoff, using 0.03.\n\nClustering splitby.matrix.dist.column.dist.1.temp\n\ntp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0\t3569\t0\t1\t0\t1\t0\t0.99972\t0\t0.99972\t0\t0\t\n\n\nYou did not set a cutoff, using 0.03.\n\nClustering splitby.matrix.dist.column.dist.4.temp\n\ntp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0\t3569\t0\t1\t0\t1\t0\t0.99972\t0\t0.99972\t0\t0\t\n\nIt took 0 seconds to cluster\nMerging the clustered files...\nIt took 0 seconds to merge.\n/**************************************/\nRunning command: sens.spec(cutoff=0.03, list=splitby.matrix.dist.column.opti_mcc.list, phylip=splitby.matrix.dist.dat, name=splitby.matrix.dist.dat.names)\n\nNOTE: sens.spec assumes that only unique sequences were used to generate the distance matrix.\n\n0.03\nIt took 0 to run sens.spec.\n\nOutput File Names: \nsplitby.matrix.dist.column.opti_mcc.sensspec\n\n/***************************************/\nDone.\n\n\nlabel\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0.03\t0.03\t0\t4736\t0\t17\t0\t1\t0\t0.9964\t0\t0.9964\t0\t0\n\nOutput File Names: \nsplitby.matrix.dist.column.opti_mcc.sabund\nsplitby.matrix.dist.column.opti_mcc.rabund\nsplitby.matrix.dist.column.opti_mcc.list\nsplitby.matrix.dist.column.opti_mcc.sensspec\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_417.dat' splitby.matrix.dist.dat && ln -s 'None' splitby.matrix.nameOrCount.dat && echo 'cluster.split( splitmethod=distance, phylip=splitby.matrix.dist.dat, method=opti, metric=mcc, initialize=singleton, delta=0.0001, iters=100, precision=100, large=false, cluster=true, runsensspec=true, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:11:45.894758", "params": {"runsensspec": "\"true\"", "cutoff": "\"0.0\"", "splitby": "{\"splitmethod\": \"distance\", \"condmethod\": {\"iters\": \"100\", \"metric\": \"mcc\", \"__current_case__\": 3, \"delta\": \"0.0001\", \"initialize\": \"singleton\", \"method\": \"opti\"}, \"matrix\": {\"nameOrCount\": null, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 417}]}, \"__current_case__\": 1, \"format\": \"phylip\"}, \"__current_case__\": 0}", "precision": "\"100\"", "dbkey": "\"hg17\"", "large": "\"false\"", "cluster": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "13078", "id": "b7d4a98a7bb9e1bc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_split.test_tool_000006", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "6eb09fe0ca80e9ad"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "6eb09fe0ca80e9ad", "uuid": "d2d740da-4498-40f5-b809-01cb26b7e829"}}, "update_time": "2018-02-08T17:12:25.413981", "tool_id": "mothur_collect_shared", "outputs": {"__new_primary_file_thetayc\|jabund__": {"src": "hda", "id": "09dbeac489d85549", "uuid": "d9c1ae28-881d-4501-85d5-33667b47309f"}, "__new_primary_file_thetayc\|jest__": {"src": "hda", "id": "3a07e8fa101f66c3", "uuid": "3aa67a68-55bc-49be-970a-065c3e3f022b"}, "__new_primary_file_thetayc\|sorclass__": {"src": "hda", "id": "457390d412d4922c", "uuid": "a9107de5-1ffa-412d-ab9a-c2b6f14ead9f"}, "__new_primary_file_thetayc\|thetayc__": {"src": "hda", "id": "6c12052addbdbf10", "uuid": "99933db3-30b7-4f45-b0ca-e4e3cc1da9ee"}, "__new_primary_file_thetayc\|sorabund__": {"src": "hda", "id": "7b32cfe10869d24e", "uuid": "7fa144d9-5695-473c-83a5-341fa500b861"}, "__new_primary_file_thetayc\|shared.chao__": {"src": "hda", "id": "a8b7bad9a0464ba9", "uuid": "849e6208-1c61-4b1e-b3e2-4f29352f74bd"}, "__new_primary_file_thetayc\|sorest__": {"src": "hda", "id": "3fc9b5ca07992501", "uuid": "34314ff0-2518-43f0-b5dc-d1129b3ad0fc"}, "__new_primary_file_thetayc\|shared.sobs__": {"src": "hda", "id": "5f49ccb40e6bf114", "uuid": "7db453f9-365a-4cba-b0ec-97f034dd5d49"}, "__new_primary_file_thetayc\|thetan__": {"src": "hda", "id": "2cfb598380799c5c", "uuid": "35caf54a-a243-4695-80a1-377ce870793a"}, "logfile": {"src": "hda", "id": "41fcf23659876b66", "uuid": "9c77450f-0cb7-4dac-baaa-ff4336aa23ed"}, "__new_primary_file_thetayc\|jclass__": {"src": "hda", "id": "43c7ced58110ff4d", "uuid": "0d2d47c8-e779-425c-ad2f-cfa734b53eff"}, "__new_primary_file_thetayc\|shared.ace__": {"src": "hda", "id": "07efabe7adaf6e12", "uuid": "cea5d499-2702-4f2f-9405-3d70e3d681a1"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > collect.shared(shared=otu.dat,calc=sharedsobs-sharedchao-sharedace-jcla \rss-jest-sorclass-sorest-jabund-sorabund-thetan-thetayc,freq=100.0,all=true)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.shared.sobs\notu.shared.chao\notu.shared.ace\notu.jclass\notu.jest\notu.sorclass\notu.sorest\notu.jabund\notu.sorabund\notu.thetan\notu.thetayc\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_423.dat' otu.dat && echo 'collect.shared( shared=otu.dat, calc=sharedsobs-sharedchao-sharedace-jclass-jest-sorclass-sorest-jabund-sorabund-thetan-thetayc, freq=100.0, all=true )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && rm otu.dat", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:12:21.966900", "params": {"dbkey": "\"hg17\"", "label": "null", "groups": "null", "freq": "\"100.0\"", "calc": "[\"sharedsobs\", \"sharedchao\", \"sharedace\", \"jclass\", \"jest\", \"sorclass\", \"sorest\", \"jabund\", \"sorabund\", \"thetan\", \"thetayc\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "13205", "id": "8984b162f62c6c24", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_collect_shared.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"calc": ["sharedsobs", "sharedchao", "sharedace", "anderberg", "jclass", "jest", "kulczynski", "kulczynskicody", "kstest", "lennon", "ochiai", "sorclass", "sorest", "whittaker", "hamming", "memchi2", "memchord", "memeuclidean", "mempearson", "braycurtis", "jabund", "morisitahorn", "sorabund", "thetan", "thetayc", "canberra", "gower", "hellinger", "manhattan", "odum", "soergel", "spearman", "speciesprofile", "structchi2", "structchord", "structeuclidean", "structkulczynski", "structpearson", "sharednseqs"], "otu": {"src": "hda", "id": "3e47ebdf403a2dd1"}, "groups": ["forest", "pasture"], "label": ["0.03", "0.05", "0.22"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "3e47ebdf403a2dd1", "uuid": "c4207529-1bc3-44b7-9110-967e843f2544"}}, "update_time": "2018-02-08T17:12:45.362338", "tool_id": "mothur_collect_shared", "outputs": {"__new_primary_file_whittaker\|mempearson__": {"src": "hda", "id": "2b215f192af96e2f", "uuid": "cecc2250-db1a-4c37-9d24-d73c011d1abc"}, "__new_primary_file_whittaker\|manhattan__": {"src": "hda", "id": "07fd9a413201852e", "uuid": "d70a8e27-c95d-4554-a285-459f0e18354c"}, "__new_primary_file_whittaker\|gower__": {"src": "hda", "id": "fd1e10e0f0d76fac", "uuid": "03420e9a-6924-4dc9-a224-b72db0e5558a"}, "__new_primary_file_whittaker\|structpearson__": {"src": "hda", "id": "82d89e614ebda5c1", "uuid": "51ab641a-5e2e-40a9-88e8-e8037d9f1e6a"}, "__new_primary_file_whittaker\|thetayc__": {"src": "hda", "id": "3df0a01a3ae34d52", "uuid": "546e7e77-f2c3-49f5-a1a0-014e2f5f400c"}, "__new_primary_file_whittaker\|sorclass__": {"src": "hda", "id": "0d63eb5c811d9a5b", "uuid": "e1c6c74f-2af8-436e-ad8c-b688e7791215"}, "__new_primary_file_whittaker\|whittaker__": {"src": "hda", "id": "fc6a9ef5f7630e87", "uuid": "7b5512d4-aa1f-48bf-bc5a-295406139240"}, "__new_primary_file_whittaker\|hellinger__": {"src": "hda", "id": "78fdca853d645da8", "uuid": "c9c7c063-bdea-4576-9c17-707aa732667e"}, "__new_primary_file_whittaker\|lennon__": {"src": "hda", "id": "eb492223fe45a3a1", "uuid": "55ecafe7-fdc9-4d09-821a-69a7bea023fa"}, "__new_primary_file_whittaker\|anderberg__": {"src": "hda", "id": "f7cac463734b28ae", "uuid": "010a3fd5-5254-4d09-8562-fa3f38c26ae0"}, "__new_primary_file_whittaker\|hamming__": {"src": "hda", "id": "032dc790b013bafc", "uuid": "4a8d06b3-ac49-431f-a96c-932e23af81c9"}, "__new_primary_file_whittaker\|shared.sobs__": {"src": "hda", "id": "c9e276c91d77be76", "uuid": "5eeba6a8-f91f-491a-95ad-00b655abba36"}, "__new_primary_file_whittaker\|sorabund__": {"src": "hda", "id": "cf6f5650773911ff", "uuid": "45d9148b-2992-46cf-ae88-a4024e68acd2"}, "__new_primary_file_whittaker\|speciesprofile__": {"src": "hda", "id": "dd09e5318fcac9cd", "uuid": "21ec4299-981e-472f-9ee4-1af55871c4a4"}, "__new_primary_file_whittaker\|structchi2__": {"src": "hda", "id": "cc61617d359bbeb4", "uuid": "98e5435d-ab04-4c9c-a8ef-bbcf8a0b396b"}, "__new_primary_file_whittaker\|jest__": {"src": "hda", "id": "06134b0ededad71e", "uuid": "083dbc1c-3adb-4333-aac5-fc487c02b14b"}, "__new_primary_file_whittaker\|thetan__": {"src": "hda", "id": "ace828d96e9bc93f", "uuid": "85aa130c-ed1d-4bc6-b4ae-bab5a4229910"}, "__new_primary_file_whittaker\|shared.chao__": {"src": "hda", "id": "d27681472e68c286", "uuid": "d22d8971-fb37-4dab-a896-3c16da9cd88d"}, "__new_primary_file_whittaker\|morisitahorn__": {"src": "hda", "id": "89eb04d15155113e", "uuid": "c5a36a03-64be-44d8-a3b1-9ac4042bc8ae"}, "__new_primary_file_whittaker\|memchi2__": {"src": "hda", "id": "c70fd0f87d1321b9", "uuid": "cccbdcb1-95ea-4b3e-a01e-4389fe29dcf1"}, "__new_primary_file_whittaker\|jclass__": {"src": "hda", "id": "4a03c449ab1f345a", "uuid": "7b7910a3-a461-4a15-97b6-0b6b5b0028dd"}, "__new_primary_file_whittaker\|structeuclidean__": {"src": "hda", "id": "64eba53a47060775", "uuid": "0d3b86ba-b129-40f6-b7a7-17c6df06a266"}, "__new_primary_file_whittaker\|structkulczynski__": {"src": "hda", "id": "8617c587cd9e4e77", "uuid": "b69d8972-f8c4-44ae-80f8-fbcd73a74e0f"}, "__new_primary_file_whittaker\|memeuclidean__": {"src": "hda", "id": "5c48130196180838", "uuid": "5654d852-104b-46d4-b850-ba523b238c7f"}, "__new_primary_file_whittaker\|structchord__": {"src": "hda", "id": "7206901401158c4a", "uuid": "677b89a0-54b2-43f5-96f8-df5422cea5ff"}, "__new_primary_file_whittaker\|ochiai__": {"src": "hda", "id": "c9ef78ff932a2539", "uuid": "69a341de-3ccc-4e20-94b4-eead506e8d14"}, "__new_primary_file_whittaker\|braycurtis__": {"src": "hda", "id": "3cb3ad12c0574547", "uuid": "cec9891f-dbec-40d8-bc6a-63c99c85f3d0"}, "__new_primary_file_whittaker\|canberra__": {"src": "hda", "id": "010d772e12940e81", "uuid": "c484d80a-c5da-4b7d-b280-a49020407453"}, "__new_primary_file_whittaker\|shared.nseqs__": {"src": "hda", "id": "11fff4f70c354168", "uuid": "66154bc9-063b-4970-b223-8f4734d31bf6"}, "logfile": {"src": "hda", "id": "36f33e00653500e8", "uuid": "25e5fc6d-b192-48f2-9a37-98afbb5e8744"}, "__new_primary_file_whittaker\|memchord__": {"src": "hda", "id": "5c0379f640540f7d", "uuid": "12c00f31-5beb-4d47-89f8-2bc512ed9336"}, "__new_primary_file_whittaker\|kulczynskicody__": {"src": "hda", "id": "0a0eeda241196907", "uuid": "41b900b0-e92e-4bd6-a8b9-6162181f6f3f"}, "__new_primary_file_whittaker\|spearman__": {"src": "hda", "id": "6e055b0f6b730971", "uuid": "54ad0a10-a404-48f7-aeb8-1c0c12137878"}, "__new_primary_file_whittaker\|shared.ace__": {"src": "hda", "id": "864ad45f69d33ad2", "uuid": "c34a956f-7b6d-44ac-abcd-13568970b2bf"}, "__new_primary_file_whittaker\|soergel__": {"src": "hda", "id": "7536865915d87753", "uuid": "6f387274-a14a-4ade-ac1c-22d001bdf696"}, "__new_primary_file_whittaker\|odum__": {"src": "hda", "id": "ab313dd72b645b75", "uuid": "a7ad4d37-2d02-4eb8-99fa-c6ff83f4ccf8"}, "__new_primary_file_whittaker\|kstest__": {"src": "hda", "id": "446f6e70c8f6f247", "uuid": "4bdc0101-cb98-43a5-b4be-8673e035ca1d"}, "__new_primary_file_whittaker\|sorest__": {"src": "hda", "id": "b8252606b6759e88", "uuid": "9577bc6a-357f-4bc0-8d49-c141496fd520"}, "__new_primary_file_whittaker\|jabund__": {"src": "hda", "id": "a12cdd35a80cbdf3", "uuid": "f3c84a67-78c1-4581-8e51-e270e5baa92b"}, "__new_primary_file_whittaker\|kulczynski__": {"src": "hda", "id": "2afa7a4578b8f4fd", "uuid": "18326c68-5ed7-49eb-9fe9-f1e23139b73a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > collect.shared(shared=otu.dat,label=0.03-0.05-0.22,calc=sharedsobs-shar \redchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-kstest-lennon-o \rchiai-sorclass-sorest-whittaker-hamming-memchi2-memchord-memeuclidean-mempearson \r-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc-canberra-gower-hellinger \r-manhattan-odum-soergel-spearman-speciesprofile-structchi2-structchord-structeuc \rlidean-structkulczynski-structpearson-sharednseqs,groups=forest-pasture,freq=100 \r.0,all=true)\n0.03\n0.05\n0.22\n\nOutput File Names: \notu.shared.sobs\notu.shared.chao\notu.shared.ace\notu.anderberg\notu.jclass\notu.jest\notu.kulczynski\notu.kulczynskicody\notu.kstest\notu.lennon\notu.ochiai\notu.sorclass\notu.sorest\notu.whittaker\notu.hamming\notu.memchi2\notu.memchord\notu.memeuclidean\notu.mempearson\notu.braycurtis\notu.jabund\notu.morisitahorn\notu.sorabund\notu.thetan\notu.thetayc\notu.canberra\notu.gower\notu.hellinger\notu.manhattan\notu.odum\notu.soergel\notu.spearman\notu.speciesprofile\notu.structchi2\notu.structchord\notu.structeuclidean\notu.structkulczynski\notu.structpearson\notu.shared.nseqs\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_436.dat' otu.dat && echo 'collect.shared( shared=otu.dat, label=0.03-0.05-0.22, calc=sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-kstest-lennon-ochiai-sorclass-sorest-whittaker-hamming-memchi2-memchord-memeuclidean-mempearson-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc-canberra-gower-hellinger-manhattan-odum-soergel-spearman-speciesprofile-structchi2-structchord-structeuclidean-structkulczynski-structpearson-sharednseqs, groups=forest-pasture, freq=100.0, all=true )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && rm otu.dat", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:12:40.316603", "params": {"dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\", \"0.22\"]", "groups": "[\"forest\", \"pasture\"]", "freq": "\"100.0\"", "calc": "[\"sharedsobs\", \"sharedchao\", \"sharedace\", \"anderberg\", \"jclass\", \"jest\", \"kulczynski\", \"kulczynskicody\", \"kstest\", \"lennon\", \"ochiai\", \"sorclass\", \"sorest\", \"whittaker\", \"hamming\", \"memchi2\", \"memchord\", \"memeuclidean\", \"mempearson\", \"braycurtis\", \"jabund\", \"morisitahorn\", \"sorabund\", \"thetan\", \"thetayc\", \"canberra\", \"gower\", \"hellinger\", \"manhattan\", \"odum\", \"soergel\", \"spearman\", \"speciesprofile\", \"structchi2\", \"structchord\", \"structeuclidean\", \"structkulczynski\", \"structpearson\", \"sharednseqs\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "13306", "id": "71db30c33f7a1d97", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_collect_shared.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "77c3626ab0594697"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "77c3626ab0594697", "uuid": "b215e272-d061-4228-b42c-f2ceb82e2668"}}, "update_time": "2018-02-08T17:13:04.454824", "tool_id": "mothur_collect_single", "outputs": {"__new_primary_file_sobs\|ace__": {"src": "hda", "id": "191434f645ec622f", "uuid": "027519e4-1115-40a8-b787-fef65bb75865"}, "__new_primary_file_sobs\|shannon__": {"src": "hda", "id": "9ee2e00a0d8ff0c1", "uuid": "db8e108e-cd33-4eb1-8889-a7214a6da043"}, "__new_primary_file_sobs\|sobs__": {"src": "hda", "id": "f060dd6bec0b0c91", "uuid": "9aa5224d-5d1a-47b8-825a-a0ebdf95c615"}, "__new_primary_file_sobs\|chao__": {"src": "hda", "id": "dd28ab0e62f6c657", "uuid": "6cc80384-1ab4-45fd-9747-33db889e16d8"}, "__new_primary_file_sobs\|jack__": {"src": "hda", "id": "982b968aefffd7e6", "uuid": "ece0b874-fdca-4647-b5f0-340b0c38aa54"}, "__new_primary_file_sobs\|npshannon__": {"src": "hda", "id": "4dfde39352bb574f", "uuid": "e53eda85-f247-4cfa-a1be-f1a80608d29f"}, "logfile": {"src": "hda", "id": "50eb45139d0d6a93", "uuid": "113d9767-5ec5-441d-8a41-ed74b6095e1b"}, "__new_primary_file_sobs\|simpson__": {"src": "hda", "id": "2e7d279ca3333738", "uuid": "53f30268-939b-4087-9e34-adcd6250a341"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > collect.single(list=otu.dat,calc=ace-chao-jack-sobs-simpson-shannon-nps \rhannon,abund=10,freq=100.0)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.ace\notu.chao\notu.jack\notu.sobs\notu.simpson\notu.shannon\notu.npshannon\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_477.dat' otu.dat && echo 'collect.single( list=otu.dat, calc=ace-chao-jack-sobs-simpson-shannon-npshannon, abund=10, freq=100.0 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && rm otu.dat", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:13:00.966122", "params": {"abund": "\"10\"", "dbkey": "\"hg17\"", "label": "null", "freq": "\"100.0\"", "calc": "[\"ace\", \"chao\", \"jack\", \"sobs\", \"simpson\", \"shannon\", \"npshannon\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "13392", "id": "c6239e5379f31f0f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_collect_single.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"calc": ["ace", "bootstrap", "chao", "jack", "sobs", "simpsoneven", "shannoneven", "heip", "smithwilson", "bergerparker", "coverage", "goodscoverage", "simpson", "invsimpson", "qstat", "shannon", "npshannon", "boneh", "efron", "shen", "solow", "logseries", "geometric", "bstick", "nseqs"], "otu": {"src": "hda", "id": "599aa42a6f638c3c"}, "label": ["0.36", "0.38", "0.41"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "599aa42a6f638c3c", "uuid": "0933dde9-2f47-471a-a6d3-abec09250959"}}, "update_time": "2018-02-08T17:13:26.296010", "tool_id": "mothur_collect_single", "outputs": {"__new_primary_file_solow\|simpson__": {"src": "hda", "id": "ddfa564d1c57beab", "uuid": "75ff5504-acd1-40aa-9031-5097db7dd66b"}, "__new_primary_file_solow\|simpsoneven__": {"src": "hda", "id": "3808e741d551ae79", "uuid": "deb08319-362f-4c01-a945-2cce9b31fbc8"}, "__new_primary_file_solow\|chao__": {"src": "hda", "id": "4c17a0c0b24f3d2a", "uuid": "62ed1247-d5d3-402f-af91-87380a3b9a17"}, "__new_primary_file_solow\|sobs__": {"src": "hda", "id": "bd9ebfe83c09a924", "uuid": "2ee19aa2-3b9b-4e4c-a3f2-1ceb4fc294dc"}, "__new_primary_file_solow\|bootstrap__": {"src": "hda", "id": "c33192ec797333a8", "uuid": "a7124b13-6151-4e62-a30a-59f6e1efd035"}, "__new_primary_file_solow\|logseries__": {"src": "hda", "id": "30389f7c5465c626", "uuid": "d72c0749-4314-4300-9965-cb8ccec89074"}, "__new_primary_file_solow\|ace__": {"src": "hda", "id": "d13b0aeade1f3b9f", "uuid": "9100a533-4087-4376-80dc-9892685d7a8b"}, "__new_primary_file_solow\|shen__": {"src": "hda", "id": "b0746254f283297c", "uuid": "d6ef866c-0e64-4db7-8899-b45492e2cb44"}, "__new_primary_file_solow\|shannoneven__": {"src": "hda", "id": "5300091d026f85af", "uuid": "088ccdc7-fd4d-4506-8531-2353c772eaa4"}, "__new_primary_file_solow\|invsimpson__": {"src": "hda", "id": "b3c2b8853f254e86", "uuid": "72cefb8a-92dc-406f-8ea8-0478f9c8baf3"}, "__new_primary_file_solow\|jack__": {"src": "hda", "id": "5932136d963c1318", "uuid": "af006a66-4002-4656-b6c7-1b5c105e8851"}, "__new_primary_file_solow\|smithwilson__": {"src": "hda", "id": "de3955fb86630a7e", "uuid": "cb2307ab-a198-48e6-a9ee-93d01df34577"}, "__new_primary_file_solow\|boneh__": {"src": "hda", "id": "98cd146bafa9f05e", "uuid": "e42d3b64-8117-4b4f-9930-e7ea9ce7d3d0"}, "__new_primary_file_solow\|heip__": {"src": "hda", "id": "7a298366c9388d2f", "uuid": "81e2119b-a66b-4ff1-9796-90458fdc87bd"}, "__new_primary_file_solow\|geometric__": {"src": "hda", "id": "2c905c266975a822", "uuid": "19e08439-6a2d-45e3-884e-ad716a4bdb6b"}, "__new_primary_file_solow\|shannon__": {"src": "hda", "id": "9bebc27cdf46e887", "uuid": "9fc5a622-8063-41bb-8926-262d0bbe7a37"}, "__new_primary_file_solow\|bergerparker__": {"src": "hda", "id": "a8a72597d313e674", "uuid": "6de9fb48-8aed-441e-9732-7ea6008adb0b"}, "__new_primary_file_solow\|coverage__": {"src": "hda", "id": "5989b468f72bfcf5", "uuid": "5ddbac9d-e350-4d10-b2d0-b71c34a9da9f"}, "__new_primary_file_solow\|npshannon__": {"src": "hda", "id": "3307079e08296ced", "uuid": "0c946a77-8e44-44a9-bb6d-b3b81b9c4d63"}, "__new_primary_file_solow\|qstat__": {"src": "hda", "id": "bdfaaa58b77537a7", "uuid": "69617fe1-149e-4f11-952b-d2ffeb16d878"}, "logfile": {"src": "hda", "id": "480b3d56ed97c000", "uuid": "47827789-b03e-43e5-a90f-a3572067b330"}, "__new_primary_file_solow\|goodscoverage__": {"src": "hda", "id": "d8859fda823215ee", "uuid": "069b6dc7-a02b-42d6-bf83-e8b5a99d8b83"}, "__new_primary_file_solow\|nseqs__": {"src": "hda", "id": "b7c449f860774475", "uuid": "ab61d3db-886d-434c-9f90-b7e17ef7951c"}, "__new_primary_file_solow\|bstick__": {"src": "hda", "id": "b0c02b917db38b13", "uuid": "1a591dcb-9e93-4488-afcb-7d14e6acb6ba"}, "__new_primary_file_solow\|solow__": {"src": "hda", "id": "3679dac861a4e053", "uuid": "9d5f072d-49c9-413d-a968-364281350165"}, "__new_primary_file_solow\|efron__": {"src": "hda", "id": "37b49f3ca84157b5", "uuid": "41d7ec1e-3b60-4640-ba13-dd2405473bea"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > collect.single(sabund=otu.dat,label=0.36-0.38-0.41,calc=ace-bootstrap-c \rhao-jack-sobs-simpsoneven-shannoneven-heip-smithwilson-bergerparker-coverage-goo \rdscoverage-simpson-invsimpson-qstat-shannon-npshannon-boneh-efron-shen-solow-log \rseries-geometric-bstick-nseqs,abund=10,freq=100.0)\n0.36\n0.38\n0.41\n\nOutput File Names: \notu.ace\notu.bootstrap\notu.chao\notu.jack\notu.sobs\notu.simpsoneven\notu.shannoneven\notu.heip\notu.smithwilson\notu.bergerparker\notu.coverage\notu.goodscoverage\notu.simpson\notu.invsimpson\notu.qstat\notu.shannon\notu.npshannon\notu.boneh\notu.efron\notu.shen\notu.solow\notu.logseries\notu.geometric\notu.bstick\notu.nseqs\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_486.dat' otu.dat && echo 'collect.single( sabund=otu.dat, label=0.36-0.38-0.41, calc=ace-bootstrap-chao-jack-sobs-simpsoneven-shannoneven-heip-smithwilson-bergerparker-coverage-goodscoverage-simpson-invsimpson-qstat-shannon-npshannon-boneh-efron-shen-solow-logseries-geometric-bstick-nseqs, abund=10, freq=100.0 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && rm otu.dat", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:13:22.030750", "params": {"abund": "\"10\"", "dbkey": "\"hg17\"", "label": "[\"0.36\", \"0.38\", \"0.41\"]", "freq": "\"100.0\"", "calc": "[\"ace\", \"bootstrap\", \"chao\", \"jack\", \"sobs\", \"simpsoneven\", \"shannoneven\", \"heip\", \"smithwilson\", \"bergerparker\", \"coverage\", \"goodscoverage\", \"simpson\", \"invsimpson\", \"qstat\", \"shannon\", \"npshannon\", \"boneh\", \"efron\", \"shen\", \"solow\", \"logseries\", \"geometric\", \"bstick\", \"nseqs\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "13485", "id": "cd5f25030bbf4788", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_collect_single.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "966d85c09a3ba224"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "966d85c09a3ba224", "uuid": "4e106005-f312-4492-9215-949aa781008a"}}, "update_time": "2018-02-08T17:13:46.721790", "tool_id": "mothur_consensus_seqs", "outputs": {"logfile": {"src": "hda", "id": "7dabb5bd245b7e86", "uuid": "3be51f90-2742-4388-a1ab-2fefa8ee76d8"}, "cons_fasta": {"src": "hda", "id": "e4b28fee36db3ded", "uuid": "f4dee734-7be1-4e34-82aa-6186612713aa"}, "summary": {"src": "hda", "id": "499ab5633737b2d3", "uuid": "213fe84b-bf79-40b9-9b5a-3e504993a354"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > consensus.seqs(fasta=fasta.dat)\nIt took 0 secs to find the consensus sequences.\nOutput File Names: \nfasta.cons.summary\nfasta.cons.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_513.dat' fasta.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && echo 'consensus.seqs( fasta=fasta.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:13:42.630431", "params": {"count": "null", "cutoff": "\"\"", "name": "null", "dbkey": "\"hg17\"", "perotu": "{\"use\": \"no\", \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "13578", "id": "33d716567e7a5529", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_consensus_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"count": {"src": "hda", "id": "83dfe49f50126b60"}, "perotu\|otu": {"src": "hda", "id": "93ee5b88b9257311"}, "fasta": {"src": "hda", "id": "ed149d1c3c9443b2"}, "perotu\|use": "yes"}, "job": {"inputs": {"count": {"src": "hda", "id": "83dfe49f50126b60", "uuid": "3620f06b-5ed4-4d25-8e52-d35f73c0e498"}, "fasta": {"src": "hda", "id": "ed149d1c3c9443b2", "uuid": "dadc920c-ef1b-476d-a7ad-c9abca0a2882"}, "otu": {"src": "hda", "id": "93ee5b88b9257311", "uuid": "e3746a8a-8017-4045-a09c-eb7e45d10277"}}, "update_time": "2018-02-08T17:14:23.581097", "tool_id": "mothur_consensus_seqs", "outputs": {"__new_primary_file_unique\|0.30__": {"src": "hda", "id": "c9376b9862484ed4", "uuid": "1e9d5969-e4a9-4f38-b87f-401e7ca8b6c9"}, "logfile": {"src": "hda", "id": "6d049149a6f947d3", "uuid": "cb42d6d1-fa4d-4359-bb3b-0e99648b5f8d"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "a15361ef356dda4c", "uuid": "3abca939-41b6-4841-8cb9-2bdc41db1d6d"}, "__new_primary_file_unique\|0.33__": {"src": "hda", "id": "270b3503788ebdd6", "uuid": "160db0d3-3bb6-4f56-84c5-d915cf2ff6b0"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > consensus.seqs(fasta=fasta.dat,list=perotu.otu.dat,count=count.dat)\nunique\n0.30\n0.33\nIt took 1 secs to find the consensus sequences.\nOutput File Names: \nfasta.unique.cons.summary\nfasta.unique.cons.names\nfasta.unique.cons.fasta\nfasta.0.30.cons.summary\nfasta.0.30.cons.names\nfasta.0.30.cons.fasta\nfasta.0.33.cons.summary\nfasta.0.33.cons.names\nfasta.0.33.cons.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_517.dat' fasta.dat && ln -s 'None' name.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_519.dat' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_518.dat' perotu.otu.dat && echo 'consensus.seqs( fasta=fasta.dat ,list=perotu.otu.dat ,count=count.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:14:15.579381", "params": {"cutoff": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name": "null", "dbkey": "\"hg17\"", "perotu": "{\"use\": \"yes\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 518}]}, \"__current_case__\": 0, \"label\": null}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "13712", "id": "89c96313ae93d0a8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_consensus_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "c661245d3c9c7a1b"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "c661245d3c9c7a1b", "uuid": "ef8e6508-b2c1-41ba-99a7-48b8f91816aa"}}, "update_time": "2018-02-08T17:14:56.139601", "tool_id": "mothur_cooccurrence", "outputs": {"logfile": {"src": "hda", "id": "691344dc3af3bae5", "uuid": "bf5e2572-adc7-48af-97ba-de7fbc4c5d67"}, "out_summary": {"src": "hda", "id": "9cb939e9f07d29cd", "uuid": "e5d7ca81-706e-4320-8012-af7c59eb71e9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > cooccurrence(shared=otu.dat,metric=cscore,matrixmodel=sim2,iters=1000)\nunique\nInitial c score: 0.505263\n\naverage metric score: 0.49971\nzscore: 0.688308\nstandard deviation: 0.00806771\nnon-parametric p-value: 0.081\n0.01\nInitial c score: 0.505495\n\naverage metric score: 0.499899\nzscore: 0.689761\nstandard deviation: 0.00811162\nnon-parametric p-value: 0.085\n0.02\nInitial c score: 0.505107\n\naverage metric score: 0.499893\nzscore: 0.603707\nstandard deviation: 0.00863748\nnon-parametric p-value: 0.334\n0.03\nInitial c score: 0.505609\n\naverage metric score: 0.500176\nzscore: 0.672499\nstandard deviation: 0.00807817\nnon-parametric p-value: 0.256\n0.04\nInitial c score: 0.506329\n\naverage metric score: 0.500085\nzscore: 0.730838\nstandard deviation: 0.00854372\nnon-parametric p-value: 0.17\n0.05\nInitial c score: 0.507042\n\naverage metric score: 0.499892\nzscore: 0.727804\nstandard deviation: 0.00982421\nnon-parametric p-value: 0.181\n0.06\nInitial c score: 0.508475\n\naverage metric score: 0.499489\nzscore: 0.738319\nstandard deviation: 0.01217\nnon-parametric p-value: 0.097\n0.07\nInitial c score: 0.509091\n\naverage metric score: 0.500385\nzscore: 0.7394\nstandard deviation: 0.0117742\nnon-parametric p-value: 0.106\n0.08\nInitial c score: 0.510638\n\naverage metric score: 0.500255\nzscore: 0.668373\nstandard deviation: 0.0155347\nnon-parametric p-value: 0.241\n0.09\nInitial c score: 0.511111\n\naverage metric score: 0.49986\nzscore: 0.739436\nstandard deviation: 0.0152159\nnon-parametric p-value: 0.117\n0.10\nInitial c score: 0.509756\n\naverage metric score: 0.500649\nzscore: 0.529354\nstandard deviation: 0.0172046\nnon-parametric p-value: 0.488\n0.11\nInitial c score: 0.513514\n\naverage metric score: 0.500045\nzscore: 0.691855\nstandard deviation: 0.0194672\nnon-parametric p-value: 0.262\n0.12\nInitial c score: 0.514286\n\naverage metric score: 0.500101\nzscore: 0.715402\nstandard deviation: 0.0198278\nnon-parametric p-value: 0.262\n0.13\nInitial c score: 0.516129\n\naverage metric score: 0.499629\nzscore: 0.670815\nstandard deviation: 0.024597\nnon-parametric p-value: 0.146\n0.14\nInitial c score: 0.518519\n\naverage metric score: 0.499396\nzscore: 0.660312\nstandard deviation: 0.0289598\nnon-parametric p-value: 0.29\n0.15\nInitial c score: 0.516923\n\naverage metric score: 0.50024\nzscore: 0.594084\nstandard deviation: 0.028082\nnon-parametric p-value: 0.446\n0.16\nInitial c score: 0.513333\n\naverage metric score: 0.499947\nzscore: 0.475889\nstandard deviation: 0.0281298\nnon-parametric p-value: 0.57\n0.17\nInitial c score: 0.513834\n\naverage metric score: 0.500664\nzscore: 0.406264\nstandard deviation: 0.0324173\nnon-parametric p-value: 0.615\n0.18\nInitial c score: 0.514286\n\naverage metric score: 0.499648\nzscore: 0.421505\nstandard deviation: 0.0347281\nnon-parametric p-value: 0.611\n0.19\nInitial c score: 0.51462\n\naverage metric score: 0.499287\nzscore: 0.382877\nstandard deviation: 0.0400476\nnon-parametric p-value: 0.645\n0.20\nInitial c score: 0.514706\n\naverage metric score: 0.501265\nzscore: 0.295044\nstandard deviation: 0.0455565\nnon-parametric p-value: 0.7\n0.21\nInitial c score: 0.525\n\naverage metric score: 0.501542\nzscore: 0.523122\nstandard deviation: 0.0448429\nnon-parametric p-value: 0.55\n0.22\nInitial c score: 0.527473\n\naverage metric score: 0.499813\nzscore: 0.515418\nstandard deviation: 0.0536639\nnon-parametric p-value: 0.582\n0.23\nInitial c score: 0.538462\n\naverage metric score: 0.498821\nzscore: 0.702445\nstandard deviation: 0.0564329\nnon-parametric p-value: 0.425\n0.24\nInitial c score: 0.533333\n\naverage metric score: 0.4974\nzscore: 0.468581\nstandard deviation: 0.0766854\nnon-parametric p-value: 0.65\n0.25\nInitial c score: 0.535714\n\naverage metric score: 0.5005\nzscore: 0.367823\nstandard deviation: 0.095737\nnon-parametric p-value: 0.708\n0.26\nInitial c score: 0.533333\n\naverage metric score: 0.4956\nzscore: 0.288774\nstandard deviation: 0.130667\nnon-parametric p-value: 0.761\n0.27\nInitial c score: 0.533333\n\naverage metric score: 0.4974\nzscore: 0.272986\nstandard deviation: 0.13163\nnon-parametric p-value: 0.776\n0.29\nInitial c score: 0.6\n\naverage metric score: 0.4894\nzscore: 0.65946\nstandard deviation: 0.167713\nnon-parametric p-value: 0.599\n0.32\nInitial c score: 0.5\n\naverage metric score: 0.496\nzscore: 0.0191454\nstandard deviation: 0.208927\nnon-parametric p-value: 0.867\n0.33\nInitial c score: 0.5\n\naverage metric score: 0.499833\nzscore: 0.000833623\nstandard deviation: 0.19993\nnon-parametric p-value: 0.88\n0.36\nInitial c score: 0.666667\n\naverage metric score: 0.503333\nzscore: 0.569652\nstandard deviation: 0.286725\nnon-parametric p-value: 0.755\n0.38\nInitial c score: 1\n\naverage metric score: 0.477\nzscore: 1.04711\nstandard deviation: 0.499471\nnon-parametric p-value: 0.477\n0.41\nInitial c score: 1\n\naverage metric score: 0.52\nzscore: 0.960769\nstandard deviation: 0.4996\nnon-parametric p-value: 0.52\n0.45\nInitial c score: -nan\n\naverage metric score: -nan\nzscore: -nan\nstandard deviation: -nan\nnon-parametric p-value: 0\n0.55\nNot enough OTUs for co-occurrence analysis, skipping\n\nOutput File Names: \notu.cooccurence.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_530.dat' otu.dat && echo 'cooccurrence( shared=otu.dat, metric=cscore, matrixmodel=sim2, iters=1000 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:14:52.638168", "params": {"matrixmodel": "\"sim2\"", "iters": "\"1000\"", "metric": "\"cscore\"", "dbkey": "\"hg17\"", "label": "null", "groups": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "13806", "id": "8b9818d7842d6e75", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cooccurrence.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"metric": "vratio", "otu": {"src": "hda", "id": "f1cb956746b7222f"}, "groups": ["forest", "pasture"], "label": ["0.05", "0.22", "0.41"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "f1cb956746b7222f", "uuid": "2253cdd5-860c-4546-bfcd-80b05a1479c9"}}, "update_time": "2018-02-08T17:15:16.391349", "tool_id": "mothur_cooccurrence", "outputs": {"logfile": {"src": "hda", "id": "9c51eb665ea2103a", "uuid": "12b819be-425e-44e4-91c8-36522b833d89"}, "out_summary": {"src": "hda", "id": "c59b1eb3addb92c6", "uuid": "6650870a-9871-4e0d-aa08-a94a01a4e784"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > cooccurrence(shared=otu.dat,metric=vratio,matrixmodel=sim2,iters=1000,l \rabel=0.05-0.22-0.41,groups=forest-pasture)\n0.05\nInitial c score: 0.0140845\n\naverage metric score: 0.0140845\nzscore: -1\nstandard deviation: 2.98372e-16\nnon-parametric p-value: 1\n0.22\nInitial c score: 0.285714\n\naverage metric score: 0.285714\nzscore: 1\nstandard deviation: 3.27516e-15\nnon-parametric p-value: 1\n0.41\nInitial c score: 0\n\naverage metric score: 0\nzscore: -nan\nstandard deviation: 0\nnon-parametric p-value: 1\n\nOutput File Names: \notu.cooccurence.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_533.dat' otu.dat && echo 'cooccurrence( shared=otu.dat, metric=vratio, matrixmodel=sim2, iters=1000 ,label=0.05-0.22-0.41 ,groups=forest-pasture )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:15:13.250684", "params": {"matrixmodel": "\"sim2\"", "iters": "\"1000\"", "metric": "\"vratio\"", "dbkey": "\"hg17\"", "label": "[\"0.05\", \"0.22\", \"0.41\"]", "groups": "[\"forest\", \"pasture\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "13891", "id": "b3dbb33ff37f6ca1", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cooccurrence.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"axes": {"src": "hda", "id": "3511dc9f211ca562"}, "input\|source": "shared", "input\|otu": {"src": "hda", "id": "b7614d7298eb8371"}}, "job": {"inputs": {"axes": {"src": "hda", "id": "3511dc9f211ca562", "uuid": "ad7e52e8-f6da-42c3-9118-9a115f5f0914"}, "otu": {"src": "hda", "id": "b7614d7298eb8371", "uuid": "b1349374-8445-467e-943b-25973a860ae3"}}, "update_time": "2018-02-08T17:15:37.113599", "tool_id": "mothur_corr_axes", "outputs": {"logfile": {"src": "hda", "id": "c068ba61abe27ec2", "uuid": "51756d9e-0966-4007-b404-9c56634d51fd"}, "corr_axes": {"src": "hda", "id": "751af820aa10c307", "uuid": "923c2fd2-a3bc-40ea-9eb2-abfc3900dc9b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > corr.axes(shared=input.otu.dat,method=pearson,axes=/tmp/saskia/tmpKSDp0 \rp/files/000/dataset_536.dat,numaxes=3)\nYou did not provide a label, I will use the first label in your inputfile.\n\nOutput File Names: \ninput.otu.pearson.corr.axes\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_537.dat' input.otu.dat && echo 'corr.axes( shared=input.otu.dat, method=pearson, axes=/tmp/saskia/tmpKSDp0p/files/000/dataset_536.dat, numaxes=3 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:15:33.982854", "params": {"numaxes": "\"3\"", "input": "{\"groups\": null, \"source\": \"shared\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 537}]}, \"__current_case__\": 0, \"label\": null}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"pearson\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14013", "id": "a6edf8654f66f4d6", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_corr_axes.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|metadata": {"src": "hda", "id": "c2b0116e87929f66"}, "axes": {"src": "hda", "id": "aa43a28a12fcf867"}, "input\|source": "metadata"}, "job": {"inputs": {"axes": {"src": "hda", "id": "aa43a28a12fcf867", "uuid": "f4234459-a2f4-4fdb-8fa6-6cbcf5638eb3"}, "metadata": {"src": "hda", "id": "c2b0116e87929f66", "uuid": "2431fcfc-cdbb-4eba-a953-4ee99eaefe3a"}}, "update_time": "2018-02-08T17:15:58.839796", "tool_id": "mothur_corr_axes", "outputs": {"logfile": {"src": "hda", "id": "bb9931d062678360", "uuid": "556cb252-2dda-42fd-9167-6f44e15d12b2"}, "corr_axes": {"src": "hda", "id": "828c366ec88b9842", "uuid": "92def415-ab6a-42f2-935c-c574aad0b57c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > corr.axes(metadata=input.metadata.dat,method=pearson,axes=/tmp/saskia/t \rmpKSDp0p/files/000/dataset_540.dat,numaxes=3)\nYou did not provide a label, I will use the first label in your inputfile.\n\nOutput File Names: \ninput.metadata.pearson.corr.axes\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_541.dat' input.metadata.dat && echo 'corr.axes( metadata=input.metadata.dat, method=pearson, axes=/tmp/saskia/tmpKSDp0p/files/000/dataset_540.dat, numaxes=3 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:15:55.632585", "params": {"numaxes": "\"3\"", "input": "{\"source\": \"metadata\", \"__current_case__\": 1, \"metadata\": {\"values\": [{\"src\": \"hda\", \"id\": 541}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"pearson\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14126", "id": "e8a2248405ed0640", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_corr_axes.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|label": "0.05", "input\|source": "shared", "input\|groups": ["forest", "pasture"], "axes": {"src": "hda", "id": "76880adb125efe03"}, "input\|otu": {"src": "hda", "id": "eafd24481bcc96df"}}, "job": {"inputs": {"axes": {"src": "hda", "id": "76880adb125efe03", "uuid": "49bbc3a7-5968-436f-b8bf-1c7d863a9a9a"}, "otu": {"src": "hda", "id": "eafd24481bcc96df", "uuid": "e53ae831-a4e6-4710-a763-420abb52caf2"}}, "update_time": "2018-02-08T17:16:19.486444", "tool_id": "mothur_corr_axes", "outputs": {"logfile": {"src": "hda", "id": "d36e0ad5b4ecc523", "uuid": "d9f1e3db-30eb-4d51-8fea-d9150db896a8"}, "corr_axes": {"src": "hda", "id": "f71b4098ab6a1836", "uuid": "b0f94268-023d-4674-be3f-a1562438a6fb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > corr.axes(relabund=input.otu.dat,label=0.05,groups=forest-pasture,metho \rd=pearson,axes=/tmp/saskia/tmpKSDp0p/files/000/dataset_544.dat,numaxes=3)\n\nOutput File Names: \ninput.otu.pearson.corr.axes\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_545.dat' input.otu.dat && echo 'corr.axes( relabund=input.otu.dat, label=0.05, groups=forest-pasture, method=pearson, axes=/tmp/saskia/tmpKSDp0p/files/000/dataset_544.dat, numaxes=3 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:16:16.360411", "params": {"numaxes": "\"3\"", "input": "{\"groups\": [\"forest\", \"pasture\"], \"source\": \"shared\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 545}]}, \"__current_case__\": 0, \"label\": \"0.05\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"pearson\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14234", "id": "168b8fc92b5c87b9", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_corr_axes.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"group": {"src": "hda", "id": "2055ef0ee953a321"}}, "job": {"inputs": {"group": {"src": "hda", "id": "2055ef0ee953a321", "uuid": "85f8a4fb-c98f-4e67-959c-8fa7b160350e"}}, "update_time": "2018-02-08T17:16:37.211383", "tool_id": "mothur_count_groups", "outputs": {"logfile": {"src": "hda", "id": "d1010cb72bf991e5", "uuid": "b339060b-210b-4a0e-8ca3-cfaeb05bab93"}, "grp_count": {"src": "hda", "id": "2b91a5aff526e014", "uuid": "330704c8-aa6d-489c-b5e0-4f3a1cd28aa8"}, "summary": {"src": "hda", "id": "39ed0b190e5aa078", "uuid": "be37c436-d733-40aa-9d3b-3ceec97a6a22"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > count.groups(shared=group.dat)\nforest contains 49.\npasture contains 49.\n\nTotal seqs: 98.\n\nOutput File Names: \ngroup.count.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_548.dat' group.dat && echo 'count.groups( shared=group.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && cat mothur..logfile \| head -n-7 \| sed '1,30d' > '/tmp/saskia/tmpKSDp0p/files/000/dataset_550.dat'", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:16:34.007477", "params": {"groupnames": "{\"source\": \"none\", \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14320", "id": "f28875befd5fbf72", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_count_groups.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"groupnames\|groups": ["forest", "pasture"], "group": {"src": "hda", "id": "731d7fc7f6176125"}, "groupnames\|source": "groups"}, "job": {"inputs": {"group": {"src": "hda", "id": "731d7fc7f6176125", "uuid": "2fb9ef4d-8299-4dab-abb7-022dac7f5b56"}}, "update_time": "2018-02-08T17:16:49.634091", "tool_id": "mothur_count_groups", "outputs": {"logfile": {"src": "hda", "id": "8710e509865c9aaa", "uuid": "0b718802-5d6d-4b8d-ae15-4b7a7c207bcb"}, "grp_count": {"src": "hda", "id": "64f19a468d4ecfd5", "uuid": "54dfe4be-87cd-4ddd-9a46-7a98f76edb5d"}, "summary": {"src": "hda", "id": "ced3352a0235cd8b", "uuid": "22d85b3f-4e99-41ca-b1b6-525a68e0a595"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > count.groups(shared=group.dat,groups=forest-pasture)\nforest contains 49.\npasture contains 49.\n\nTotal seqs: 98.\n\nOutput File Names: \ngroup.count.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_552.dat' group.dat && echo 'count.groups( shared=group.dat ,groups=forest-pasture )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && cat mothur..logfile \| head -n-7 \| sed '1,30d' > '/tmp/saskia/tmpKSDp0p/files/000/dataset_554.dat'", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:16:46.402985", "params": {"groupnames": "{\"source\": \"groups\", \"groups\": [\"forest\", \"pasture\"], \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14410", "id": "0805ac7051fb8901", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_count_groups.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"name": {"src": "hda", "id": "2768baa09f52abc1"}}, "job": {"inputs": {"name": {"src": "hda", "id": "2768baa09f52abc1", "uuid": "877d12b1-a9ae-43bd-bd42-826b4b94e910"}}, "update_time": "2018-02-08T17:17:02.896150", "tool_id": "mothur_count_seqs", "outputs": {"logfile": {"src": "hda", "id": "8e15e2c734ba9663", "uuid": "a7bef60f-dcf4-4097-b6cc-dae34ad58be5"}, "seq_count": {"src": "hda", "id": "f4b2790380ce04e0", "uuid": "2c11e730-b181-4268-8b2b-1304ec1671b5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > count.seqs(name=name.dat)\n\nUsing 1 processors.\nIt took 0 secs to create a table for 98 sequences.\n\n\nTotal number of sequences: 98\n\nOutput File Names: \nname.count_table\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_556.dat' name.dat && echo 'count.seqs( name=name.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:16:59.097828", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "grouping": "{\"use\": \"no\", \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14500", "id": "6b84be122359b58b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_count_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"grouping\|group": {"src": "hda", "id": "1e4cd37e942f1647"}, "grouping\|use": "yes", "name": {"src": "hda", "id": "2ea80d0e66f18b07"}}, "job": {"inputs": {"group": {"src": "hda", "id": "1e4cd37e942f1647", "uuid": "103a5eb2-d49e-43d3-bac3-ccb2e1a53715"}, "name": {"src": "hda", "id": "2ea80d0e66f18b07", "uuid": "18a1e998-a6c8-4f4f-96dd-24a69a4d7652"}}, "update_time": "2018-02-08T17:17:25.704500", "tool_id": "mothur_count_seqs", "outputs": {"logfile": {"src": "hda", "id": "e57e8f741b8c587a", "uuid": "9bf1e448-c3f1-45f0-9192-20330890bfb6"}, "seq_count": {"src": "hda", "id": "9a68e8442a2ae0ec", "uuid": "efc00a4e-2573-489d-a8dd-58a6193eea62"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > count.seqs(group=grouping.group.dat,name=name.dat)\n\nUsing 1 processors.\nIt took 0 secs to create a table for 98 sequences.\n\n\nTotal number of sequences: 98\n\nOutput File Names: \nname.count_table\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_559.dat' name.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_560.dat' grouping.group.dat && echo 'count.seqs( group=grouping.group.dat, name=name.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:17:22.636543", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "grouping": "{\"use\": \"yes\", \"group\": {\"values\": [{\"src\": \"hda\", \"id\": 560}]}, \"groups\": null, \"__current_case__\": 0}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14615", "id": "eb96e852c39cc9f1", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_count_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"grouping\|group": {"src": "hda", "id": "ba8874b7e3e0c2f3"}, "grouping\|use": "yes", "name": {"src": "hda", "id": "60e341e237cd70c8"}, "grouping\|groups": "pasture"}, "job": {"inputs": {"group": {"src": "hda", "id": "ba8874b7e3e0c2f3", "uuid": "536927dc-c192-4c3e-a6eb-a8c2fc4ce4ee"}, "name": {"src": "hda", "id": "60e341e237cd70c8", "uuid": "deb928d4-ad1e-4c1f-8098-30f2aea5b1e5"}}, "update_time": "2018-02-08T17:17:46.294616", "tool_id": "mothur_count_seqs", "outputs": {"logfile": {"src": "hda", "id": "ec153c27faccd8c3", "uuid": "60bf6227-8266-4dff-afe0-b41eddfc98e5"}, "seq_count": {"src": "hda", "id": "7e283a4b4d60f5b4", "uuid": "10feb9e6-0a1b-42a1-a03d-c040f1369ce4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > count.seqs(group=grouping.group.dat,groups=pasture,name=name.dat)\n\nUsing 1 processors.\nIt took 0 secs to create a table for 98 sequences.\n\n\nTotal number of sequences: 98\n\nOutput File Names: \nname.count_table\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_563.dat' name.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_564.dat' grouping.group.dat && echo 'count.seqs( group=grouping.group.dat, groups=pasture, name=name.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:17:43.317222", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "grouping": "{\"use\": \"yes\", \"group\": {\"values\": [{\"src\": \"hda\", \"id\": 564}]}, \"groups\": \"pasture\", \"__current_case__\": 0}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14731", "id": "e63663c4a976dc8c", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_count_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"grouping\|group": {"src": "hda", "id": "632f677f352f3520"}, "grouping\|use": "yes", "name": {"src": "hda", "id": "cdf5fcd4ad6fb5ef"}, "grouping\|groups": ["pasture", "forest"]}, "job": {"inputs": {"group": {"src": "hda", "id": "632f677f352f3520", "uuid": "2acbeca9-34f4-4ae5-9bd4-3a8f8d73b8b6"}, "name": {"src": "hda", "id": "cdf5fcd4ad6fb5ef", "uuid": "1883ab42-717c-4697-8567-f10bb2313628"}}, "update_time": "2018-02-08T17:18:06.896417", "tool_id": "mothur_count_seqs", "outputs": {"logfile": {"src": "hda", "id": "723d087f45888e63", "uuid": "30655e8b-a706-46a1-8f4b-907424e4e5a6"}, "seq_count": {"src": "hda", "id": "536b558fd30defca", "uuid": "d6e04181-dee8-45d0-9972-97111e7b319c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > count.seqs(group=grouping.group.dat,groups=pasture-forest,name=name.dat \r)\n\nUsing 1 processors.\nIt took 0 secs to create a table for 98 sequences.\n\n\nTotal number of sequences: 98\n\nOutput File Names: \nname.count_table\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_567.dat' name.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_568.dat' grouping.group.dat && echo 'count.seqs( group=grouping.group.dat, groups=pasture-forest, name=name.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:18:03.744174", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "grouping": "{\"use\": \"yes\", \"group\": {\"values\": [{\"src\": \"hda\", \"id\": 568}]}, \"groups\": [\"pasture\", \"forest\"], \"__current_case__\": 0}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14840", "id": "ea1cd3f6f7bfdbc8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_count_seqs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"nameOrCount": {"src": "hda", "id": "aa616977935bece4"}, "repfasta": {"src": "hda", "id": "b82be0a67dfc3ead"}, "otu": {"src": "hda", "id": "ecbb26f6b49a2189"}, "constaxonomy": {"src": "hda", "id": "c097cce02f6efe06"}, "label": "unique"}, "job": {"inputs": {"nameOrCount": {"src": "hda", "id": "aa616977935bece4", "uuid": "23d0a8a9-8cd1-4e1f-8066-e4f4c023df8c"}, "repfasta": {"src": "hda", "id": "b82be0a67dfc3ead", "uuid": "0c5fca4c-acb1-4344-91dd-3567a08e7173"}, "otu": {"src": "hda", "id": "ecbb26f6b49a2189", "uuid": "1cc67aa9-8f9f-4d4f-902f-47e2bbafd6a1"}, "constaxonomy": {"src": "hda", "id": "c097cce02f6efe06", "uuid": "44a0f4ed-ce6e-4a99-8c7f-fd15e74d7657"}}, "update_time": "2018-02-08T17:18:33.797429", "tool_id": "mothur_create_database", "outputs": {"logfile": {"src": "hda", "id": "4fcb2862e39bce1b", "uuid": "50452c1e-8865-490b-a150-ca3c4a03c0db"}, "database": {"src": "hda", "id": "0507eab7257c99fb", "uuid": "dd8a2598-7156-4ff5-8dd4-aa02af6af4cb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > create.database(list=otu.dat,repfasta=repfasta.dat,repname=nameOrCount. \rdat,constaxonomy=constaxonomy.dat,label=unique)\n\nOutput File Names: \notu.database\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_571.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_572.dat' repfasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_573.dat' nameOrCount.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_574.dat' constaxonomy.dat && ln -s 'None' group.dat && echo 'create.database( list=otu.dat ,repfasta=repfasta.dat ,repname=nameOrCount.dat ,constaxonomy=constaxonomy.dat ,label=unique )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:18:30.660644", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "group": "null", "dbkey": "\"hg17\"", "label": "\"unique\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14992", "id": "1f643d6293754887", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_create_database.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"nameOrCount": {"src": "hda", "id": "66041b9fc316678f"}, "repfasta": {"src": "hda", "id": "ea961441905a3251"}, "otu": {"src": "hda", "id": "dad37bad3e582a03"}, "constaxonomy": {"src": "hda", "id": "f706247abc458287"}, "label": "unique"}, "job": {"inputs": {"nameOrCount": {"src": "hda", "id": "66041b9fc316678f", "uuid": "f8944112-9c77-460e-81c2-a543787690b9"}, "repfasta": {"src": "hda", "id": "ea961441905a3251", "uuid": "225fe3e4-bc37-4cb5-95a8-ed3b69f59be8"}, "otu": {"src": "hda", "id": "dad37bad3e582a03", "uuid": "8650be9a-feff-4bdb-8343-002b66ccf18b"}, "constaxonomy": {"src": "hda", "id": "f706247abc458287", "uuid": "063fc1c5-72fa-4744-b007-61c8c5f4ef78"}}, "update_time": "2018-02-08T17:19:01.552810", "tool_id": "mothur_create_database", "outputs": {"logfile": {"src": "hda", "id": "f39983d675d72056", "uuid": "0351c5e2-e001-48a3-a0d4-51c562891382"}, "database": {"src": "hda", "id": "c338e0c0b90362b9", "uuid": "69043eb9-dcfe-4429-8847-34dc04d2e380"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > create.database(list=otu.dat,repfasta=repfasta.dat,count=nameOrCount.da \rt,constaxonomy=constaxonomy.dat,label=unique)\n\nOutput File Names: \notu.database\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_577.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_578.dat' repfasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_579.dat' nameOrCount.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_580.dat' constaxonomy.dat && ln -s 'None' group.dat && echo 'create.database( list=otu.dat ,repfasta=repfasta.dat ,count=nameOrCount.dat ,constaxonomy=constaxonomy.dat ,label=unique )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:18:58.396784", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "group": "null", "dbkey": "\"hg17\"", "label": "\"unique\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15165", "id": "73f3912444e9fea9", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_create_database.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "445fd010406004cf"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "445fd010406004cf", "uuid": "350fa411-824d-4347-a194-594deaff7c95"}}, "update_time": "2018-02-08T17:19:19.237084", "tool_id": "mothur_degap_seqs", "outputs": {"logfile": {"src": "hda", "id": "acb17c34a39829bc", "uuid": "e5f43689-a962-449c-984b-3d0bd77b6e20"}, "out_fasta": {"src": "hda", "id": "756973d6ae6b9fe0", "uuid": "0b910abc-af11-48a8-b277-3b80ba2ba8bb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > degap.seqs(fasta=fasta.dat)\n\nUsing 1 processors.\nDegapping sequences from fasta.dat ...\n10\nIt took 0 secs to degap 10 sequences.\n\n\nOutput File Names: \nfasta.ng.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_583.dat' fasta.dat && echo 'degap.seqs( fasta=fasta.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:19:16.126712", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15261", "id": "714401c2c9d376cc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_degap_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "e06eaaa480b62987"}, "inputtype\|intype": "namesfile", "inputtype\|names": {"src": "hda", "id": "bd5643b7bad6c5ee"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "e06eaaa480b62987", "uuid": "dc2e9af9-d7d9-436c-9619-c65fb4a17e58"}, "names": {"src": "hda", "id": "bd5643b7bad6c5ee", "uuid": "f76d6979-2c69-45f4-adb6-e30bd6908377"}}, "update_time": "2018-02-08T17:19:34.833603", "tool_id": "mothur_deunique_seqs", "outputs": {"groups_file": {"src": "hda", "id": "2e05a675c8e4effa", "uuid": "26b8ee44-3d29-4469-b2fd-b87f6522251a"}, "logfile": {"src": "hda", "id": "0326414b4e40019a", "uuid": "d990da53-bd56-4fb2-b0b6-f47de25d7270"}, "out_fasta": {"src": "hda", "id": "533f5f02878a870d", "uuid": "c25ac10e-52b9-49e8-9c10-6cdbe901225b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > deunique.seqs(name=names.dat,fasta=fasta.dat)\n\nOutput File Names: \nfasta.redundant.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_586.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_587.dat' names.dat && echo 'deunique.seqs( name=names.dat, fasta=fasta.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:19:31.626015", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "inputtype": "{\"intype\": \"namesfile\", \"names\": {\"values\": [{\"src\": \"hda\", \"id\": 587}]}, \"__current_case__\": 0}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15371", "id": "32b5b014fd8ff7d7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_deunique_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "fea2f59e598c220b"}, "inputtype\|intype": "countfile", "inputtype\|names": {"src": "hda", "id": "89c39e6bc9d1ed43"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "fea2f59e598c220b", "uuid": "e91472b1-dad8-42dd-94d8-b94dadafed05"}, "names": {"src": "hda", "id": "89c39e6bc9d1ed43", "uuid": "59c434e9-21eb-4c7e-b650-d415e4c681fa"}}, "update_time": "2018-02-08T17:19:55.584258", "tool_id": "mothur_deunique_seqs", "outputs": {"groups_file": {"src": "hda", "id": "78187af971523bc5", "uuid": "a69e189f-7e4c-4720-bb47-ca41b7bcb0fc"}, "logfile": {"src": "hda", "id": "808438a09599e30a", "uuid": "172c6010-537e-44eb-a61d-c7d8ead283ea"}, "out_fasta": {"src": "hda", "id": "5f0fd33b40be7b90", "uuid": "29cc005e-a38f-4461-9f5a-7f6fec1ff42d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > deunique.seqs(count=names.dat,fasta=fasta.dat)\n\nOutput File Names: \nfasta.redundant.fasta\nnames.redundant.groups\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_591.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_592.dat' names.dat && echo 'deunique.seqs( count=names.dat, fasta=fasta.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:19:52.400579", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "inputtype": "{\"intype\": \"countfile\", \"names\": {\"values\": [{\"src\": \"hda\", \"id\": 592}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15487", "id": "b722e15494aaed88", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_deunique_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "0fd8e817110724fa"}, "inputtype\|intype": "countfile", "inputtype\|names": {"src": "hda", "id": "8cf2c4d96fac8f30"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "0fd8e817110724fa", "uuid": "0ab27f57-35d3-414a-b873-a2a3638f8dc3"}, "names": {"src": "hda", "id": "8cf2c4d96fac8f30", "uuid": "2d94fcfa-9ec9-49e5-b797-a27b3680b1f3"}}, "update_time": "2018-02-08T17:20:21.581063", "tool_id": "mothur_deunique_seqs", "outputs": {"groups_file": {"src": "hda", "id": "26a7a34cb9e5bfcc", "uuid": "6ff5666d-cc51-457d-9faa-68081fcbbf0a"}, "logfile": {"src": "hda", "id": "d0739bd14cbff0fb", "uuid": "15127adf-a761-4cd5-b404-0dd5aefac5fa"}, "out_fasta": {"src": "hda", "id": "aaec100bcea4a774", "uuid": "6b20f501-a458-4912-84a8-f1f5db2ee785"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > deunique.seqs(count=names.dat,fasta=fasta.dat)\n\nOutput File Names: \nfasta.redundant.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_596.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_597.dat' names.dat && echo 'deunique.seqs( count=names.dat, fasta=fasta.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:20:18.330376", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "inputtype": "{\"intype\": \"countfile\", \"names\": {\"values\": [{\"src\": \"hda\", \"id\": 597}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15598", "id": "3837873dd5f5f1f7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_deunique_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"tree": {"src": "hda", "id": "ed97b3e2ab207f95"}, "names": {"src": "hda", "id": "3e9d65cd9bd3cb5b"}}, "job": {"inputs": {"tree": {"src": "hda", "id": "ed97b3e2ab207f95", "uuid": "8171afc5-b70b-43d9-8cb2-54983b923226"}, "names": {"src": "hda", "id": "3e9d65cd9bd3cb5b", "uuid": "afc58f8a-27fd-448f-b908-bd15cad5024d"}}, "update_time": "2018-02-08T17:20:47.056523", "tool_id": "mothur_deunique_tree", "outputs": {"logfile": {"src": "hda", "id": "8733d0796a352268", "uuid": "49007554-1f8e-40d2-b876-b55356ff1837"}, "out_tree": {"src": "hda", "id": "9fbd2c401152ab55", "uuid": "440ed4e6-2f7e-4907-b481-13820836e2ad"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > deunique.tree(tree=tree.dat,name=names.dat)\n\nOutput File Names: \ntree.deunique.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_601.dat' tree.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_602.dat' names.dat && echo 'deunique.tree( tree=tree.dat, name=names.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:20:43.954435", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15720", "id": "12eb47432b3fa224", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_deunique_tree.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "4611eaf69222f4fc"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "4611eaf69222f4fc", "uuid": "e855b896-9810-401a-b333-c4e23384496d"}}, "update_time": "2018-02-08T17:20:59.418904", "tool_id": "mothur_dist_seqs", "outputs": {"logfile": {"src": "hda", "id": "11f90d7d2e7018d3", "uuid": "92e6a2d8-dc1e-4fae-bd9b-fc4cd45473ac"}, "out_dist": {"src": "hda", "id": "e310ea5c66f14aec", "uuid": "dd2805ef-d7e6-4ea6-8c2e-75f8d788f8f9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > dist.seqs(fasta=fasta.dat,countends=true,processors=1)\n\nUsing 1 processors.\n0\t0\n31\t0\n\nOutput File Names: \nfasta.dist\n\nIt took 0 seconds to calculate the distances for 32 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_605.dat' fasta.dat && echo 'dist.seqs( fasta=fasta.dat, countends=true, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:20:56.286624", "params": {"cutoff": "\"\"", "countends": "\"true\"", "dbkey": "\"hg17\"", "output": "\"\"", "calc": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15806", "id": "6194a3cf14a0177a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_dist_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"cutoff": "0.3", "fasta": {"src": "hda", "id": "3d3fb87387ce837c"}, "calc": "nogaps", "countends": false, "output": "lt"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "3d3fb87387ce837c", "uuid": "e197838d-144e-44fb-bac1-ca8ec8e3b339"}}, "update_time": "2018-02-08T17:21:16.984539", "tool_id": "mothur_dist_seqs", "outputs": {"logfile": {"src": "hda", "id": "619ac1d452a0c845", "uuid": "083fae16-a130-4737-91eb-0fef578c6f86"}, "out_dist": {"src": "hda", "id": "e150414f34961064", "uuid": "dc360c82-95d6-45f2-9ba7-591e518829a7"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > dist.seqs(fasta=fasta.dat,calc=nogaps,countends=false,cutoff=0.3,output \r=lt,processors=1)\n\nUsing 1 processors.\n0\t0\n31\t0\n\nOutput File Names: \nfasta.phylip.dist\n\nIt took 0 seconds to calculate the distances for 32 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_608.dat' fasta.dat && echo 'dist.seqs( fasta=fasta.dat, calc=nogaps, countends=false, cutoff=0.3, output=lt, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:21:13.826483", "params": {"cutoff": "\"0.3\"", "countends": "\"false\"", "dbkey": "\"hg17\"", "output": "\"lt\"", "calc": "\"nogaps\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15891", "id": "ce239e512e8f2197", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_dist_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "24493ccad6413f6e"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "24493ccad6413f6e", "uuid": "11f606c6-1b88-4fbc-a277-1b2d16fc55a2"}}, "update_time": "2018-02-08T17:21:38.102240", "tool_id": "mothur_dist_shared", "outputs": {"__new_primary_file_thetayc.unique.lt\|jclass.0.18.lt__": {"src": "hda", "id": "0a063fcbe434cf24", "uuid": "6fd33918-5c64-4b5f-b40b-bce477f11d44"}, "__new_primary_file_thetayc.unique.lt\|jclass.0.32.lt__": {"src": "hda", "id": "c7f95f7f9cd38954", "uuid": "63ade87b-4250-48bc-a55e-3a01cec0669b"}, "__new_primary_file_thetayc.unique.lt\|jclass.0.24.lt__": {"src": "hda", "id": "0ab5259e4af4b72d", "uuid": "3a5a830b-ff9f-4f6f-8a24-4211042cfd6e"}, "__new_primary_file_thetayc.unique.lt\|jclass.0.36.lt__": {"src": "hda", "id": "38956bd0aa358c3f", "uuid": "61d147dc-9a9c-474a-b48d-e1ad6330fcb7"}, "__new_primary_file_thetayc.unique.lt\|jclass.0.38.lt__": {"src": "hda", "id": "4ece32d755307fe6", "uuid": "a0d2a58a-39b1-4a2f-a7d8-38679890e1e2"}, "__new_primary_file_thetayc.unique.lt\|thetayc.0.02.lt__": {"src": "hda", "id": "f85272b32a0e3096", "uuid": "9ac744ce-34a1-495f-9637-c9b08543095e"}, "__new_primary_file_thetayc.unique.lt\|thetayc.0.14.lt__": {"src": "hda", "id": "311536be0a100aff", "uuid": 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"__new_primary_file_thetayc.unique.lt\|thetayc.0.21.lt__": {"src": "hda", "id": "b55d88427b65723f", "uuid": "8eff059b-de68-4d40-acd1-210d558a3b81"}, "__new_primary_file_thetayc.unique.lt\|thetayc.unique.lt__": {"src": "hda", "id": "d19d4ec68e7448b5", "uuid": "7f768e59-7cb6-4a7d-bc9e-1227f3a56372"}, "__new_primary_file_thetayc.unique.lt\|thetayc.0.19.lt__": {"src": "hda", "id": "d1af14f4da906d66", "uuid": "be3446ce-69c6-49b1-9c97-667f153ac558"}, "__new_primary_file_thetayc.unique.lt\|jclass.0.15.lt__": {"src": "hda", "id": "825dec33847777b5", "uuid": "adb13a7f-e79e-4b3f-9f42-47430d91174d"}, "__new_primary_file_thetayc.unique.lt\|jclass.0.16.lt__": {"src": "hda", "id": "ee234bf95ca1c311", "uuid": "55f3b565-c35a-446f-acda-1a80a908b9e7"}, "__new_primary_file_thetayc.unique.lt\|jclass.0.20.lt__": {"src": "hda", "id": "53dfc6f5f1ee9e8c", "uuid": "fcec0cce-78e6-4410-a5b4-60ea38791156"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > dist.shared(shared=otu.dat,calc=jclass-thetayc,output=lt,processors=1)\n\nUsing 1 processors.\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: 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> quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_611.dat' otu.dat && echo 'dist.shared( shared=otu.dat, calc=jclass-thetayc, output=lt, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:21:31.443852", "params": {"dbkey": "\"hg17\"", "label": "null", "groups": "null", "output": "\"lt\"", "subsampling": "{\"use\": \"no\", \"__current_case__\": 1}", "calc": "[\"jclass\", \"thetayc\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15979", "id": "c786be9a5c4573e3", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_dist_shared.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"calc": ["sharedsobs", "sharedchao", "sharedace", "anderberg", "jclass", "jest", "kulczynski", "kulczynskicody", "kstest", "lennon", "ochiai", "sorclass", "sorest", "whittaker", "hamming", "memchi2", "memchord", "memeuclidean", "mempearson", "braycurtis", "jabund", "morisitahorn", "sorabund", "thetan", "thetayc", "canberra", "gower", "hellinger", "manhattan", "odum", "soergel", "spearman", "speciesprofile", "structchi2", "structeuclidean", "structpearson", "sharednseqs", "sharedobserved"], "otu": {"src": "hda", "id": "41cb101ab8c7143d"}, "groups": ["forest", "pasture"], "label": ["0.05", "0.22"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "41cb101ab8c7143d", "uuid": "512586be-d3ce-458b-bc04-d6f1f8f5ec90"}}, "update_time": "2018-02-08T17:22:05.537905", 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"__new_primary_file_whittaker.0.22.lt\|whittaker.0.05.lt__": {"src": "hda", "id": "faf4e505dc24cb4d", "uuid": "f88894b5-973d-4d7e-aa1e-b25df9e4ae86"}, "__new_primary_file_whittaker.0.22.lt\|sorest.0.05.lt__": {"src": "hda", "id": "5d14d4d6e1b26e70", "uuid": "b6e81a3a-bf3e-4705-85ae-9db7a8a1fefb"}, "__new_primary_file_whittaker.0.22.lt\|kulczynskicody.0.22.lt__": {"src": "hda", "id": "0a2f8c1113cd2df5", "uuid": "f769fe63-c783-4969-87e5-54be177029e8"}, "__new_primary_file_whittaker.0.22.lt\|jest.0.05.lt__": {"src": "hda", "id": "821ad9bcbb2bbe9b", "uuid": "5286828e-32a2-4413-90ef-0626c3446fc4"}, "__new_primary_file_whittaker.0.22.lt\|sorabund.0.22.lt__": {"src": "hda", "id": "25d0f693a44d3b63", "uuid": "0bb75d42-b881-4f10-9e26-843a452c79b2"}, "__new_primary_file_whittaker.0.22.lt\|sharedace.0.22.lt__": {"src": "hda", "id": "f4140b0f3e683fb7", "uuid": "e1f9a4e0-5150-4dd0-9654-d4fd1a8cfb10"}, "__new_primary_file_whittaker.0.22.lt\|mempearson.0.22.lt__": {"src": "hda", "id": "27dd330ceb35c837", "uuid": "4dc9b5df-0826-4faa-b01e-859fe5726867"}, "__new_primary_file_whittaker.0.22.lt\|gower.0.05.lt__": {"src": "hda", "id": "a4a6e47454aeba8e", "uuid": "35129200-5454-46ab-9498-584451cb60fd"}, "__new_primary_file_whittaker.0.22.lt\|structpearson.0.22.lt__": {"src": "hda", "id": "45a4f11c8f7e7223", "uuid": "2bdde3cd-797c-40d3-bd31-70325d55d785"}, "__new_primary_file_whittaker.0.22.lt\|sharednseqs.0.22.lt__": {"src": "hda", "id": "b726424360e35364", "uuid": "1d58ebaa-35df-4000-8fb3-966eb5384dc0"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > dist.shared(shared=otu.dat,label=0.05-0.22,groups=forest-pasture,calc=s \rharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-k \rstest-lennon-ochiai-sorclass-sorest-whittaker-hamming-memchi2-memchord-memeuclid \rean-mempearson-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc-canberra-g \rower-hellinger-manhattan-odum-soergel-spearman-speciesprofile-structchi2-structe \ruclidean-structpearson-sharednseqs-sharedobserved,output=lt,processors=1)\n\nUsing 1 processors.\nsharedobserved is not a valid estimator for the matrix.output command and will be disregarded. Valid estimators are anderberg, braycurtis, canberra, gower, hamming, hellinger, jabund, jclass, jest, jsd, kstest, kulczynski, kulczynskicody, lennon, manhattan, memchi2, memchord, memeuclidean, mempearson, morisitahorn, ochiai, odum, rjsd, sharedace, sharedchao, sharednseqs, sharedsobs, soergel, sorabund, sorclass, sorest, spearman, speciesprofile, structchi2, structchord, structeuclidean, structkulczynski, structpearson, thetan, thetayc, whittaker, \n0.05\n0.22\n\nOutput File Names: \notu.sharedsobs.0.05.lt.dist\notu.sharedchao.0.05.lt.dist\notu.sharedace.0.05.lt.dist\notu.anderberg.0.05.lt.dist\notu.jclass.0.05.lt.dist\notu.jest.0.05.lt.dist\notu.kulczynski.0.05.lt.dist\notu.kulczynskicody.0.05.lt.dist\notu.kstest.0.05.lt.dist\notu.lennon.0.05.lt.dist\notu.ochiai.0.05.lt.dist\notu.sorclass.0.05.lt.dist\notu.sorest.0.05.lt.dist\notu.whittaker.0.05.lt.dist\notu.hamming.0.05.lt.dist\notu.memchi2.0.05.lt.dist\notu.memchord.0.05.lt.dist\notu.memeuclidean.0.05.lt.dist\notu.mempearson.0.05.lt.dist\notu.braycurtis.0.05.lt.dist\notu.jabund.0.05.lt.dist\notu.morisitahorn.0.05.lt.dist\notu.sorabund.0.05.lt.dist\notu.thetan.0.05.lt.dist\notu.thetayc.0.05.lt.dist\notu.canberra.0.05.lt.dist\notu.gower.0.05.lt.dist\notu.hellinger.0.05.lt.dist\notu.manhattan.0.05.lt.dist\notu.odum.0.05.lt.dist\notu.soergel.0.05.lt.dist\notu.spearman.0.05.lt.dist\notu.speciesprofile.0.05.lt.dist\notu.structchi2.0.05.lt.dist\notu.structeuclidean.0.05.lt.dist\notu.structpearson.0.05.lt.dist\notu.sharednseqs.0.05.lt.dist\notu.sharedsobs.0.22.lt.dist\notu.sharedchao.0.22.lt.dist\notu.sharedace.0.22.lt.dist\notu.anderberg.0.22.lt.dist\notu.jclass.0.22.lt.dist\notu.jest.0.22.lt.dist\notu.kulczynski.0.22.lt.dist\notu.kulczynskicody.0.22.lt.dist\notu.kstest.0.22.lt.dist\notu.lennon.0.22.lt.dist\notu.ochiai.0.22.lt.dist\notu.sorclass.0.22.lt.dist\notu.sorest.0.22.lt.dist\notu.whittaker.0.22.lt.dist\notu.hamming.0.22.lt.dist\notu.memchi2.0.22.lt.dist\notu.memchord.0.22.lt.dist\notu.memeuclidean.0.22.lt.dist\notu.mempearson.0.22.lt.dist\notu.braycurtis.0.22.lt.dist\notu.jabund.0.22.lt.dist\notu.morisitahorn.0.22.lt.dist\notu.sorabund.0.22.lt.dist\notu.thetan.0.22.lt.dist\notu.thetayc.0.22.lt.dist\notu.canberra.0.22.lt.dist\notu.gower.0.22.lt.dist\notu.hellinger.0.22.lt.dist\notu.manhattan.0.22.lt.dist\notu.odum.0.22.lt.dist\notu.soergel.0.22.lt.dist\notu.spearman.0.22.lt.dist\notu.speciesprofile.0.22.lt.dist\notu.structchi2.0.22.lt.dist\notu.structeuclidean.0.22.lt.dist\notu.structpearson.0.22.lt.dist\notu.sharednseqs.0.22.lt.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_685.dat' otu.dat && echo 'dist.shared( shared=otu.dat, label=0.05-0.22, groups=forest-pasture, calc=sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-kstest-lennon-ochiai-sorclass-sorest-whittaker-hamming-memchi2-memchord-memeuclidean-mempearson-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc-canberra-gower-hellinger-manhattan-odum-soergel-spearman-speciesprofile-structchi2-structeuclidean-structpearson-sharednseqs-sharedobserved, output=lt, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:21:58.880697", "params": {"dbkey": "\"hg17\"", "label": "[\"0.05\", \"0.22\"]", "groups": "[\"forest\", \"pasture\"]", "output": "\"lt\"", "subsampling": "{\"use\": \"no\", \"__current_case__\": 1}", "calc": "[\"sharedsobs\", \"sharedchao\", \"sharedace\", \"anderberg\", \"jclass\", \"jest\", \"kulczynski\", \"kulczynskicody\", \"kstest\", \"lennon\", \"ochiai\", \"sorclass\", \"sorest\", \"whittaker\", \"hamming\", \"memchi2\", \"memchord\", \"memeuclidean\", \"mempearson\", \"braycurtis\", \"jabund\", \"morisitahorn\", \"sorabund\", \"thetan\", \"thetayc\", \"canberra\", \"gower\", \"hellinger\", \"manhattan\", \"odum\", \"soergel\", \"spearman\", \"speciesprofile\", \"structchi2\", \"structeuclidean\", \"structpearson\", \"sharednseqs\", \"sharedobserved\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16068", "id": "90653ba0c3bbef25", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_dist_shared.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"output": "square", "calc": "canberra", "otu": {"src": "hda", "id": "baf2364ee29b3107"}, "subsampling\|use": "yes", "label": ["0.03", "0.33"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "baf2364ee29b3107", "uuid": "d4951c32-9e65-48e0-a3e6-c87cd597d149"}}, "update_time": "2018-02-08T17:22:29.803485", "tool_id": "mothur_dist_shared", "outputs": {"__new_primary_file_canberra.0.33.square.std\|canberra.0.03.square.ave__": {"src": "hda", "id": "0cc52239f966e8d8", "uuid": "1e0e7251-b715-4310-9902-f07e202040a9"}, "__new_primary_file_canberra.0.33.square.std\|canberra.0.33.square__": {"src": "hda", "id": "26abeaa977847256", "uuid": "24dd2c79-5195-41b7-a6db-cb56d8fe607f"}, "__new_primary_file_canberra.0.33.square.std\|canberra.0.33.square.ave__": {"src": "hda", "id": "20daa85480c5e233", "uuid": "c644c065-62d7-4f8c-b217-9b8a45e0d06c"}, "__new_primary_file_canberra.0.33.square.std\|canberra.0.33.square.std__": {"src": "hda", "id": "68b1b014e79dbbac", "uuid": "0bee9b58-e601-4cdc-9005-442df905d104"}, "__new_primary_file_canberra.0.33.square.std\|canberra.0.03.square__": {"src": "hda", "id": "9aa847d0f9b17c8b", "uuid": "7fc00040-a3e2-44b2-814f-12d3f0f9c5e7"}, "logfile": {"src": "hda", "id": "b46b161a6298a88e", "uuid": "00339ae5-b634-4c23-8bd4-3ba23fb04806"}, "__new_primary_file_canberra.0.33.square.std\|canberra.0.03.square.std__": {"src": "hda", "id": "4a18607ffedf0072", "uuid": "799afe6d-3a56-4571-a4a0-ebcb0ad5a168"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > dist.shared(shared=otu.dat,label=0.03-0.33,calc=canberra,subsample=T,it \rers=1000,output=square,processors=1)\n\nUsing 1 processors.\n0.03\n100\n200\n300\n400\n500\n600\n700\n800\n900\n1000\n0.33\n100\n200\n300\n400\n500\n600\n700\n800\n900\n1000\n\nOutput File Names: \notu.canberra.0.03.square.dist\notu.canberra.0.03.square.ave.dist\notu.canberra.0.03.square.std.dist\notu.canberra.0.33.square.dist\notu.canberra.0.33.square.ave.dist\notu.canberra.0.33.square.std.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_761.dat' otu.dat && echo 'dist.shared( shared=otu.dat, label=0.03-0.33, calc=canberra, subsample=T, iters=1000, output=square, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:22:26.360733", "params": {"dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.33\"]", "groups": "null", "output": "\"square\"", "subsampling": "{\"iters\": \"1000\", \"subsample\": \"\", \"use\": \"yes\", \"__current_case__\": 0}", "calc": "\"canberra\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16161", "id": "06bb318fcaf8f1eb", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_dist_shared.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"subsampling\|use": "yes", "label": "0.10", "otu": {"src": "hda", "id": "cfc54229b67d91e3"}, "subsampling\|subsample": "2", "output": "square", "calc": "canberra", "subsampling\|iters": "42"}, "job": {"inputs": {"otu": {"src": "hda", "id": "cfc54229b67d91e3", "uuid": "20daefca-def5-4876-946d-4cf232dfb9b0"}}, "update_time": "2018-02-08T17:22:47.020234", "tool_id": "mothur_dist_shared", "outputs": {"__new_primary_file_canberra.0.10.square.std\|canberra.0.10.square.ave__": {"src": "hda", "id": "e6723b9768a74d82", "uuid": "79dcde89-0d4b-440f-ad9b-335794b42c15"}, "logfile": {"src": "hda", "id": "71eba17e79d46ea5", "uuid": "bcc4be41-17fa-4a06-b847-718aa331d440"}, "__new_primary_file_canberra.0.10.square.std\|canberra.0.10.square__": {"src": "hda", "id": "617cf9f340bd6e86", "uuid": "2ce97851-6f4d-4494-9ef3-797b888ad973"}, "__new_primary_file_canberra.0.10.square.std\|canberra.0.10.square.std__": {"src": "hda", "id": "ed1b8cbf308ff665", "uuid": "d49683ab-1105-4341-983b-1203f49ab877"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > dist.shared(shared=otu.dat,label=0.10,calc=canberra,subsample=2,iters=4 \r2,output=square,processors=1)\n\nUsing 1 processors.\n0.10\n\nOutput File Names: \notu.canberra.0.10.square.dist\notu.canberra.0.10.square.ave.dist\notu.canberra.0.10.square.std.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_769.dat' otu.dat && echo 'dist.shared( shared=otu.dat, label=0.10, calc=canberra, subsample=2, iters=42, output=square, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:22:43.797807", "params": {"dbkey": "\"hg17\"", "label": "\"0.10\"", "groups": "null", "output": "\"square\"", "subsampling": "{\"iters\": \"42\", \"subsample\": \"2\", \"use\": \"yes\", \"__current_case__\": 0}", "calc": "\"canberra\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16253", "id": "dec5e0baf08c9f80", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_dist_shared.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"oligo\|add": "no", "fastq": {"src": "hda", "id": "e033f1f6a16a5fdb"}, "pacbio": false, "format": "sanger"}, "job": {"inputs": {"fastq": {"src": "hda", "id": "e033f1f6a16a5fdb", "uuid": "77438fba-535e-4216-8327-0e768915addb"}}, "update_time": "2018-02-08T17:23:04.684646", "tool_id": "mothur_fastq_info", "outputs": {"qfile_out": {"src": "hda", "id": "6c35ab7e615cea5a", "uuid": "dcefa944-94d0-4b60-97bd-2c4dc8eaecd0"}, "qfile_scrap_out": {"src": "hda", "id": "030656b247de0efe", "uuid": "9b1c11b7-5927-4d58-8b93-e90c055527c0"}, "fasta_scrap_out": {"src": "hda", "id": "a32e6dbc1964b80f", "uuid": "10697ffc-6f5b-49e7-9485-bdcba92bedeb"}, "fasta_out": {"src": "hda", "id": "f691a5951523571b", "uuid": "ed80280c-a610-4d2a-8521-7b0cde8c8754"}, "logfile": {"src": "hda", "id": "aa4dc5fa9f74231b", "uuid": "22ec9601-e7f9-40ca-b8d9-171c3ecbc0bd"}, "fastq_scrap_out": {"src": "hda", "id": "824db84bb730ff40", "uuid": "267a7c53-6bc5-4dde-850b-682f61bf72f7"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > fastq.info(fastq=fastq.dat,pacbio=false,format=sanger)\n25\n\nOutput File Names: \nfastq.fasta\nfastq.qual\n\n[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_774.dat' fastq.dat && echo 'fastq.info( fastq=fastq.dat, pacbio=false, format=sanger )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:23:01.321492", "params": {"oligo": "{\"add\": \"no\", \"__current_case__\": 1}", "format": "\"sanger\"", "pacbio": "\"false\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16337", "id": "01949e60fe484dc7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_fastq_info.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"oligo\|tdiffs": "3", "oligo\|oligos": {"src": "hda", "id": "35610b944eae1662"}, "format": "sanger", "oligo\|add": "yes", "fastq": {"src": "hda", "id": "bf2647e7c02a9611"}, "oligo\|pdiffs": "3", "pacbio": false, "oligo\|sdiffs": "7", "oligo\|bdiffs": "1", "oligo\|ldiffs": "3"}, "job": {"inputs": {"oligos": {"src": "hda", "id": "35610b944eae1662", "uuid": "81848543-318d-40ec-9f24-7e56a060ab4d"}, "fastq": {"src": "hda", "id": "bf2647e7c02a9611", "uuid": "7809aabd-ef88-4cbe-9bed-d0d4bde19717"}}, "update_time": "2018-02-08T17:23:25.374084", "tool_id": "mothur_fastq_info", "outputs": {"qfile_out": {"src": "hda", "id": "fdd788dd2ce60116", "uuid": "0d1ddeba-9f32-4378-9f89-54550cfe540f"}, "qfile_scrap_out": {"src": "hda", "id": "d1ff5636c3d156c1", "uuid": "ecc11736-d5b3-433a-99a7-5bfe26291fd9"}, "fasta_scrap_out": {"src": "hda", "id": "0a9daec53650332d", "uuid": "3ced0477-7b8f-4826-9fa3-dc8c00c7c3a9"}, "fasta_out": {"src": "hda", "id": "0f7bfbeda1808692", "uuid": "439b73c1-c987-439f-b470-01fca30b9187"}, "logfile": {"src": "hda", "id": "8e338a85ec192878", "uuid": "39bb7c9b-3632-4e54-a7af-06f6f0ced455"}, "fastq_scrap_out": {"src": "hda", "id": "32e4cd7ce068c585", "uuid": "4265a7df-7cb5-49ab-9add-e74293195c8a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > fastq.info(fastq=fastq.dat,pacbio=false,format=sanger,oligos=oligo.olig \ros.dat,bdiffs=1,pdiffs=3,tdiffs=3,ldiffs=3,sdiffs=7)\n25\n\nOutput File Names: \nfastq.fasta\nfastq.qual\nfastq.scrap.fastq\nfastq.scrap.fasta\nfastq.scrap.qual\n\n[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_781.dat' fastq.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_782.dat' oligo.oligos.dat && echo 'fastq.info( fastq=fastq.dat, pacbio=false, format=sanger ,oligos=oligo.oligos.dat ,bdiffs=1 ,pdiffs=3 ,tdiffs=3 ,ldiffs=3 ,sdiffs=7 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv fastq.scrap.fasta scrap.fasta && mv fastq.scrap.qual scrap.qual", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:23:21.806144", "params": {"oligo": "{\"bdiffs\": \"1\", \"sdiffs\": \"7\", \"ldiffs\": \"3\", \"pdiffs\": \"3\", \"tdiffs\": \"3\", \"add\": \"yes\", \"__current_case__\": 0, \"oligos\": {\"values\": [{\"src\": \"hda\", \"id\": 782}]}}", "format": "\"sanger\"", "pacbio": "\"false\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16448", "id": "10a6a0683c3e243b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_fastq_info.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"oligo\|tdiffs": "3", "oligo\|oligos": {"src": "hda", "id": "1380d0b9d445228e"}, "format": "sanger", "oligo\|add": "yes", "fastq": {"src": "hda", "id": "9926857060044181"}, "oligo\|pdiffs": "3", "pacbio": false, "oligo\|sdiffs": "7", "oligo\|bdiffs": "1", "oligo\|ldiffs": "3"}, "job": {"inputs": {"oligos": {"src": "hda", "id": "1380d0b9d445228e", "uuid": "8c307d4a-4b92-49ff-a385-b7e66a389056"}, "fastq": {"src": "hda", "id": "9926857060044181", "uuid": "eaf7180b-c799-4fd3-b0c0-e3813deaac9d"}}, "update_time": "2018-02-08T17:24:09.682399", "tool_id": "mothur_fastq_info", "outputs": {"qfile_out": {"src": "hda", "id": "1c98d06fd14cd58f", "uuid": "890802e0-d230-4124-8616-65dc4330f583"}, "qfile_scrap_out": {"src": "hda", "id": "743a8d5f0b93543f", "uuid": "8fd611e9-658c-4b48-b9c7-2bc7030b1ffa"}, "fasta_scrap_out": {"src": "hda", "id": "d2877f6f2610c2e2", "uuid": "8b46de15-d1f8-476f-b274-7dae66d698af"}, "fasta_out": {"src": "hda", "id": "0127e3e8a6471eea", "uuid": "c62929d1-5324-4bd1-b277-4e260a3f43d1"}, "logfile": {"src": "hda", "id": "36389a8523644138", "uuid": "edadd9bc-8711-4aa2-b098-b0871e3c3982"}, "fastq_scrap_out": {"src": "hda", "id": "da235095819aad8a", "uuid": "4ac12252-aa96-4911-90a0-c582f5cadc8c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > fastq.info(fastq=fastq.dat,pacbio=false,format=sanger,oligos=oligo.olig \ros.dat,bdiffs=1,pdiffs=3,tdiffs=3,ldiffs=3,sdiffs=7)\n[WARNING]: your oligos file does not contain any group names. mothur will not create a groupfile.\n25\n\nOutput File Names: \nfastq.fasta\nfastq.qual\nfastq.scrap.fastq\nfastq.scrap.fasta\nfastq.scrap.qual\n\n[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 2 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_789.dat' fastq.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_790.dat' oligo.oligos.dat && echo 'fastq.info( fastq=fastq.dat, pacbio=false, format=sanger ,oligos=oligo.oligos.dat ,bdiffs=1 ,pdiffs=3 ,tdiffs=3 ,ldiffs=3 ,sdiffs=7 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv fastq.scrap.fasta scrap.fasta && mv fastq.scrap.qual scrap.qual", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:24:05.898702", "params": {"oligo": "{\"bdiffs\": \"1\", \"sdiffs\": \"7\", \"ldiffs\": \"3\", \"pdiffs\": \"3\", \"tdiffs\": \"3\", \"add\": \"yes\", \"__current_case__\": 0, \"oligos\": {\"values\": [{\"src\": \"hda\", \"id\": 790}]}}", "format": "\"sanger\"", "pacbio": "\"false\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16578", "id": "e4a1e6f57e384175", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_fastq_info.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "8cd4beb5cf8a2f93"}, "inputs_0\|fasta": {"src": "hda", "id": "c6b012dc2ec4a20b"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "8cd4beb5cf8a2f93", "uuid": "c9633e87-92ec-41e8-8681-cd3853616f18"}, "inputs_0\|fasta": {"src": "hda", "id": "c6b012dc2ec4a20b", "uuid": "f202689a-78a7-4f16-a06c-193c6b7cadb5"}}, "update_time": "2018-02-08T17:24:28.595502", "tool_id": "mothur_filter_seqs", "outputs": {"__new_primary_file_Mock_S280_L001_R1_001_small.trim.contigs.good.align_head\|HMP_MOCK.v35.align__": {"src": "hda", "id": "d12daff1a3ddfe3f", "uuid": "59b94fbc-28e9-478b-a3be-6f31b037432e"}, "__new_primary_file_Mock_S280_L001_R1_001_small.trim.contigs.good.align_head\|Mock_S280_L001_R1_001_small.trim.contigs.good.align_head__": {"src": "hda", "id": "c9ec74100d9952dd", "uuid": "efb1b48b-884a-432c-b896-0f79354137c3"}, "logfile": {"src": "hda", "id": "e81ccf1738866a34", "uuid": "5253fc43-d4ff-48b4-b4bb-318955c58886"}, "out_filter": {"src": "hda", "id": "e400af07ae3fa77f", "uuid": "3d6ac024-1b0e-47fc-bcfc-4e19cf5b1c57"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > filter.seqs(fasta=fasta.dat-fasta0.dat,vertical=true,soft=0,processors= \r1)\n\nUsing 1 processors.\nCreating Filter... \n32\n10\n\n\nRunning Filter... \n32\n10\n\n\n\nLength of filtered alignment: 553\nNumber of columns removed: 49447\nLength of the original alignment: 50000\nNumber of sequences used to construct filter: 42\n\nOutput File Names: \nfastafasta0.filter\nfasta.filter.fasta\nfasta0.filter.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_797.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_798.dat' fasta0.dat && ln -s 'None' hard.dat && echo 'filter.seqs( fasta=fasta.dat-fasta0.dat, vertical=true, soft=0, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv fasta.filter.fasta \"HMP_MOCK.v35.align\".filter.fasta && mv fasta0.filter.fasta \"Mock_S280_L001_R1_001_small.trim.contigs.good.align_head\".filter.fasta", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:24:25.233007", "params": {"inputs": "[{\"__index__\": 0, \"fasta\": {\"values\": [{\"src\": \"hda\", \"id\": 798}]}}]", "trump": "\"\"", "vertical": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "hard": "null", "dbkey": "\"hg17\"", "soft": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16693", "id": "3318d523831bcec2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_filter_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "d9eeaf6b2b0ea17f"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "d9eeaf6b2b0ea17f", "uuid": "d7d2e1f4-b3aa-4e9a-8a9b-cbffc910044f"}}, "update_time": "2018-02-08T17:24:49.016571", "tool_id": "mothur_filter_seqs", "outputs": {"filteredfasta": {"src": "hda", "id": "92afd254baae3cac", "uuid": "be76b447-ba3b-42ca-b0ea-02f97b7c93a5"}, "logfile": {"src": "hda", "id": "dc72314d29258a13", "uuid": "d09ac3a3-1577-4b8a-a837-2c45eb5a49f5"}, "out_filter": {"src": "hda", "id": "766e222ad152fb61", "uuid": "c46e69b4-a17e-43f6-a069-7b1a71eee36c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > filter.seqs(fasta=fasta.dat,vertical=true,soft=0,processors=1)\n\nUsing 1 processors.\nCreating Filter... \n32\n\n\nRunning Filter... \n32\n\n\n\nLength of filtered alignment: 553\nNumber of columns removed: 49447\nLength of the original alignment: 50000\nNumber of sequences used to construct filter: 32\n\nOutput File Names: \nfasta.filter\nfasta.filter.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_803.dat' fasta.dat && ln -s 'None' hard.dat && echo 'filter.seqs( fasta=fasta.dat, vertical=true, soft=0, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv fasta.filter.fasta \"HMP_MOCK.v35.align\".filter.fasta", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:24:45.943706", "params": {"inputs": "[]", "trump": "\"\"", "vertical": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "hard": "null", "dbkey": "\"hg17\"", "soft": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16789", "id": "2c6815fe89528bcf", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_filter_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "4a879c43cb8448df"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "4a879c43cb8448df", "uuid": "82a3f9b7-2c8c-4581-99a3-28ee8ab509cf"}}, "update_time": "2018-02-08T17:25:01.250499", "tool_id": "mothur_filter_shared", "outputs": {"__new_primary_file_unique\|unique__": {"src": "hda", "id": "093ebc9d412c603b", "uuid": "768abf77-cedd-4a5a-bddc-0b554cdf7081"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "b20d09ab9f40b4f6", "uuid": "2871a8d8-7e54-446f-b6b7-903707315190"}, "logfile": {"src": "hda", "id": "e39481c9f084a332", "uuid": "457b2a64-4e88-40ac-8c94-eb99e65a950c"}, "__new_primary_file_unique\|0.10__": {"src": "hda", "id": "aab4584d69f5e8dc", "uuid": "3e67925b-3f5d-433f-9a0c-95ba91b13bab"}, "__new_primary_file_unique\|0.03__": {"src": "hda", "id": "ab005d4cdb71cef2", "uuid": "0a08a2d9-2415-4eb2-a834-bb5367999485"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > filter.shared(shared=otu.dat,minabund=0,minpercent=0,rarepercent=0,keep \rties=true,minnumsamples=0,minpercentsamples=0,mintotal=0,makerare=true)\nunique\n\nRemoved 0 OTUs.\n0.03\n\nRemoved 0 OTUs.\n0.05\n\nRemoved 0 OTUs.\n0.10\n\nRemoved 0 OTUs.\n\nOutput File Names: \notu.unique.filter.dat\notu.0.03.filter.dat\notu.0.05.filter.dat\notu.0.10.filter.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_807.dat' otu.dat && echo 'filter.shared( shared=otu.dat, minabund=0, minpercent=0, rarepercent=0, keepties=true, minnumsamples=0, minpercentsamples=0, mintotal=0, makerare=true )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:24:58.042706", "params": {"rarepercent": "\"0\"", "mintotal": "\"0\"", "makerare": "\"true\"", "minabund": "\"0\"", "keepties": "\"true\"", "label": "null", "dbkey": "\"hg17\"", "groups": "null", "minnumsamples": "\"0\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "minpercent": "\"0\"", "minpercentsamples": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16884", "id": "1475351371259894", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_filter_shared.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"minabund": "1", "otu": {"src": "hda", "id": "3b15c7f26dc0569d"}, "groups": ["forest", "pasture"], "label": ["0.05", "0.29", "0.33"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "3b15c7f26dc0569d", "uuid": "5fb0d6d8-3073-4326-a70a-191ff53c54aa"}}, "update_time": "2018-02-08T17:25:18.973667", "tool_id": "mothur_filter_shared", "outputs": {"__new_primary_file_0.33\|0.29__": {"src": "hda", "id": "6535d25f5d400f01", "uuid": "8e5e98b5-ad5e-42e7-85f6-e1460da8e9e1"}, "__new_primary_file_0.33\|0.05__": {"src": "hda", "id": "ef11ae9dd5e1ab5d", "uuid": "247b8f50-45f4-4926-955a-c6c15494ecf3"}, "logfile": {"src": "hda", "id": "4065036011f723eb", "uuid": "6b0186d1-9972-485c-b3b4-4c252d55df05"}, "__new_primary_file_0.33\|0.33__": {"src": "hda", "id": "72b2b39740f9703c", "uuid": "07092db3-77f7-4bf4-ac2b-167b728f30d0"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > filter.shared(shared=otu.dat,label=0.05-0.29-0.33,groups=forest-pasture \r,minabund=1,minpercent=0,rarepercent=0,keepties=true,minnumsamples=0,minpercents \ramples=0,mintotal=0,makerare=true)\n0.05\n\nRemoved 71 OTUs.\n0.29\n\nRemoved 5 OTUs.\n0.33\n\nRemoved 4 OTUs.\n\nOutput File Names: \notu.0.05.filter.dat\notu.0.29.filter.dat\notu.0.33.filter.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_813.dat' otu.dat && echo 'filter.shared( shared=otu.dat, label=0.05-0.29-0.33, groups=forest-pasture, minabund=1, minpercent=0, rarepercent=0, keepties=true, minnumsamples=0, minpercentsamples=0, mintotal=0, makerare=true )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:25:15.440162", "params": {"rarepercent": "\"0\"", "mintotal": "\"0\"", "makerare": "\"true\"", "minabund": "\"1\"", "keepties": "\"true\"", "label": "[\"0.05\", \"0.29\", \"0.33\"]", "dbkey": "\"hg17\"", "groups": "[\"forest\", \"pasture\"]", "minnumsamples": "\"0\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "minpercent": "\"0\"", "minpercentsamples": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16968", "id": "8c2787e62639209d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_filter_shared.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "da36c3eb2b3d65a2"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "da36c3eb2b3d65a2", "uuid": "cba3d5fe-09fc-4e04-91ab-7bbc05d36321"}}, "update_time": "2018-02-08T17:25:37.273222", "tool_id": "mothur_get_communitytype", "outputs": {"__new_primary_file_1.dmm.5.mix\|1.dmm.2.mix__": {"src": "hda", "id": "46d9987333936090", "uuid": "b0623781-62e3-4150-ac7f-239be4a71b70"}, "parameters": {"src": "hda", "id": "dd4d919ea4ea0b29", "uuid": "d612eb45-53ea-47b8-95d4-873e5618fb69"}, "fit": {"src": "hda", "id": "e3f91a060b9b80d1", "uuid": "6a770929-dc86-4bc0-8900-c47fd74aaf88"}, "__new_primary_file_1.dmm.5.mix\|1.dmm.4.mix__": {"src": "hda", "id": "80bd938d1e1607e1", "uuid": "1235a90e-f5b0-48e0-8831-411fc5e6dd2f"}, "__new_primary_file_1.dmm.5.mix\|1.dmm.3.mix__": {"src": "hda", "id": "9140d1ef204facd8", "uuid": "1bf8cde3-d372-4fb5-b7e1-177508ce896f"}, "summary": {"src": "hda", "id": "45ca4a044ef44e98", "uuid": "51c92525-d990-4b94-aeb0-5f4b88275daf"}, "__new_primary_file_1.dmm.5.mix\|1.dmm.5.mix__": {"src": "hda", "id": "fd784843823fdc6f", "uuid": "aad19a5d-9410-4cff-8b9a-20900d8dc2b7"}, "design": {"src": "hda", "id": "1fb72aa777fd09ee", "uuid": "3509ad1e-3446-40e3-aec1-788fa6b63e6d"}, "logfile": {"src": "hda", "id": "957ab5f6bc45f41a", "uuid": "8648dd7f-d3e4-45d9-974a-511fb5a40d0b"}, "__new_primary_file_1.dmm.5.mix\|1.dmm.1.mix__": {"src": "hda", "id": "512bef0a5c0a6baf", "uuid": "fdc4d9b4-eca5-4859-ace7-6cb87f40b831"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.communitytype(shared=shared.dat,method=dmm,minpartitions=5,maxparti \rtions=10,optimizegap=3,processors=1)\nUsing 1 processor\n1\nK\tNLE\t\tlogDet\tBIC\t\tAIC\t\tLaplace\n1\t1216.81\t81.07\t1265.15\t1260.81\t1216.91\n2\t1277.35\t93.64\t1375.12\t1366.35\t1242.39\n3\t1394.29\t95.07\t1541.51\t1528.29\t1318.69\n4\t1506.74\t56.14\t1703.39\t1685.74\t1370.32\n5\t1609.90\t33.23\t1855.99\t1833.90\t1420.67\n\nOutput File Names: \nshared.1.dmm.mix.fit\nshared.1.dmm.1.mix.posterior\nshared.1.dmm.1.mix.relabund\nshared.1.dmm.2.mix.posterior\nshared.1.dmm.2.mix.relabund\nshared.1.dmm.3.mix.posterior\nshared.1.dmm.3.mix.relabund\nshared.1.dmm.4.mix.posterior\nshared.1.dmm.4.mix.relabund\nshared.1.dmm.5.mix.posterior\nshared.1.dmm.5.mix.relabund\nshared.1.dmm.mix.design\nshared.1.dmm.mix.parameters\nshared.1.dmm.mix.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_818.dat' shared.dat && echo 'get.communitytype( shared=shared.dat, method=dmm, minpartitions=5, maxpartitions=10, optimizegap=3, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:25:32.972501", "params": {"optimizegap": "\"3\"", "m": "{\"method\": \"dmm\", \"__current_case__\": 0}", "dbkey": "\"hg17\"", "label": "null", "subsample": "\"-1\"", "minpartitions": "\"5\"", "groups": "null", "maxpartitions": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17059", "id": "1347e273f5270371", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_communitytype.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"m\|method": "kmeans", "label": "1", "subsample": "0", "groups": ["F003D000", "F003D002", "F003D006", "F003D008", "F003D142"], "m\|iters": "100", "maxpartitions": "4", "otu": {"src": "hda", "id": "fa032b562e153122"}, "m\|calc": "manhattan"}, "job": {"inputs": {"otu": {"src": "hda", "id": "fa032b562e153122", "uuid": "5bfd8e93-46fe-453c-a4da-48ec58a85d3e"}}, "update_time": "2018-02-08T17:26:23.046397", "tool_id": "mothur_get_communitytype", "outputs": {"__new_primary_file_1.kmeans.4.mix\|1.kmeans.1.mix__": {"src": "hda", "id": "d094c18f3f0c4217", "uuid": "84368f6d-4d9c-4113-9bd6-257309aed486"}, "__new_primary_file_1.kmeans.4.mix\|1.kmeans.4.mix__": {"src": "hda", "id": "af3fae2a84d45574", "uuid": "c2b87b12-c748-4afe-8fe5-c6df9b709939"}, "fit": {"src": "hda", "id": "b1d26ebda0776d51", "uuid": "58f10d11-2ccf-4f31-a25c-de3108ef4496"}, "__new_primary_file_1.kmeans.4.mix\|1.kmeans.2.mix__": {"src": "hda", "id": "5498b8b462f50992", "uuid": "1248da22-bd19-4fd6-ad84-b8bb15632ed6"}, "__new_primary_file_1.kmeans.4.mix\|1.kmeans.3.mix__": {"src": "hda", "id": "172394607370a660", "uuid": "31f888f5-2ccb-4958-a217-4eac5900c86e"}, "design": {"src": "hda", "id": "c1aa962b6790390b", "uuid": "a10310a9-90b9-4c09-9d30-bc836823e2d4"}, "logfile": {"src": "hda", "id": "8d9b160acaa0feca", "uuid": "d19c3919-9eb7-4dac-a914-7c053983d7b3"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.communitytype(shared=shared.dat,label=1,groups=F003D000-F003D002-F0 \r03D006-F003D008-F003D142,method=kmeans,calc=manhattan,iters=100,subsample=T,minp \rartitions=5,maxpartitions=4,optimizegap=3,processors=1)\nUsing 1 processor\n1\nK\tCH\tF003D000\tF003D002\tF003D006\tF003D008\tF003D142\n100\n1\t0.000000\t0.000000\t0.000000\t0.000000\t0.000000\t0.000000\n2\t4.168014\t0.296084\t0.201078\t0.496841\t0.122851\t0.606822\n3\t0.646053\t-0.138889\t0.000000\t0.399794\t-0.239057\t0.594163\n4\t0.182272\t-0.138889\t0.000000\t0.000000\t-0.239057\t0.000000\n\nOutput File Names: \nshared.1.kmeans.mix.fit\nshared.1.kmeans.1.mix.posterior\nshared.1.kmeans.1.mix.relabund\nshared.1.kmeans.2.mix.posterior\nshared.1.kmeans.2.mix.relabund\nshared.1.kmeans.3.mix.posterior\nshared.1.kmeans.3.mix.relabund\nshared.1.kmeans.4.mix.posterior\nshared.1.kmeans.4.mix.relabund\nshared.1.kmeans.mix.design\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_834.dat' shared.dat && echo 'get.communitytype( shared=shared.dat, label=1, groups=F003D000-F003D002-F003D006-F003D008-F003D142, method=kmeans, calc=manhattan, iters=100, subsample=T, minpartitions=5, maxpartitions=4, optimizegap=3, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:26:19.082655", "params": {"optimizegap": "\"3\"", "m": "{\"iters\": \"100\", \"calc\": \"manhattan\", \"method\": \"kmeans\", \"__current_case__\": 1}", "dbkey": "\"hg17\"", "label": "\"1\"", "subsample": "\"0\"", "minpartitions": "\"5\"", "groups": "[\"F003D000\", \"F003D002\", \"F003D006\", \"F003D008\", \"F003D142\"]", "maxpartitions": "\"4\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17158", "id": "4ffe0c6ec86fa835", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_communitytype.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "b7e286a9dc222a5c"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "b7e286a9dc222a5c", "uuid": "bdec2f8f-1198-44cc-b57e-a04799d0e832"}}, "update_time": "2018-02-08T17:26:59.775503", "tool_id": "mothur_get_coremicrobiome", "outputs": {"__new_primary_file_unique\|0.10__": {"src": "hda", "id": "a6d2cc1cc42ebc8f", "uuid": "233065b3-98ac-4c29-b30e-3b306f62aff7"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "2359309399418ebc", "uuid": "d78b6caa-de9d-4319-ada9-88432db48511"}, "__new_primary_file_unique\|0.17__": {"src": "hda", "id": "075a237cd5260f96", "uuid": "4f8c8914-582b-4740-b421-c7e4d86ec21e"}, "__new_primary_file_unique\|0.02__": {"src": "hda", "id": "ec7711f2346cbca2", "uuid": "654e2c05-b90c-4435-860a-97156d892f09"}, "__new_primary_file_unique\|0.21__": {"src": "hda", "id": "793e3e9c6f59a42d", "uuid": "3fc8cb23-3378-4f70-9b14-ee4904c6fff6"}, "__new_primary_file_unique\|0.16__": {"src": "hda", "id": "b870f50c8df3ba43", "uuid": "be1c738a-4a78-48d2-97cf-739fb8a700cf"}, "__new_primary_file_unique\|0.45__": {"src": "hda", "id": "464c0ed74865d74c", "uuid": "8171f1de-f71d-42a8-a7e3-447b4be12d61"}, "__new_primary_file_unique\|0.03__": {"src": "hda", "id": "1000d2466fcfad34", "uuid": "736b8b91-4f88-4616-9c7e-d0a27458847f"}, "__new_primary_file_unique\|0.15__": {"src": "hda", "id": "fbe5f3e3e3e03570", "uuid": "c79935f9-a980-4a16-8ee1-734ad89f89d1"}, "__new_primary_file_unique\|0.08__": {"src": "hda", "id": "dd222fd69f0dcf77", "uuid": "593ab8a8-e41a-467f-9e5f-73864cc64489"}, "__new_primary_file_unique\|0.14__": {"src": "hda", "id": "ff8b3978bcf080b9", "uuid": "634b157a-6818-4084-bb17-2a5e387c40f2"}, "__new_primary_file_unique\|0.13__": {"src": "hda", "id": "9f2ff1f2038a0454", "uuid": "078e742d-b87a-413f-aaaf-a67611bc6951"}, "__new_primary_file_unique\|0.09__": {"src": "hda", "id": "3d4c423d57259fbe", "uuid": "2985e026-f0ee-41dc-9889-62be13ea052f"}, "__new_primary_file_unique\|0.12__": {"src": "hda", "id": "aeb3a7d27531d8af", "uuid": "ad4e98b4-c643-4d4a-a391-e2b966da62aa"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "306d83d29e038396", "uuid": "6f9746f6-d36b-425a-bf6b-960f1f3e2b66"}, "__new_primary_file_unique\|0.11__": {"src": "hda", "id": "1bdec2d5353dc7ac", "uuid": "ab5376c5-c51d-4ef7-b34f-e9f1e8d7fa48"}, "__new_primary_file_unique\|0.41__": {"src": "hda", "id": "753f526c4fe64c6a", "uuid": "1d767ed6-fed9-4555-86b8-b7e57cb0ecff"}, "__new_primary_file_unique\|0.06__": {"src": "hda", "id": "0e57173360853a16", "uuid": "c68d169e-4ce1-4884-97e3-74695ade4348"}, "__new_primary_file_unique\|0.25__": {"src": "hda", "id": "6d4181f50c48e719", "uuid": "224c4143-b35f-41ec-ac34-4d49db58eeed"}, "__new_primary_file_unique\|0.22__": {"src": "hda", "id": "39aace9ebf1f79e7", "uuid": "dff73c25-fa2e-4d9d-bbba-c5bb39012224"}, "__new_primary_file_unique\|0.36__": {"src": "hda", "id": "9009f3fbd6374ed9", "uuid": "62b406ba-bcea-487a-befd-2df70395590b"}, "__new_primary_file_unique\|0.04__": {"src": "hda", "id": "e5cb57ff5e9a2036", "uuid": "142511d9-525c-4498-8b73-e6d5a6af8882"}, "__new_primary_file_unique\|0.23__": {"src": "hda", "id": "3a712f92b35e894a", "uuid": "39100123-be01-44f0-a652-52508139227c"}, "__new_primary_file_unique\|0.33__": {"src": "hda", "id": "ab53f78f19a8abb1", "uuid": "51d68092-e60d-400c-bf47-d6dd75569dba"}, "logfile": {"src": "hda", "id": "7bfed31e5ec18c3b", "uuid": "2d37f2f3-9ea3-4c56-babd-56e719ca5cad"}, "__new_primary_file_unique\|0.20__": {"src": "hda", "id": "a015212d4be18feb", "uuid": "ece7a697-24a6-42bc-a04c-2567edc4f37d"}, "__new_primary_file_unique\|0.29__": {"src": "hda", "id": "06d05dea0c9ced7b", "uuid": "74c220de-4196-497d-9a83-497883ef5336"}, "__new_primary_file_unique\|0.38__": {"src": "hda", "id": "c26638b7e7264d47", "uuid": "2a4a43d5-d028-44c6-9e80-401e0c943d70"}, "__new_primary_file_unique\|0.55__": {"src": "hda", "id": "cfd269e45b767b10", "uuid": "91742f4b-eca2-4b50-b0dd-f58a9bb2ea12"}, "__new_primary_file_unique\|0.07__": {"src": "hda", "id": "86305fdc0e529488", "uuid": "295d95a4-8e81-45c9-ba14-9df0fbc7a735"}, "__new_primary_file_unique\|0.26__": {"src": "hda", "id": "fd5c24c1cb65fd09", "uuid": "60e02f42-5541-40b7-ad8d-6a799983f01f"}, "__new_primary_file_unique\|0.32__": {"src": "hda", "id": "d0db08ce3cbc8382", "uuid": "f25a63c1-78e3-4655-86f4-e58b5b012e51"}, "__new_primary_file_unique\|0.27__": {"src": "hda", "id": "e2424d83ba170c8a", "uuid": "d0bb553a-75f1-4097-8a16-9b50032c5694"}, "__new_primary_file_unique\|0.19__": {"src": "hda", "id": "90ebacaedc3e1f42", "uuid": "0c90a057-a0f3-4382-a45b-8838caa3515b"}, "__new_primary_file_unique\|0.01__": {"src": "hda", "id": "2d9271a917bcfaf1", "uuid": "d2bee9b2-9f4e-4c58-b86a-07de1c2a2779"}, "__new_primary_file_unique\|0.24__": {"src": "hda", "id": "b13eb5b1dace709b", "uuid": "6f9bf0fa-95a7-44db-ae7d-0f44bf126dbc"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "fd9f0efd7554e81c", "uuid": "94481846-0b13-4170-b7b2-e96063435573"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.coremicrobiome(shared=otu.dat)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.unique.core.microbiome\notu.0.01.core.microbiome\notu.0.02.core.microbiome\notu.0.03.core.microbiome\notu.0.04.core.microbiome\notu.0.05.core.microbiome\notu.0.06.core.microbiome\notu.0.07.core.microbiome\notu.0.08.core.microbiome\notu.0.09.core.microbiome\notu.0.10.core.microbiome\notu.0.11.core.microbiome\notu.0.12.core.microbiome\notu.0.13.core.microbiome\notu.0.14.core.microbiome\notu.0.15.core.microbiome\notu.0.16.core.microbiome\notu.0.17.core.microbiome\notu.0.18.core.microbiome\notu.0.19.core.microbiome\notu.0.20.core.microbiome\notu.0.21.core.microbiome\notu.0.22.core.microbiome\notu.0.23.core.microbiome\notu.0.24.core.microbiome\notu.0.25.core.microbiome\notu.0.26.core.microbiome\notu.0.27.core.microbiome\notu.0.29.core.microbiome\notu.0.32.core.microbiome\notu.0.33.core.microbiome\notu.0.36.core.microbiome\notu.0.38.core.microbiome\notu.0.41.core.microbiome\notu.0.45.core.microbiome\notu.0.55.core.microbiome\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_846.dat' otu.dat && echo 'get.coremicrobiome( shared=otu.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:26:55.029493", "params": {"abundance": "\"\"", "samples": "\"\"", "dbkey": "\"hg17\"", "label": "null", "groups": "null", "output": "\"fraction\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17250", "id": "6fb508dbe1736155", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_coremicrobiome.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"abundance": "30", "otu": {"src": "hda", "id": "58c9e52c4a64b228"}, "label": ["0.05", "0.22", "0.45"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "58c9e52c4a64b228", "uuid": "8ce00b7a-a8a2-430e-8bc6-84d7fbd2a3bf"}}, "update_time": "2018-02-08T17:27:19.754618", "tool_id": "mothur_get_coremicrobiome", "outputs": {"__new_primary_file_0.45\|0.22__": {"src": "hda", "id": "afce6c63a9e7aea5", "uuid": "1845c435-5d48-4b12-b043-c80f08244f67"}, "logfile": {"src": "hda", "id": "c09e2ca1f1e4cd99", "uuid": "082703a5-d021-4379-b991-d1c9af2b43c6"}, "__new_primary_file_0.45\|0.45__": {"src": "hda", "id": "9c87d501351cb89f", "uuid": "f88274c8-a2e6-41b8-849b-9f24bc40bdaf"}, "__new_primary_file_0.45\|0.05__": {"src": "hda", "id": "816dd7bcb4c0fa93", "uuid": "60ee11c0-8707-40a1-afb8-324a92eecba5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.coremicrobiome(shared=otu.dat,label=0.05-0.22-0.45,abundance=30)\n0.05\n0.22\n0.45\n\nOutput File Names: \notu.0.05.core.microbiome\notu.0.05.core.microbiomelist\notu.0.22.core.microbiome\notu.0.22.core.microbiomelist\notu.0.45.core.microbiome\notu.0.45.core.microbiomelist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_884.dat' otu.dat && echo 'get.coremicrobiome( shared=otu.dat ,label=0.05-0.22-0.45 ,abundance=30 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:27:16.293030", "params": {"abundance": "\"30\"", "samples": "\"\"", "dbkey": "\"hg17\"", "label": "[\"0.05\", \"0.22\", \"0.45\"]", "groups": "null", "output": "\"fraction\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17337", "id": "38f13aa9fc15acbf", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_coremicrobiome.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|dist": {"src": "hda", "id": "da06cbb007a4cb61"}, "input\|source": "phylip", "accnos": {"src": "hda", "id": "0126412added8c8e"}}, "job": {"inputs": {"accnos": {"src": "hda", "id": "0126412added8c8e", "uuid": "c191f3eb-cc95-4db0-9524-2f70d2b5e647"}, "dist": {"src": "hda", "id": "da06cbb007a4cb61", "uuid": "b1ed6156-408c-4f43-80fc-5536243e55e7"}}, "update_time": "2018-02-08T17:27:48.325338", "tool_id": "mothur_get_dists", "outputs": {"logfile": {"src": "hda", "id": "b3cba6951cf833ad", "uuid": "9013f911-7f16-4fbe-b982-75d3c13d2ab8"}, "pick_dist": {"src": "hda", "id": "26507515799dee2a", "uuid": "e3b28f5f-eb02-4fe6-bdd2-7b45e1539df4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.dists(accnos=accnos.dat,phylip=input.dist.dat)\nSelected 8 groups or sequences from your phylip file.\n\nOutput File names: \ninput.dist.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_893.dat' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_892.dat' input.dist.dat && echo 'get.dists( accnos=accnos.dat, phylip=input.dist.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:27:45.313518", "params": {"input": "{\"source\": \"phylip\", \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 892}]}, \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17452", "id": "3ecde483422ba55d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_dists.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"shared": {"src": "hda", "id": "b792db3724607288"}}, "job": {"inputs": {"shared": {"src": "hda", "id": "b792db3724607288", "uuid": "ee9810f6-620b-469e-939d-54f8b55afc92"}}, "update_time": "2018-02-08T17:28:05.694410", "tool_id": "mothur_get_group", "outputs": {"bootgroups": {"src": "hda", "id": "f9be15f92a6fe6ec", "uuid": "5c5c9da1-3a70-476f-bef4-df34961637b2"}, "logfile": {"src": "hda", "id": "668671b8705dc162", "uuid": "0a519a4e-a481-4c50-bfea-ab7139416da0"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.group(shared=shared.dat)\nforest\npasture\n\nOutput File Names: \n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_896.dat' shared.dat && echo 'get.group( shared=shared.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && cat mothur..logfile \| head -n-6 \| sed '1,30d' > \"/tmp/saskia/tmpKSDp0p/files/000/dataset_898.dat\"", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:28:02.572268", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17539", "id": "6776b4c51106726f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_group.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"group_in": {"src": "hda", "id": "847f267ec407e762"}, "groupnames\|groups": ["forest", "pasture"], "groupnames\|source": "groups"}, "job": {"inputs": {"group_in": {"src": "hda", "id": "847f267ec407e762", "uuid": "52ca1b29-6082-4531-bade-d86f51e9f447"}}, "update_time": "2018-02-08T17:28:18.288203", "tool_id": "mothur_get_groups", "outputs": {"group_out": {"src": "hda", "id": "4561df7fd732de3f", "uuid": "3cda55f1-262a-4201-b49a-9e0c022a36e4"}, "logfile": {"src": "hda", "id": "aab4e8dd7c444bc2", "uuid": "4a0646f7-9b7f-472f-8bdd-7af6a790339d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.groups(group=group_in.dat,groups=forest-pasture)\nSelected 98 sequences from your group file.\n\nOutput File names: \ngroup_in.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_899.dat' group_in.dat && ln -s 'None' fasta_in.dat && ln -s 'None' name_in.dat && ln -s 'None' list_in.dat && ln -s 'None' shared_in.dat && ln -s 'None' taxonomy_in.dat && ln -s 'None' design_in.dat && echo 'get.groups( group=group_in.dat ,groups=forest-pasture )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:28:15.314231", "params": {"design_in": "null", "shared_in": "null", "fasta_in": "null", "dbkey": "\"hg17\"", "groupnames": "{\"source\": \"groups\", \"groups\": [\"forest\", \"pasture\"], \"__current_case__\": 0}", "taxonomy_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17626", "id": "7e438c048dc73282", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_groups.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"group_in": {"src": "hda", "id": "0650f1de48127da2"}, "groupnames\|accnos": {"src": "hda", "id": "a614724d012c5b21"}, "groupnames\|source": "accnos"}, "job": {"inputs": {"group_in": {"src": "hda", "id": "0650f1de48127da2", "uuid": "fd50498c-4bc4-4221-9e90-73e70d2a37ad"}, "accnos": {"src": "hda", "id": "a614724d012c5b21", "uuid": "e4dab025-9ff2-4b5a-81fb-f5519760b90d"}}, "update_time": "2018-02-08T17:28:38.840237", "tool_id": "mothur_get_groups", "outputs": {"group_out": {"src": "hda", "id": "4420605beb7b8bfb", "uuid": "2cd9f556-01d6-4537-b6a4-cfb46c181f17"}, "logfile": {"src": "hda", "id": "5bea13ccc5be4601", "uuid": "54f9eb15-cd81-4161-abe4-6a5298ccc88e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.groups(group=group_in.dat,accnos=groupnames.accnos.dat)\nSelected 98 sequences from your group file.\n\nOutput File names: \ngroup_in.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_902.dat' group_in.dat && ln -s 'None' fasta_in.dat && ln -s 'None' name_in.dat && ln -s 'None' list_in.dat && ln -s 'None' shared_in.dat && ln -s 'None' taxonomy_in.dat && ln -s 'None' design_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_903.dat' groupnames.accnos.dat && echo 'get.groups( group=group_in.dat ,accnos=groupnames.accnos.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:28:35.903967", "params": {"design_in": "null", "shared_in": "null", "fasta_in": "null", "dbkey": "\"hg17\"", "groupnames": "{\"source\": \"accnos\", \"accnos\": {\"values\": [{\"src\": \"hda\", \"id\": 903}]}, \"__current_case__\": 1}", "taxonomy_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17749", "id": "daf78d18ceb29125", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_groups.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"shared_in": {"src": "hda", "id": "d67967a926798f5f"}, "fasta_in": {"src": "hda", "id": "35283c805171c447"}, "list_in": {"src": "hda", "id": "f607da3436fbec2f"}, "group_in": {"src": "hda", "id": "2678f705a638379e"}, "groupnames\|source": "accnos", "groupnames\|accnos": {"src": "hda", "id": "0cb926f24836ac7c"}, "name_in": {"src": "hda", "id": "cfe031a04a60c053"}}, "job": {"inputs": {"shared_in": {"src": "hda", "id": "d67967a926798f5f", "uuid": "51ef0239-4c60-46ca-968b-309399b500fe"}, "fasta_in": {"src": "hda", "id": "35283c805171c447", "uuid": "57d4d1b8-7ada-432f-9f75-b44c0176ba84"}, "group_in": {"src": "hda", "id": "2678f705a638379e", "uuid": "123b585d-dd83-4d4d-ad63-a21cca9786c2"}, "accnos": {"src": "hda", "id": "0cb926f24836ac7c", "uuid": "12c17915-dd32-45eb-a48a-2f7302e6b71f"}, "list_in": {"src": "hda", "id": "f607da3436fbec2f", "uuid": "642ba2bd-7ef7-491e-b46b-89ad138d6c91"}, "name_in": {"src": "hda", "id": "cfe031a04a60c053", "uuid": "7dadd403-a404-4254-8947-6231ad67f1d4"}}, "update_time": "2018-02-08T17:29:19.880133", "tool_id": "mothur_get_groups", "outputs": {"__new_primary_file_unique\|0.10__": {"src": "hda", "id": "e7b2fbcbe0130dc5", "uuid": "0fc85bad-a4cd-487b-9d9e-917735e5f337"}, "fasta_out": {"src": "hda", "id": "e3d34fd694cc8229", "uuid": "df83ec03-d83a-471f-9667-05c4c355b36d"}, "__new_primary_file_unique\|0.17__": {"src": "hda", "id": "49e0d2540b109fa1", "uuid": "0512e81e-973d-4e2c-b6aa-76f587ab07ae"}, "name_out": {"src": "hda", "id": "dc3d09c4b8e0106b", "uuid": "e2ef3817-ebec-4af6-9523-3162b6396cf0"}, "__new_primary_file_unique\|0.02__": {"src": "hda", "id": "28f4914f81d01a57", "uuid": "11bd60dd-fb43-41f9-a092-217e04111f0f"}, "__new_primary_file_unique\|0.21__": {"src": "hda", "id": "0c74b38aee0a0707", "uuid": "e22ad6ae-070b-4a3c-bf25-aa64d1b9ed46"}, "__new_primary_file_unique\|0.16__": {"src": "hda", "id": "d81fd9932dcc170a", "uuid": "041d0e7f-db5b-44eb-9fea-dcf4b2fb87c7"}, "__new_primary_file_unique\|0.45__": {"src": "hda", "id": "69399224f9256324", "uuid": "2ce57bef-5a87-49c8-9fb0-d8875771706a"}, "__new_primary_file_unique\|0.25__": {"src": "hda", "id": "f0a1b060065d5446", "uuid": "6cc32651-11ef-4e7f-9f83-92e41535b9a2"}, "__new_primary_file_unique\|0.15__": {"src": "hda", "id": "59577937f74245aa", "uuid": "8495987e-d861-4ba0-b99d-336fddc547e1"}, "__new_primary_file_unique\|0.08__": {"src": "hda", "id": "2b396abc964fbea2", "uuid": "8978e23d-4166-47e6-b9b2-5752815535b6"}, "__new_primary_file_unique\|0.14__": {"src": "hda", "id": "f21afe41a9b1581c", "uuid": "dc1d3cba-9e86-4969-9b92-b9a176495360"}, "__new_primary_file_unique\|0.13__": {"src": "hda", "id": "1ed3e70d24b98524", "uuid": "45b7a913-f48a-43d0-a013-afddb51f8ea6"}, "__new_primary_file_unique\|0.09__": {"src": "hda", "id": "1fd6dc2cbb454726", "uuid": "17866495-61a1-4938-a035-15962d8ab6d0"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "64114e2b118e5c93", "uuid": "5f3900a8-63e5-4c6d-b6fa-37f6c4e5cf66"}, "__new_primary_file_unique\|0.12__": {"src": "hda", "id": "0edc42988cb29650", "uuid": "6db90c67-7578-49e9-b756-d816a9106382"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "ba68b57cc8005e59", "uuid": "789ba415-6a47-4be9-a6b7-5dfd4b42ceec"}, "__new_primary_file_unique\|0.11__": {"src": "hda", "id": "00df4bed4eb73805", "uuid": "80186821-a510-4bcb-8006-c6b0c41c193c"}, "__new_primary_file_unique\|0.41__": {"src": "hda", "id": "63acbb87262a1307", "uuid": "0b55ba95-3740-4d53-bd41-150e5b5fc8dd"}, "__new_primary_file_unique\|0.06__": {"src": "hda", "id": "5c0d4def21b0cc81", "uuid": "aa6c782c-87a3-4853-b401-b017615f4c6f"}, "__new_primary_file_unique\|0.03__": {"src": "hda", "id": "835154436814778d", "uuid": "09dc6d61-399d-4a0e-b140-77741c901fef"}, "__new_primary_file_unique\|0.04__": {"src": "hda", "id": "55898ade0931da26", "uuid": "b06b0390-f7d6-4ade-b33d-daa143835a10"}, "__new_primary_file_unique\|0.36__": {"src": "hda", "id": "d10947b9879b82b2", "uuid": "c1bee6d0-b738-4568-9372-7ae85bdc2952"}, "__new_primary_file_unique\|0.22__": {"src": "hda", "id": "d30ef2c42df90932", "uuid": "1c58dab4-07f1-459a-aadb-6708836de56e"}, "__new_primary_file_unique\|0.23__": {"src": "hda", "id": "8b5aaaded4e2744a", "uuid": "ddd0691d-4c4a-480e-b33c-682dec6fd1a9"}, "__new_primary_file_unique\|0.33__": {"src": "hda", "id": "e4bf668168cf4d28", "uuid": "f61f63c3-eb97-4c8f-b84f-f83c84fc7029"}, "logfile": {"src": "hda", "id": "9991dcf0fd7f0858", "uuid": "f8771e9a-bf6e-416a-b94f-daff5d8d95d6"}, "__new_primary_file_unique\|0.20__": {"src": "hda", "id": "6106d47609a22f86", "uuid": "2afdba2a-cc11-4655-9ccc-b744a34bff5f"}, "__new_primary_file_unique\|0.29__": {"src": "hda", "id": "7ebdd79957123fd3", "uuid": "938d5e9a-2fdb-40fa-b33b-e4214fb89732"}, "__new_primary_file_unique\|0.38__": {"src": "hda", "id": "884d04d1bc49fbdb", "uuid": "a592c21e-ecf3-4904-9e4e-e737b0745087"}, "__new_primary_file_unique\|0.55__": {"src": "hda", "id": "498289f2374aaabc", "uuid": "2d5e7e5f-eb29-4c83-8ee2-76e8c2b04364"}, "group_out": {"src": "hda", "id": "f5bbc78947a4eedf", "uuid": "9d342395-a884-438a-a94a-869933812708"}, "__new_primary_file_unique\|0.07__": {"src": "hda", "id": "9b47053a34d461cf", "uuid": "bbfa83f3-3cf1-4a5a-8203-45444602993e"}, "__new_primary_file_unique\|0.26__": {"src": "hda", "id": "de60620e584e5f58", "uuid": "5934793a-5722-4ed0-a76d-002a7dc64b89"}, "__new_primary_file_unique\|0.32__": {"src": "hda", "id": "9d84a8c0f8b83109", "uuid": "6b911bb6-5197-49a3-a901-25346bf3ac3c"}, "__new_primary_file_unique\|0.27__": {"src": "hda", "id": "c2a06a3a7a66a110", "uuid": "57f7b1b4-b2f9-4724-b60b-48b5474918d6"}, "__new_primary_file_unique\|0.19__": {"src": "hda", "id": "e6fa111c52a4ac04", "uuid": "3d9d4e51-96cc-46e0-a698-edc16d5368ea"}, "__new_primary_file_unique\|0.01__": {"src": "hda", "id": "27741565111063db", "uuid": "4e53bb98-a46f-4c49-af70-69c408fadbd6"}, "__new_primary_file_unique\|0.24__": {"src": "hda", "id": "0bc7636427d365b6", "uuid": "473f7936-2596-4bf1-9ca1-07604f66f8a3"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "db7df1b0dd9c9f66", "uuid": "eaa9fc5a-aecb-45fc-abc5-3c51a2ea1257"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.groups(group=group_in.dat,accnos=groupnames.accnos.dat,fasta=fasta_ \rin.dat,name=name_in.dat,list=list_in.dat,shared=shared_in.dat)\nSelected 98 sequences from your name file.\nSelected 98 sequences from your fasta file.\nSelected 98 sequences from your group file.\nSelected 98 sequences from your list file.\nSelected groups: forest, pasture from your shared file.\n\nOutput File names: \nname_in.pick.dat\nfasta_in.pick.dat\ngroup_in.pick.dat\nlist_in.unique.pick.dat\nlist_in.0.01.pick.dat\nlist_in.0.02.pick.dat\nlist_in.0.03.pick.dat\nlist_in.0.04.pick.dat\nlist_in.0.05.pick.dat\nlist_in.0.06.pick.dat\nlist_in.0.07.pick.dat\nlist_in.0.08.pick.dat\nlist_in.0.09.pick.dat\nlist_in.0.10.pick.dat\nlist_in.0.11.pick.dat\nlist_in.0.12.pick.dat\nlist_in.0.13.pick.dat\nlist_in.0.14.pick.dat\nlist_in.0.15.pick.dat\nlist_in.0.16.pick.dat\nlist_in.0.17.pick.dat\nlist_in.0.18.pick.dat\nlist_in.0.19.pick.dat\nlist_in.0.20.pick.dat\nlist_in.0.21.pick.dat\nlist_in.0.22.pick.dat\nlist_in.0.23.pick.dat\nlist_in.0.24.pick.dat\nlist_in.0.25.pick.dat\nlist_in.0.26.pick.dat\nlist_in.0.27.pick.dat\nlist_in.0.29.pick.dat\nlist_in.0.32.pick.dat\nlist_in.0.33.pick.dat\nlist_in.0.36.pick.dat\nlist_in.0.38.pick.dat\nlist_in.0.41.pick.dat\nlist_in.0.45.pick.dat\nlist_in.0.55.pick.dat\nshared_in.unique.pick.dat\nshared_in.0.01.pick.dat\nshared_in.0.02.pick.dat\nshared_in.0.03.pick.dat\nshared_in.0.04.pick.dat\nshared_in.0.05.pick.dat\nshared_in.0.06.pick.dat\nshared_in.0.07.pick.dat\nshared_in.0.08.pick.dat\nshared_in.0.09.pick.dat\nshared_in.0.10.pick.dat\nshared_in.0.11.pick.dat\nshared_in.0.12.pick.dat\nshared_in.0.13.pick.dat\nshared_in.0.14.pick.dat\nshared_in.0.15.pick.dat\nshared_in.0.16.pick.dat\nshared_in.0.17.pick.dat\nshared_in.0.18.pick.dat\nshared_in.0.19.pick.dat\nshared_in.0.20.pick.dat\nshared_in.0.21.pick.dat\nshared_in.0.22.pick.dat\nshared_in.0.23.pick.dat\nshared_in.0.24.pick.dat\nshared_in.0.25.pick.dat\nshared_in.0.26.pick.dat\nshared_in.0.27.pick.dat\nshared_in.0.29.pick.dat\nshared_in.0.32.pick.dat\nshared_in.0.33.pick.dat\nshared_in.0.36.pick.dat\nshared_in.0.38.pick.dat\nshared_in.0.41.pick.dat\nshared_in.0.45.pick.dat\nshared_in.0.55.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_906.dat' group_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_908.dat' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_909.dat' name_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_910.dat' list_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_911.dat' shared_in.dat && ln -s 'None' taxonomy_in.dat && ln -s 'None' design_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_907.dat' groupnames.accnos.dat && echo 'get.groups( group=group_in.dat ,accnos=groupnames.accnos.dat ,fasta=fasta_in.dat ,name=name_in.dat ,list=list_in.dat ,shared=shared_in.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:29:09.781970", "params": {"design_in": "null", "taxonomy_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groupnames": "{\"source\": \"accnos\", \"accnos\": {\"values\": [{\"src\": \"hda\", \"id\": 907}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17947", "id": "cda64434023ac031", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_groups.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "57529f16d280395b"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "57529f16d280395b", "uuid": "32739e7b-3636-46fd-b3ac-cea446510cfb"}}, "update_time": "2018-02-08T17:30:01.971982", "tool_id": "mothur_get_label", "outputs": {"logfile": {"src": "hda", "id": "bc9fca4354129cac", "uuid": "067bdef1-3a84-4829-8c96-a48e32186d48"}, "labels_list": {"src": "hda", "id": "201e02e237ed0c72", "uuid": "4ba5be37-6f34-4c01-8556-825aa312902f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.label(sabund=otu.dat)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_988.dat' otu.dat && echo 'get.label( sabund=otu.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && cat mothur..logfile \| head -n-3 \| sed '1,30d' > '/tmp/saskia/tmpKSDp0p/files/000/dataset_990.dat'", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:29:58.831218", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18052", "id": "e038b12fcc34712c", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_label.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "49cb3d1841241873"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "49cb3d1841241873", "uuid": "3a2bc5f4-1e07-46cd-a0be-4cca2b665959"}}, "update_time": "2018-02-08T17:30:19.631582", "tool_id": "mothur_get_label", "outputs": {"logfile": {"src": "hda", "id": "ba98875ce3cc6214", "uuid": "f9116359-0d6b-4f41-b691-665ce1d3a1a7"}, "labels_list": {"src": "hda", "id": "ca6dcdef942ee1ff", "uuid": "8263f4f7-7637-44d9-8018-af63e1aaa888"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.label(rabund=otu.dat)\n0.03\n0.05\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_991.dat' otu.dat && echo 'get.label( rabund=otu.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && cat mothur..logfile \| head -n-3 \| sed '1,30d' > '/tmp/saskia/tmpKSDp0p/files/000/dataset_993.dat'", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:30:16.297205", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18142", "id": "57d21b82f66bdde1", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_label.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "8c90b885b85c197b"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "8c90b885b85c197b", "uuid": "14ef5623-7a0b-48ec-a0f1-b67dfcf3c3df"}}, "update_time": "2018-02-08T17:30:37.243891", "tool_id": "mothur_get_label", "outputs": {"logfile": {"src": "hda", "id": "d0915a2b5dcfc5c8", "uuid": "4f7aa13b-d0c7-447d-b1ac-d33bfe1cd0c1"}, "labels_list": {"src": "hda", "id": "d63ffe6d4f3dca3c", "uuid": "7e207c4c-5c60-4eb8-9b35-7c17721e16b6"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.label(list=otu.dat)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_994.dat' otu.dat && echo 'get.label( list=otu.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && cat mothur..logfile \| head -n-3 \| sed '1,30d' > '/tmp/saskia/tmpKSDp0p/files/000/dataset_996.dat'", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:30:34.086402", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18244", "id": "b76e2c1d909ec95b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_label.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"file\|taxonomy": {"src": "hda", "id": "e42f3afaf409615c"}, "file\|filetype": "usetaxonomy", "taxon": "Bacteria;Firmicutes;"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "e42f3afaf409615c", "uuid": "e7dc8e71-b2d3-4775-aac9-a05c3db431de"}}, "update_time": "2018-02-08T17:30:54.719853", "tool_id": "mothur_get_lineage", "outputs": {"logfile": {"src": "hda", "id": "7ea54b244028000c", "uuid": "54d577a5-2051-4705-a621-041d2df19088"}, "taxonomy_out": {"src": "hda", "id": "370469ee2a7f9bfc", "uuid": "2d258268-f5c1-4efa-a6cd-1640a8072a07"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.lineage(taxonomy=file.taxonomy.dat,taxon='Bacteria;Firmicutes;')\n\nOutput File Names: \nfile.taxonomy.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_997.dat' file.taxonomy.dat && ln -s 'None' fasta_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat && echo 'get.lineage( taxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Firmicutes;'\"' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:30:51.569064", "params": {"count": "null", "dups": "\"true\"", "fasta_in": "null", "taxon": "\"Bacteria;Firmicutes;\"", "dbkey": "\"hg17\"", "group_in": "null", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 997}]}, \"filetype\": \"usetaxonomy\", \"taxons\": null, \"__current_case__\": 0}", "alignreport_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18333", "id": "6cafac5eedb91caf", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_lineage.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta_in": {"src": "hda", "id": "9430897aec45eb57"}, "taxon": "Bacteria;Firmicutes;,Bacteria;Actinobacteria;", "list_in": {"src": "hda", "id": "c9e1a49c1225960d"}, "group_in": {"src": "hda", "id": "842c471bdfd9c887"}, "file\|taxonomy": {"src": "hda", "id": "8e944aefd2c834c6"}, "alignreport_in": {"src": "hda", "id": "11a8d37cccceb071"}, "file\|filetype": "usetaxonomy", "name_in": {"src": "hda", "id": "70c3e648e0bbdb1c"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "8e944aefd2c834c6", "uuid": "7c0d62a8-03c2-4142-8222-f461f4e3f089"}, "fasta_in": {"src": "hda", "id": "9430897aec45eb57", "uuid": "61c83e2c-ffd2-4517-8353-c672a56d39e9"}, "group_in": {"src": "hda", "id": "842c471bdfd9c887", "uuid": "517541bb-1156-4c61-bda2-341c4bdbc22d"}, "alignreport_in": {"src": "hda", "id": "11a8d37cccceb071", "uuid": "137a99fb-0157-4241-9d36-1f71de3a69be"}, "list_in": {"src": "hda", "id": "c9e1a49c1225960d", "uuid": "cc505d11-a571-4e10-a752-a7f3a0e884b7"}, "name_in": {"src": "hda", "id": "70c3e648e0bbdb1c", "uuid": "353c65e1-e56a-4583-be0b-444eda6d964f"}}, "update_time": "2018-02-08T17:31:21.642906", "tool_id": "mothur_get_lineage", "outputs": {"__new_primary_file_unique\|0.10__": {"src": "hda", "id": "1be6bbaba2ffb15b", "uuid": "7ca3cacf-7b8c-4c88-b17e-422f35c7a299"}, "fasta_out": {"src": "hda", "id": "72a1145ce219300b", "uuid": "30f3f211-b8b0-4603-b9c8-c33ed578429b"}, "__new_primary_file_unique\|0.17__": {"src": "hda", "id": "cc260ebfc536bb4b", "uuid": "987a49be-eefe-4d4f-9ae4-f72c618fbfb0"}, "name_out": {"src": "hda", "id": "ab97b488b33c6246", "uuid": "35a651dd-bed5-4a1a-b77d-b8b25f7d88e2"}, "__new_primary_file_unique\|0.02__": {"src": "hda", "id": "efc416652e1b4600", "uuid": "4ed1729d-b356-48bf-b60c-e0fb10ee177f"}, "__new_primary_file_unique\|0.21__": {"src": "hda", "id": "b6539af83432ffdf", "uuid": "e4dd59a4-8400-4c8b-8179-b00ccc99bf8f"}, "__new_primary_file_unique\|0.16__": {"src": "hda", "id": "31b6d67921f34be7", "uuid": "8e72d679-cfd8-47d7-b98c-9f6f22111f49"}, "__new_primary_file_unique\|0.45__": {"src": "hda", "id": "702034d3254f766a", "uuid": "e4f68036-9f09-44a8-a763-e05a6de05098"}, "__new_primary_file_unique\|0.25__": {"src": "hda", "id": "41e9dee505e6f6ca", "uuid": "bd89b938-82d9-4993-8161-276f5a35b59f"}, "__new_primary_file_unique\|0.15__": {"src": "hda", "id": "0da792b27e4b2b89", "uuid": "5185beb7-c38e-4ed2-bec0-9f2c91a67128"}, "__new_primary_file_unique\|0.08__": {"src": "hda", "id": "b5decc7b8262a098", "uuid": "532f331d-6944-4dd5-8a1c-b7441f6b8a5e"}, "__new_primary_file_unique\|0.14__": {"src": "hda", "id": "77b694bc117eb278", "uuid": "e12a1084-8f13-48ef-a3f6-146edd55811b"}, "__new_primary_file_unique\|0.13__": {"src": "hda", "id": "c8578f7fa756d7dc", "uuid": "e4eb002f-a4a4-4544-bfa4-9870a934f008"}, "__new_primary_file_unique\|0.09__": {"src": "hda", "id": "bc78784f4198424f", "uuid": "a08cc5b6-7e2d-444b-888d-112d58a2c302"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "ae6b27a2a1be3099", "uuid": "22bcbc31-0869-4336-a32f-e4d58103e730"}, "__new_primary_file_unique\|0.12__": {"src": "hda", "id": "c591040bd2b14dd3", "uuid": "9b1f67ef-057b-4613-acda-f0c5b8826759"}, "alignreport_out": {"src": "hda", "id": "1baefa50ed047fb0", "uuid": "c5b12544-fd55-41ad-a788-9decdb0f1bc3"}, "__new_primary_file_unique\|0.19__": {"src": "hda", "id": "543831fe8c81ade5", "uuid": "99208dbe-5ec3-4374-aaba-187815d1be6d"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "52c9abe36b090e71", "uuid": "4369cad3-3550-439d-a8f0-5c8c1ed28e2e"}, "__new_primary_file_unique\|0.11__": {"src": "hda", "id": "da3475a4d107f9d1", "uuid": "f25ff534-3003-4df5-8146-84e5167635e3"}, "__new_primary_file_unique\|0.41__": {"src": "hda", "id": "144a078b556f47ea", "uuid": "cdf8dcfc-f819-4c9c-9510-db1f9f05c3ce"}, "__new_primary_file_unique\|0.06__": {"src": "hda", "id": "652c409017f14add", "uuid": "ba8ee72c-2392-447e-86ad-75b27988c828"}, "__new_primary_file_unique\|0.03__": {"src": "hda", "id": "35abc15c823ac5f4", "uuid": "99be985a-c7ad-4f2f-af1d-948fec3666c1"}, "__new_primary_file_unique\|0.04__": {"src": "hda", "id": "8b2fddb4124acac3", "uuid": "17886915-baae-41ea-850b-63d48eeb1c95"}, "__new_primary_file_unique\|0.36__": {"src": "hda", "id": "3903fb6e0491d27a", "uuid": "92928c00-4d65-4244-b86f-4cf7c8dc3ea5"}, "__new_primary_file_unique\|0.22__": {"src": "hda", "id": "989b9f0457b89a0c", "uuid": "642287d6-7e73-4ac7-8fb3-bfc6d0d636b2"}, "__new_primary_file_unique\|0.23__": {"src": "hda", "id": "cd0b3415a2fdc60c", "uuid": "eac00c64-d9ee-4f7b-90ef-d55bb9b140e5"}, "__new_primary_file_unique\|0.33__": {"src": "hda", "id": "6c012b61d3ae01f5", "uuid": "c40d0e64-8dc4-4bb1-94d0-fdb98aa6a657"}, "logfile": {"src": "hda", "id": "d10cbc331e025114", "uuid": "25c3c7f7-2000-4396-b489-361f38da2e2d"}, "__new_primary_file_unique\|0.20__": {"src": "hda", "id": "8d8458d090ea7578", "uuid": "b8e4e7fa-032d-4fe8-99d0-60987b3bf8ff"}, "__new_primary_file_unique\|0.29__": {"src": "hda", "id": "a6ac437f8fe6da83", "uuid": "c961a1d0-d8aa-4859-96ec-a4b13b0e32a6"}, "__new_primary_file_unique\|0.38__": {"src": "hda", "id": "33b542efcfdd85ba", "uuid": "17c7677a-e8e1-468e-9124-3a8b486fa25f"}, "__new_primary_file_unique\|0.55__": {"src": "hda", "id": "6e25a68c2db30b46", "uuid": "fd6d2289-e2cd-4ee3-b979-0716f49fe7e4"}, "group_out": {"src": "hda", "id": "1baa7dc76fe18c68", "uuid": "f259dc8e-36fe-4e85-a55d-bf1992a8017d"}, "__new_primary_file_unique\|0.07__": {"src": "hda", "id": "2120d409550c595f", "uuid": "bed45e08-c284-49fa-9ce4-e418765ad6c8"}, "__new_primary_file_unique\|0.26__": {"src": "hda", "id": "4c9169af38dd62d7", "uuid": "bd68e773-91e9-4185-8ee9-81f4a853f391"}, "__new_primary_file_unique\|0.32__": {"src": "hda", "id": "bb3f644dc2fb6063", "uuid": "63a818fa-628d-42cb-8c21-69a8a9080aa1"}, "__new_primary_file_unique\|0.27__": {"src": "hda", "id": "38a761b89b9e6074", "uuid": "48f52554-6068-45cb-ab25-9a670e34afb6"}, "taxonomy_out": {"src": "hda", "id": "ed2ad3b822e9d9d3", "uuid": "6cf6e55c-2d40-4ae6-a182-299667b2a8cb"}, "__new_primary_file_unique\|0.01__": {"src": "hda", "id": "02434fd7d2885f87", "uuid": "a0205d2e-87a9-4052-8ce6-47d54c76632c"}, "__new_primary_file_unique\|0.24__": {"src": "hda", "id": "292bd36a691be581", "uuid": "c93c2459-e6a4-4d0e-9854-0756ffa9c70b"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "9552c7f8dd8e973e", "uuid": "3e07b209-bb24-4fff-8c0d-6db82c2c3664"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.lineage(taxonomy=file.taxonomy.dat,taxon='Bacteria;Firmicutes;-Bact \reria;Actinobacteria;',fasta=fasta_in.dat,group=group_in.dat,alignreport=alignrep \rort_in.dat,list=list_in.dat,name=name_in.dat,dups=true)\n[WARNING]: You did not provide a label, I will use the first label in your inputfile.\nYour file contains does not contain any sequences from Bacteria;Firmicutes;-Bacteria;Actinobacteria;.\nYour file contains does not contain any sequences from Bacteria;Firmicutes;-Bacteria;Actinobacteria;.\n\nOutput File Names: \nfile.taxonomy.pick.dat\nname_in.pick.dat\nfasta_in.pick.dat\ngroup_in.pick.dat\nalignreport_in.pick.align.report\nlist_in.unique.pick.dat\nlist_in.0.01.pick.dat\nlist_in.0.02.pick.dat\nlist_in.0.03.pick.dat\nlist_in.0.04.pick.dat\nlist_in.0.05.pick.dat\nlist_in.0.06.pick.dat\nlist_in.0.07.pick.dat\nlist_in.0.08.pick.dat\nlist_in.0.09.pick.dat\nlist_in.0.10.pick.dat\nlist_in.0.11.pick.dat\nlist_in.0.12.pick.dat\nlist_in.0.13.pick.dat\nlist_in.0.14.pick.dat\nlist_in.0.15.pick.dat\nlist_in.0.16.pick.dat\nlist_in.0.17.pick.dat\nlist_in.0.18.pick.dat\nlist_in.0.19.pick.dat\nlist_in.0.20.pick.dat\nlist_in.0.21.pick.dat\nlist_in.0.22.pick.dat\nlist_in.0.23.pick.dat\nlist_in.0.24.pick.dat\nlist_in.0.25.pick.dat\nlist_in.0.26.pick.dat\nlist_in.0.27.pick.dat\nlist_in.0.29.pick.dat\nlist_in.0.32.pick.dat\nlist_in.0.33.pick.dat\nlist_in.0.36.pick.dat\nlist_in.0.38.pick.dat\nlist_in.0.41.pick.dat\nlist_in.0.45.pick.dat\nlist_in.0.55.pick.dat\n\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1000.dat' file.taxonomy.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1001.dat' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1002.dat' group_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1003.dat' alignreport_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1004.dat' list_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1005.dat' name_in.dat && ln -s 'None' count.dat && echo 'get.lineage( taxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Firmicutes;-Bacteria;Actinobacteria;'\"' ,fasta=fasta_in.dat ,group=group_in.dat ,alignreport=alignreport_in.dat ,list=list_in.dat ,name=name_in.dat ,dups=true )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:31:14.507752", "params": {"count": "null", "dups": "\"true\"", "taxon": "\"Bacteria;Firmicutes;,Bacteria;Actinobacteria;\"", "dbkey": "\"hg17\"", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 1000}]}, \"filetype\": \"usetaxonomy\", \"taxons\": null, \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18531", "id": "349f287fcb778b99", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_lineage.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"file\|taxonomy": {"src": "hda", "id": "6f78f21b003042c4"}, "file\|taxons": ["Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Dorea(99);", "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(47);"], "file\|filetype": "usetaxonomy"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "6f78f21b003042c4", "uuid": "a34f0692-a2db-4929-8627-e2e626069020"}}, "update_time": "2018-02-08T17:32:00.703931", "tool_id": "mothur_get_lineage", "outputs": {"logfile": {"src": "hda", "id": "fc9d58b578cf8af3", "uuid": "2490501b-95be-4366-b70a-7ac863f83736"}, "taxonomy_out": {"src": "hda", "id": "bdb1e7b62cbbd487", "uuid": "7afddbee-f1ec-4f8a-934d-2dcf0c5ed1ea"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.lineage(taxonomy=file.taxonomy.dat,taxon='Bacteria;Firmicutes;Clost \rridia;Clostridiales;Lachnospiraceae;Dorea;-Bacteria;Firmicutes;Clostridia;Clostr \ridiales;Lachnospiraceae;Roseburia;')\n\nOutput File Names: \nfile.taxonomy.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1048.dat' file.taxonomy.dat && ln -s 'None' fasta_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat && echo 'get.lineage( taxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Dorea;-Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Roseburia;'\"' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:31:57.562198", "params": {"count": "null", "dups": "\"true\"", "fasta_in": "null", "taxon": "\"\"", "dbkey": "\"hg17\"", "group_in": "null", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 1048}]}, \"filetype\": \"usetaxonomy\", \"taxons\": [\"Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Dorea(99);\", \"Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(47);\"], \"__current_case__\": 0}", "alignreport_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18638", "id": "f66e4e467d639b46", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_lineage.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"file\|taxonomy": {"src": "hda", "id": "3747b718aaba1b94"}, "file\|filetype": "useconstaxonomy", "taxon": "Bacteria;Bacteroidetes;"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "3747b718aaba1b94", "uuid": "848176ca-3663-40b3-ad42-2ca5bf3a3aa6"}}, "update_time": "2018-02-08T17:32:07.933961", "tool_id": "mothur_get_lineage", "outputs": {"logfile": {"src": "hda", "id": "40866b2ef26dac92", "uuid": "f1d9cb2c-7f1f-4fa5-91a9-d1a7f8bf7b48"}, "taxonomy_out": {"src": "hda", "id": "ad30ab610baf0fe8", "uuid": "90c595ff-def3-4094-80f8-7aeeadd6a528"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.lineage(constaxonomy=file.taxonomy.dat,taxon='Bacteria;Bacteroidete \rs;')\n\nOutput File Names: \nfile.taxonomy.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1051.dat' file.taxonomy.dat && ln -s 'None' file.shared.dat && ln -s 'None' file.list.dat && ln -s 'None' fasta_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat && echo 'get.lineage( constaxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Bacteroidetes;'\"' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:32:04.835077", "params": {"count": "null", "dups": "\"true\"", "fasta_in": "null", "taxon": "\"Bacteria;Bacteroidetes;\"", "dbkey": "\"hg17\"", "group_in": "null", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 1051}]}, \"filetype\": \"useconstaxonomy\", \"list\": null, \"taxons\": null, \"__current_case__\": 1, \"shared\": null}", "alignreport_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18729", "id": "513510c2b856e80e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_lineage.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"file\|taxonomy": {"src": "hda", "id": "1801e6a1fcd5e06c"}, "file\|taxons": ["Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;", "Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;"], "file\|filetype": "useconstaxonomy"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "1801e6a1fcd5e06c", "uuid": "e852ff59-b576-44ec-8a29-eac7fa18e1ba"}}, "update_time": "2018-02-08T17:32:15.209631", "tool_id": "mothur_get_lineage", "outputs": {"logfile": {"src": "hda", "id": "97f0f46b65c7979f", "uuid": "2ce2929d-499b-480c-8d75-1cf4bacf3de4"}, "taxonomy_out": {"src": "hda", "id": "9a6bce08b3fe7407", "uuid": "38612f05-7677-4b22-bafc-9ecaa5766156"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.lineage(constaxonomy=file.taxonomy.dat,taxon='Bacteria;Firmicutes;C \rlostridia;Clostridiales;Lachnospiraceae;unclassified;-Bacteria;Proteobacteria;Ga \rmmaproteobacteria;unclassified;unclassified;unclassified;')\n\nOutput File Names: \nfile.taxonomy.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1054.dat' file.taxonomy.dat && ln -s 'None' file.shared.dat && ln -s 'None' file.list.dat && ln -s 'None' fasta_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat && echo 'get.lineage( constaxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;unclassified;-Bacteria;Proteobacteria;Gammaproteobacteria;unclassified;unclassified;unclassified;'\"' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:32:12.085958", "params": {"count": "null", "dups": "\"true\"", "fasta_in": "null", "taxon": "\"\"", "dbkey": "\"hg17\"", "group_in": "null", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 1054}]}, \"filetype\": \"useconstaxonomy\", \"list\": null, \"taxons\": [\"Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;\", \"Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;\"], \"__current_case__\": 1, \"shared\": null}", "alignreport_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18823", "id": "25de304670fe7732", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_lineage.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|filetype": "group", "input\|infile": {"src": "hda", "id": "89d9aa21c72ed3c7"}}, "job": {"inputs": {"infile": {"src": "hda", "id": "89d9aa21c72ed3c7", "uuid": "488e2f2d-d7ae-452d-898f-9f6f1d80ea64"}}, "update_time": "2018-02-08T17:32:22.411197", "tool_id": "mothur_get_mimarkspackage", "outputs": {"logfile": {"src": "hda", "id": "8013a1d7cf129351", "uuid": "c2d1a36f-3d5b-48c8-a2e5-ed63db8e4ec0"}, "package_out": {"src": "hda", "id": "426b952bd444adde", "uuid": "354ae98b-75db-4e76-9d1f-e7318f16b114"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.mimarkspackage(group=input.infile.dat,package=miscellaneous,require \rdonly=false)\n\nOutput File Names: \ninput.infile.tsv\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1057.dat' input.infile.dat && echo 'get.mimarkspackage( group=input.infile.dat, package=miscellaneous, requiredonly=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:32:19.295899", "params": {"input": "{\"filetype\": \"group\", \"infile\": {\"values\": [{\"src\": \"hda\", \"id\": 1057}]}, \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "requiredonly": "\"false\"", "dbkey": "\"hg17\"", "package": "\"miscellaneous\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18920", "id": "d57022ef22692475", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_mimarkspackage.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"package": "human_associated", "input\|filetype": "oligos", "requiredonly": true, "input\|infile": {"src": "hda", "id": "4a96cd4627e246f4"}}, "job": {"inputs": {"infile": {"src": "hda", "id": "4a96cd4627e246f4", "uuid": "388018a5-3429-42ff-a1c6-82941ad8176c"}}, "update_time": "2018-02-08T17:32:39.918619", "tool_id": "mothur_get_mimarkspackage", "outputs": {"logfile": {"src": "hda", "id": "3190333ac07edb13", "uuid": "227555a5-3417-4443-a05f-1a8f6b461e65"}, "package_out": {"src": "hda", "id": "234cb682c356f1ab", "uuid": "1e5c3119-a427-4614-a687-49a89283a86a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.mimarkspackage(oligos=input.infile.dat,package=human_associated,req \ruiredonly=true)\n\nOutput File Names: \ninput.infile.tsv\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1060.dat' input.infile.dat && echo 'get.mimarkspackage( oligos=input.infile.dat, package=human_associated, requiredonly=true )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:32:36.779382", "params": {"input": "{\"filetype\": \"oligos\", \"infile\": {\"values\": [{\"src\": \"hda\", \"id\": 1060}]}, \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "requiredonly": "\"true\"", "dbkey": "\"hg17\"", "package": "\"human_associated\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19016", "id": "9b36a3aa47b79bf2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_mimarkspackage.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"infile\|label": "0.22", "accnos": {"src": "hda", "id": "7655e53fa1ea970d"}, "infile\|otu": {"src": "hda", "id": "df211d5332576ec7"}, "infile\|intype": "in_shared"}, "job": {"inputs": {"accnos": {"src": "hda", "id": "7655e53fa1ea970d", "uuid": "a4d2e512-5b1e-40a8-9426-0dd4f92d86ea"}, "otu": {"src": "hda", "id": "df211d5332576ec7", "uuid": "2039f857-077f-4c50-9567-19e37479e17b"}}, "update_time": "2018-02-08T17:33:00.529600", "tool_id": "mothur_get_otulabels", "outputs": {"pick_out": {"src": "hda", "id": "75d344c42dc42fbd", "uuid": "280149a7-f5ed-42f7-8baf-92b5769c1742"}, "logfile": {"src": "hda", "id": "dca46da602361c10", "uuid": "5f8de98c-4fd6-495a-820f-be954f81dd62"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.otulabels(shared=infile.otu.dat,label=0.22,accnos=accnos.dat)\nYour file does not contain any OTUs from the .accnos file.\nSelected 0 OTUs from your shared file.\n\nOutput File Names: \ninfile.otu.0.22.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1064.dat' infile.otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1063.dat' accnos.dat && echo 'get.otulabels( shared=infile.otu.dat, label=0.22, accnos=accnos.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:32:57.371646", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_shared\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1064}]}, \"__current_case__\": 0, \"label\": \"0.22\"}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19126", "id": "24a1da3a8e5693fe", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_otulabels.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"infile\|intype": "in_other", "accnos": {"src": "hda", "id": "34e6c2e9e95d8f5b"}, "infile\|otu": {"src": "hda", "id": "99e402de1bba2f0d"}}, "job": {"inputs": {"accnos": {"src": "hda", "id": "34e6c2e9e95d8f5b", "uuid": "4929e9c0-5b6b-4f48-a881-487a21d2202c"}, "otu": {"src": "hda", "id": "99e402de1bba2f0d", "uuid": "d40ef2c8-d38f-435a-b210-2b21774b9155"}}, "update_time": "2018-02-08T17:33:21.098179", "tool_id": "mothur_get_otulabels", "outputs": {"pick_out": {"src": "hda", "id": "22857389d798733d", "uuid": "8a727fb8-62de-4743-933f-6046086727fa"}, "logfile": {"src": "hda", "id": "f079ce0ad2349821", "uuid": "fffb75ac-8124-4205-9fff-c61e61e3471b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.otulabels(corraxes=infile.otu.dat,accnos=accnos.dat)\nSelected 3 lines from your corr.axes file.\n\nOutput File Names: \ninfile.otu.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1068.dat' infile.otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1067.dat' accnos.dat && echo 'get.otulabels( corraxes=infile.otu.dat, accnos=accnos.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:33:17.955974", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_other\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1068}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19238", "id": "8543024575f6f30b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_otulabels.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "51b6da2201439bf7"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "51b6da2201439bf7", "uuid": "51f6010d-d1d0-46d1-89ee-3bfbcab06111"}}, "update_time": "2018-02-08T17:33:40.377632", "tool_id": "mothur_get_otulist", "outputs": {"__new_primary_file_unique\|0.10__": {"src": "hda", "id": "c778881db4f7e02e", "uuid": "b173a65d-467c-4045-bee3-fbdf52304014"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "eb9c10339397af09", "uuid": "be8ed080-334f-4c29-ae4e-367049fb2a97"}, "__new_primary_file_unique\|0.17__": {"src": "hda", "id": "f9a0977992bfb9ba", "uuid": "2d0a77a9-0751-4610-bc66-25ab889081d0"}, "__new_primary_file_unique\|0.02__": {"src": "hda", "id": "e6a4ded894b6f5fa", "uuid": "8beb9edc-760a-42da-af4c-953585c0ca25"}, "__new_primary_file_unique\|0.21__": {"src": "hda", "id": "3bf74cdfe204f463", "uuid": "5ab3735f-5d97-493d-b0ff-4ce508562fea"}, "__new_primary_file_unique\|0.16__": {"src": "hda", "id": "153ecf05259735e5", "uuid": "773eef8c-a03e-438f-aac0-b954b1b32ab6"}, "__new_primary_file_unique\|0.45__": {"src": "hda", "id": "4ba65871d102d69d", "uuid": "3c40c6ca-758d-4b93-8821-e375a1267e0d"}, "__new_primary_file_unique\|0.03__": {"src": "hda", "id": "1e62b3b8018b2fc6", "uuid": "600dfbaa-4811-47a3-84e3-dc7c90c84a0d"}, "__new_primary_file_unique\|0.15__": {"src": "hda", "id": "8fe9921e6d7dbafc", "uuid": "a5392bd0-046a-4266-a9a0-152c9e451f92"}, "__new_primary_file_unique\|0.08__": {"src": "hda", "id": "68a07b8eb9e4a63b", "uuid": "aee16746-2c8e-4fc6-990a-c5cee5436cdb"}, "__new_primary_file_unique\|0.14__": {"src": "hda", "id": "f2786a3b53d84563", "uuid": "a5ad18f2-5b98-45f6-802c-dc87a6d11c4a"}, "__new_primary_file_unique\|0.13__": {"src": "hda", "id": "2ddd0affa57a5a37", "uuid": "df7243a2-ecce-4d2e-a4be-430ad666cf9f"}, "__new_primary_file_unique\|0.09__": {"src": "hda", "id": "cb6f70c43fa71834", "uuid": "2947c836-d283-484c-a40e-cd893227cc87"}, "__new_primary_file_unique\|0.12__": {"src": "hda", "id": "68f8799b51cd39a2", "uuid": "7ed1c56c-a6b8-4516-a523-7026512de1df"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "62147ed004c8781f", "uuid": "4e8c99c2-5413-4073-abd2-0e3af081b082"}, "__new_primary_file_unique\|0.11__": {"src": "hda", "id": "6666372c4fab48c4", "uuid": "9af8f2b5-b3db-4d45-b716-920429a85b0f"}, "__new_primary_file_unique\|0.41__": {"src": "hda", "id": "eb38b861ea77d447", "uuid": "eea105e0-ad99-4952-a69a-d5a6761d334d"}, "__new_primary_file_unique\|0.06__": {"src": "hda", "id": "9f7279a088a67da9", "uuid": "18e2c6cf-65e7-49cd-99f3-08efa94556ce"}, "__new_primary_file_unique\|0.25__": {"src": "hda", "id": "9a4581073136ed09", "uuid": "6f6ce176-5ef2-4e40-bb91-77e7f9dedc47"}, "__new_primary_file_unique\|0.22__": {"src": "hda", "id": "f38022c92a0f7f7b", "uuid": "4cf0fa53-3f7e-45a6-ab9d-806e15f7903c"}, "__new_primary_file_unique\|0.36__": {"src": "hda", "id": "708b991ac9f806e1", "uuid": "17f747ef-57f5-49ad-aee7-458525b4ce6f"}, "__new_primary_file_unique\|0.04__": {"src": "hda", "id": "5bc01bd5935f41c1", "uuid": "683c7d93-6656-4a64-932a-f6034f55246a"}, "__new_primary_file_unique\|0.23__": {"src": "hda", "id": "2d25c0be08883c54", "uuid": "0ff99942-64cc-40cb-b1ad-96c25c2028aa"}, "__new_primary_file_unique\|0.33__": {"src": "hda", "id": "4a58f5a4317a3c0d", "uuid": "dda6a4e9-ded3-403e-8e94-9fc84e6acba7"}, "logfile": {"src": "hda", "id": "5b67fe605870f3c1", "uuid": "0ce5e213-7fb1-4789-8ded-a50cf998d596"}, "__new_primary_file_unique\|0.20__": {"src": "hda", "id": "b2e7f29c6e6f4615", "uuid": "68ac73b3-6188-4a84-9f67-803eeb8a4820"}, "__new_primary_file_unique\|0.29__": {"src": "hda", "id": "84bd3054481cbbc7", "uuid": "ff4452b9-605a-4c94-985e-81af102ec3db"}, "__new_primary_file_unique\|0.38__": {"src": "hda", "id": "ab352c0b18312637", "uuid": "531c68fc-392f-4651-9657-06386d0015c1"}, "__new_primary_file_unique\|0.55__": {"src": "hda", "id": "e47a18097101ae28", "uuid": "126ff3b8-6f66-4bd6-9c7e-d8df71e54451"}, "__new_primary_file_unique\|0.07__": {"src": "hda", "id": "e9997d6b1fbf571c", "uuid": "c43a5aec-e58e-4ba6-8157-12407ee64a4a"}, "__new_primary_file_unique\|0.26__": {"src": "hda", "id": "c1b250e6ee924774", "uuid": "d5ba1691-b71e-46e9-8035-cdbf7853d7e5"}, "__new_primary_file_unique\|0.32__": {"src": "hda", "id": "ac2a2c496e4cb460", "uuid": "67de3c2d-4d07-4d49-a71f-33e9dec1d5dd"}, "__new_primary_file_unique\|0.27__": {"src": "hda", "id": "ba8455fb60b4981e", "uuid": "c2308bf6-aa53-4d11-94a0-ce788ada056e"}, "__new_primary_file_unique\|0.19__": {"src": "hda", "id": "6c06a1831dcb5d3f", "uuid": "2eb4ca1e-3619-410f-b26e-e2f1a5f05b6e"}, "__new_primary_file_unique\|0.01__": {"src": "hda", "id": "89a5a72f6f25aac7", "uuid": "a1d0db62-1e7d-467f-96e0-c78875629ddd"}, "__new_primary_file_unique\|0.24__": {"src": "hda", "id": "71ce468762f23cf3", "uuid": "97a17ca3-ec2c-4024-8c88-04505a334415"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "6b320855e1131164", "uuid": "b47f9106-ecc3-4128-8d22-bb8ca5e63fe1"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.otulist(list=otu.dat,sort=otu)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.unique.otu\notu.0.01.otu\notu.0.02.otu\notu.0.03.otu\notu.0.04.otu\notu.0.05.otu\notu.0.06.otu\notu.0.07.otu\notu.0.08.otu\notu.0.09.otu\notu.0.10.otu\notu.0.11.otu\notu.0.12.otu\notu.0.13.otu\notu.0.14.otu\notu.0.15.otu\notu.0.16.otu\notu.0.17.otu\notu.0.18.otu\notu.0.19.otu\notu.0.20.otu\notu.0.21.otu\notu.0.22.otu\notu.0.23.otu\notu.0.24.otu\notu.0.25.otu\notu.0.26.otu\notu.0.27.otu\notu.0.29.otu\notu.0.32.otu\notu.0.33.otu\notu.0.36.otu\notu.0.38.otu\notu.0.41.otu\notu.0.45.otu\notu.0.55.otu\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1071.dat' otu.dat && echo 'get.otulist( list=otu.dat, sort=otu )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:33:35.450862", "params": {"sort": "\"otu\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19324", "id": "c8288be11b30d2bc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_otulist.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "a2c166d4f307d0c8"}, "label": ["0.03", "0.38", "0.41", "0.45"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "a2c166d4f307d0c8", "uuid": "d782722b-b6ac-4f74-9bbc-c412dec690a0"}}, "update_time": "2018-02-08T17:33:59.277768", "tool_id": "mothur_get_otulist", "outputs": {"__new_primary_file_0.45\|0.03__": {"src": "hda", "id": "3d2f7571dd3f526d", "uuid": "3a4dbde5-5d8f-4749-bae9-8cc89431844e"}, "logfile": {"src": "hda", "id": "d6e970b870fc412a", "uuid": "b4bea723-db34-4add-82fa-88018028a987"}, "__new_primary_file_0.45\|0.41__": {"src": "hda", "id": "07562b49fba381a7", "uuid": "bb6b1e54-2bcd-4c2b-9524-1b7b9116beaf"}, "__new_primary_file_0.45\|0.38__": {"src": "hda", "id": "ba7c7bcdabc0857e", "uuid": "7adf7cf1-dcd0-47fc-9848-c7882490fb65"}, "__new_primary_file_0.45\|0.45__": {"src": "hda", "id": "d2fb07980323f68c", "uuid": "6f62cad4-b96a-481b-a5a4-b8665aeb88dc"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.otulist(list=otu.dat,label=0.03-0.38-0.41-0.45,sort=otu)\n0.03\n0.38\n0.41\n0.45\n\nOutput File Names: \notu.0.03.otu\notu.0.38.otu\notu.0.41.otu\notu.0.45.otu\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1109.dat' otu.dat && echo 'get.otulist( list=otu.dat, label=0.03-0.38-0.41-0.45, sort=otu )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:33:56.020360", "params": {"sort": "\"otu\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.38\", \"0.41\", \"0.45\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19410", "id": "466b5293998bb5d6", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_otulist.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"method_condition\|matrix_condition\|dist": {"src": "hda", "id": "416075c69c435f24"}, "method_condition\|method_switch": "distance", "method_condition\|matrix_condition\|matrix_format": "phylip", "method_condition\|matrix_condition\|nameOrCount": {"src": "hda", "id": "41fd880cfa9a87dd"}, "otu": {"src": "hda", "id": "93a3cb8d32c9fc8d"}}, "job": {"inputs": {"method_condition\|dist": {"src": "hda", "id": "416075c69c435f24", "uuid": "651b1fe5-7d73-42e9-abc3-337dc0082bc4"}, "otu": {"src": "hda", "id": "93a3cb8d32c9fc8d", "uuid": "e3460105-26cd-46af-8ab3-19b8cc079558"}, "method_condition\|nameOrCount": {"src": "hda", "id": "41fd880cfa9a87dd", "uuid": "7369cd69-029a-46dd-b78d-c926c82835b4"}}, "update_time": "2018-02-08T17:34:25.314721", "tool_id": "mothur_get_oturep", "outputs": {"__new_primary_file_unique\|0.10__": {"src": "hda", "id": "30bdbac696e3ceef", "uuid": "d00fedc6-1efb-42e4-b37f-f45f957e2b92"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "da8aa8fdc0218a93", "uuid": "8361ade7-0f32-46f2-a1a8-8ee6da9ce758"}, "__new_primary_file_unique\|0.17__": {"src": "hda", "id": "730ca47799cf02d3", "uuid": "c4c5a461-029b-4cc1-a593-68c5ce286fde"}, "__new_primary_file_unique\|0.02__": {"src": "hda", "id": "40c1ea605096e77f", "uuid": "904130ae-a436-4559-8ffc-a6b7c5afe75b"}, "__new_primary_file_unique\|0.21__": {"src": "hda", "id": "2f333f7cf7d78907", "uuid": "9273fcb8-d4bb-445e-9c4f-5b6b41be00b3"}, "__new_primary_file_unique\|0.16__": {"src": "hda", "id": "b407a3967cd6ca6a", "uuid": "d369d2f3-aff3-427b-ab64-480645b2f587"}, "__new_primary_file_unique\|0.45__": {"src": "hda", "id": "6d61de378375ad0e", "uuid": "d49df779-4ccd-4711-b383-676527d79fcd"}, "__new_primary_file_unique\|0.03__": {"src": "hda", "id": "aebe4bc76827cb48", "uuid": "4e8ef798-8342-4168-853c-7614ec9bec61"}, "__new_primary_file_unique\|0.15__": {"src": "hda", "id": "977529368f8029da", "uuid": "e5d7a12b-aaea-4fc7-a31d-379fe2e8e0e9"}, "__new_primary_file_unique\|0.08__": {"src": "hda", "id": "12fc8f013fcd6fa2", "uuid": "66bda59f-99f7-4d50-8343-884cf5fb559a"}, "__new_primary_file_unique\|0.14__": {"src": "hda", "id": "8a763f8178031e3a", "uuid": "a4e2810b-5abd-40e3-8a4d-35c4a24d0ba1"}, "__new_primary_file_unique\|0.13__": {"src": "hda", "id": "3d8ba95917e241a3", "uuid": "9f08379d-c6b9-4c8a-9700-c9f9a8b5e3d9"}, "__new_primary_file_unique\|0.09__": {"src": "hda", "id": "7bb8be40a694582d", "uuid": "229d4590-77d5-4fed-89d2-09075640edde"}, "__new_primary_file_unique\|0.12__": {"src": "hda", "id": "0f0ea7742d2f7a9c", "uuid": "4c270c1a-b961-4106-afd3-5561dffb11c8"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "5b683d70bee32138", "uuid": "43437a44-842b-463d-abd6-0a5d964ea42c"}, "__new_primary_file_unique\|0.11__": {"src": "hda", "id": "24f92017f4321b90", "uuid": "9fcc26f4-d414-4037-acd8-5f5740d46cba"}, "__new_primary_file_unique\|0.41__": {"src": "hda", "id": "f9659e23aabc1e0c", "uuid": "8830819f-b9d2-4e58-9ca9-577c70136f8c"}, "__new_primary_file_unique\|0.06__": {"src": "hda", "id": "e1bf44ffb4951bed", "uuid": "32267982-3d31-4cd7-ae5d-9864dbff86c8"}, "__new_primary_file_unique\|0.25__": {"src": "hda", "id": "44b7656f117551f6", "uuid": "eb7395a0-011b-4a13-bafb-eeab65b98b20"}, "__new_primary_file_unique\|0.22__": {"src": "hda", "id": "51c23b5ceed9c18d", "uuid": "d172a29d-bb33-4b2c-a2f6-d91bde3b546f"}, "__new_primary_file_unique\|0.36__": {"src": "hda", "id": "1048228746240cdf", "uuid": "8459e654-0094-4c4e-87ce-9f5b73061296"}, "__new_primary_file_unique\|0.04__": {"src": "hda", "id": "723e4e10e4eecc59", "uuid": "029e3382-9a04-4548-baa2-e63b84d11e16"}, "__new_primary_file_unique\|0.23__": {"src": "hda", "id": "db87f06412e7adc0", "uuid": "c238c158-81e4-400b-85cf-28fcd2dd4061"}, "__new_primary_file_unique\|0.33__": {"src": "hda", "id": "00e13cdc183f52a5", "uuid": "cba7bc5b-73b3-4620-9218-7533386b618f"}, "logfile": {"src": "hda", "id": "f78a9bc7e1b3c5b0", "uuid": "a882b0e9-9a6f-4d01-915f-911d89ce8a26"}, "__new_primary_file_unique\|0.20__": {"src": "hda", "id": "8fc6a110eb2265d3", "uuid": "acbd8207-5ea5-40c0-9cd1-a60c84ddedfb"}, "__new_primary_file_unique\|0.29__": {"src": "hda", "id": "d4eed87b276e13c1", "uuid": "c9dadca8-883f-4f02-8bb8-bdc3908015c2"}, "__new_primary_file_unique\|0.38__": {"src": "hda", "id": "d19ff3dd0342839a", "uuid": "b18b0941-7b73-4b1f-a8db-5460a0cd2c57"}, "__new_primary_file_unique\|0.55__": {"src": "hda", "id": "19a46808e9dc1c5e", "uuid": "751d8de8-ddf8-40ed-863d-ba0e09096f8b"}, "__new_primary_file_unique\|0.07__": {"src": "hda", "id": "fe4f1a00cf04fcf3", "uuid": "1fca2b37-632d-40ba-b337-31b86a484895"}, "__new_primary_file_unique\|0.26__": {"src": "hda", "id": "555713c20c62ccd8", "uuid": "611a22bc-02f3-43ba-af20-d309b5e3f6db"}, "__new_primary_file_unique\|0.32__": {"src": "hda", "id": "7d80d946c53c84eb", "uuid": "7d937db3-7669-48c8-ac91-7c6f22dd7604"}, "__new_primary_file_unique\|0.27__": {"src": "hda", "id": "1fe9146927bcc3d0", "uuid": "cf5a33eb-e7c1-4396-a03b-c17a9ad4c3d0"}, "__new_primary_file_unique\|0.19__": {"src": "hda", "id": "7da19e3d7c19664a", "uuid": "35d9c97d-f75c-4881-bb73-cf9c906638f5"}, "__new_primary_file_unique\|0.01__": {"src": "hda", "id": "9c891a5a995773c1", "uuid": "485aaddf-1d54-47a0-baf6-85f127aff543"}, "__new_primary_file_unique\|0.24__": {"src": "hda", "id": "8281173e1dd8fbe2", "uuid": "5ed26988-c989-4ca7-a830-54782b46355b"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "f2d7713593c3c9fc", "uuid": "86ef6768-6f66-4e03-a4ce-127adc736dcd"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.oturep(list=otu.dat,method=distance,phylip=dist.dat,name=nameOrCoun \rt.dat,large=false)\n*****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\nunique\t96\n0.01\t93\n0.02\t90\n0.03\t88\n0.04\t83\n0.05\t78\n0.06\t69\n0.07\t65\n0.08\t56\n0.09\t55\n0.10\t49\n0.11\t45\n0.12\t43\n0.13\t40\n0.14\t36\n0.15\t35\n0.16\t34\n0.17\t33\n0.18\t31\n0.19\t30\n0.20\t27\n0.21\t25\n0.22\t23\n0.23\t21\n0.24\t17\n0.25\t15\n0.26\t13\n0.27\t12\n0.29\t9\n0.32\t7\n0.33\t6\n0.36\t5\n0.38\t4\n0.41\t3\n0.45\t2\n0.55\t1\n\nOutput File Names: \notu.unique.rep.names\notu.0.01.rep.names\notu.0.02.rep.names\notu.0.03.rep.names\notu.0.04.rep.names\notu.0.05.rep.names\notu.0.06.rep.names\notu.0.07.rep.names\notu.0.08.rep.names\notu.0.09.rep.names\notu.0.10.rep.names\notu.0.11.rep.names\notu.0.12.rep.names\notu.0.13.rep.names\notu.0.14.rep.names\notu.0.15.rep.names\notu.0.16.rep.names\notu.0.17.rep.names\notu.0.18.rep.names\notu.0.19.rep.names\notu.0.20.rep.names\notu.0.21.rep.names\notu.0.22.rep.names\notu.0.23.rep.names\notu.0.24.rep.names\notu.0.25.rep.names\notu.0.26.rep.names\notu.0.27.rep.names\notu.0.29.rep.names\notu.0.32.rep.names\notu.0.33.rep.names\notu.0.36.rep.names\notu.0.38.rep.names\notu.0.41.rep.names\notu.0.45.rep.names\notu.0.55.rep.names\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1115.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1116.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1117.dat' nameOrCount.dat && ln -s 'None' fasta.dat && echo 'get.oturep( list=otu.dat, method=distance, phylip=dist.dat, name=nameOrCount.dat, large=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:34:19.832670", "params": {"sorted": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method_condition": "{\"matrix_condition\": {\"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 1117}]}, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 1116}]}, \"__current_case__\": 1, \"matrix_format\": \"phylip\"}, \"large\": \"false\", \"__current_case__\": 0, \"pick\": {\"type\": \"no\", \"__current_case__\": 0}, \"fasta\": null, \"method_switch\": \"distance\"}", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19539", "id": "8078f99fccaa607a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_oturep.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"method_condition\|matrix_condition\|dist": {"src": "hda", "id": "aed4888e53be2c29"}, "method_condition\|method_switch": "distance", "label": ["unique", "0.05", "0.27", "0.45"], "method_condition\|matrix_condition\|matrix_format": "column", "method_condition\|matrix_condition\|nameOrCount": {"src": "hda", "id": "73d20dc7f05cb923"}, "otu": {"src": "hda", "id": "0fb95b6100ab75ac"}}, "job": {"inputs": {"method_condition\|dist": {"src": "hda", "id": "aed4888e53be2c29", "uuid": "96cd93f8-13f1-4f66-91f7-f472d543e547"}, "otu": {"src": "hda", "id": "0fb95b6100ab75ac", "uuid": "5ffb4a90-dbe5-4368-9174-0b8e26c34032"}, "method_condition\|nameOrCount": {"src": "hda", "id": "73d20dc7f05cb923", "uuid": "c6cb40a8-1e8d-44bf-a814-70d1f319f2b8"}}, "update_time": "2018-02-08T17:34:50.940943", "tool_id": "mothur_get_oturep", "outputs": {"__new_primary_file_unique\|0.27__": {"src": "hda", "id": "ca68502e42c4e7cc", "uuid": "912df286-c4c3-4ada-b486-05d0ffb119df"}, "logfile": {"src": "hda", "id": "d1da4bfb123cb5f7", "uuid": "96a5082d-9fc0-4b22-9a61-66513477c1d4"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "b385cc8f12ae4655", "uuid": "f10d0810-0145-4cba-8dbc-39c44f07d928"}, "__new_primary_file_unique\|0.45__": {"src": "hda", "id": "f5a2e6053244a622", "uuid": "e46476d5-e0a7-486f-a012-e2f903c615b5"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "13c1cf6c966b3c28", "uuid": "39f76377-6d8a-4358-94e0-b5e54fd992cb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.oturep(list=otu.dat,label=unique-0.05-0.27-0.45,method=distance,col \rumn=dist.dat,name=nameOrCount.dat,large=false)\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\nunique\t96\n0.05\t78\n0.27\t12\n0.45\t2\n\nOutput File Names: \notu.unique.rep.names\notu.0.05.rep.names\notu.0.27.rep.names\notu.0.45.rep.names\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1155.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1156.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1157.dat' nameOrCount.dat && ln -s 'None' fasta.dat && echo 'get.oturep( list=otu.dat, label=unique-0.05-0.27-0.45, method=distance, column=dist.dat, name=nameOrCount.dat, large=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:34:47.568188", "params": {"sorted": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method_condition": "{\"matrix_condition\": {\"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 1157}]}, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 1156}]}, \"__current_case__\": 0, \"matrix_format\": \"column\"}, \"large\": \"false\", \"__current_case__\": 0, \"pick\": {\"type\": \"no\", \"__current_case__\": 0}, \"fasta\": null, \"method_switch\": \"distance\"}", "dbkey": "\"hg17\"", "label": "[\"unique\", \"0.05\", \"0.27\", \"0.45\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19677", "id": "aa70baf734620bdc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_oturep.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"method_condition\|matrix_condition\|dist": {"src": "hda", "id": "b7f71ad5197d9e0a"}, "method_condition\|method_switch": "distance", "label": ["0.05", "0.27"], "method_condition\|fasta": {"src": "hda", "id": "dec68a77ca6fab55"}, "sorted": "name", "method_condition\|matrix_condition\|matrix_format": "phylip", "otu": {"src": "hda", "id": "8bcaa6ddefe62301"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "dec68a77ca6fab55", "uuid": "920ebc87-4daf-49bb-91ba-0cf172a8a7dc"}, "method_condition\|dist": {"src": "hda", "id": "b7f71ad5197d9e0a", "uuid": "92fe70a5-1c0a-49a6-935a-b931d3a5ec9f"}, "otu": {"src": "hda", "id": "8bcaa6ddefe62301", "uuid": "da9a90c4-f59b-45f4-9450-e14e8ee4c35d"}}, "update_time": "2018-02-08T17:35:18.183092", "tool_id": "mothur_get_oturep", "outputs": {"logfile": {"src": "hda", "id": "a3c766aaa70cf6ac", "uuid": "efc1c573-1a6b-41d7-81a4-76689dcc7e00"}, "__new_primary_file_0.27\|0.27__": {"src": "hda", "id": "e52776a59fe07134", "uuid": "5a7ca434-6a13-4855-8a02-e98754a14ca1"}, "__new_primary_file_0.27\|0.05__": {"src": "hda", "id": "d4a90b8ec5d7a12a", "uuid": "07714f97-9622-4c39-a222-ec47f5cf059b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.oturep(list=otu.dat,sorted=name,label=0.05-0.27,method=distance,phy \rlip=dist.dat,fasta=fasta.dat,large=false)\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n0.05\t78\n0.27\t12\n\nOutput File Names: \notu.0.05.rep.names\notu.0.27.rep.names\notu.0.05.rep.fasta\notu.0.27.rep.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1163.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1164.dat' dist.dat && ln -s 'None' nameOrCount.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1165.dat' fasta.dat && echo 'get.oturep( list=otu.dat, sorted=name, label=0.05-0.27, method=distance, phylip=dist.dat, fasta=fasta.dat, large=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:35:14.684754", "params": {"sorted": "\"name\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method_condition": "{\"matrix_condition\": {\"nameOrCount\": null, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 1164}]}, \"__current_case__\": 1, \"matrix_format\": \"phylip\"}, \"large\": \"false\", \"__current_case__\": 0, \"pick\": {\"type\": \"no\", \"__current_case__\": 0}, \"fasta\": {\"values\": [{\"src\": \"hda\", \"id\": 1165}]}, \"method_switch\": \"distance\"}", "dbkey": "\"hg17\"", "label": "[\"0.05\", \"0.27\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19808", "id": "3b972a2e0d2ad508", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_oturep.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"method_condition\|matrix_condition\|dist": {"src": "hda", "id": "bd8b611863ed9308"}, "method_condition\|pick\|type": "yes", "method_condition\|method_switch": "distance", "method_condition\|pick\|groups": ["forest", "pasture"], "label": ["unique", "0.05", "0.27", "0.45"], "method_condition\|pick\|group": {"src": "hda", "id": "880bb69112fd68b6"}, "method_condition\|matrix_condition\|matrix_format": "column", "method_condition\|matrix_condition\|nameOrCount": {"src": "hda", "id": "d3518d8bb3652466"}, "otu": {"src": "hda", "id": "99ed50059af5bb02"}}, "job": {"inputs": {"method_condition\|dist": {"src": "hda", "id": "bd8b611863ed9308", "uuid": "0cb40344-36cb-44fb-a8cc-d07691846f66"}, "method_condition\|group": {"src": "hda", "id": "880bb69112fd68b6", "uuid": "b205373d-838d-4be6-9e37-3bfa2b3382d3"}, "method_condition\|nameOrCount": {"src": "hda", "id": "d3518d8bb3652466", "uuid": "af6179b3-ab69-450c-8357-6407ea905dd6"}, "otu": {"src": "hda", "id": "99ed50059af5bb02", "uuid": "fe690c4f-e026-44af-b323-634907cdf208"}}, "update_time": "2018-02-08T17:35:53.329170", "tool_id": "mothur_get_oturep", "outputs": {"__new_primary_file_unique.pasture\|0.45.pasture__": {"src": "hda", "id": "fd31441a4aa60ede", "uuid": "544892b7-e41c-48c3-8897-89fa5c24865e"}, "__new_primary_file_unique.pasture\|0.05.forest__": {"src": "hda", "id": "777ec9c5caa78d86", "uuid": "5301c818-c0f1-4e1d-94c8-06a2fdd5667b"}, "__new_primary_file_unique.pasture\|0.45.forest__": {"src": "hda", "id": "d6f1701a9167dd73", "uuid": "814d1e54-4320-46a1-a6dd-c3d0f0d2ddc3"}, "__new_primary_file_unique.pasture\|0.27.forest__": {"src": "hda", "id": "9faf5e4358ec058f", "uuid": "3ddef2ce-68da-40ef-943a-4d7a1fa8627f"}, "__new_primary_file_unique.pasture\|0.27.pasture__": {"src": "hda", "id": "7543a3403ae6979a", "uuid": "9f91fa26-e088-4c63-853d-5f9c14989542"}, "__new_primary_file_unique.pasture\|unique.forest__": {"src": "hda", "id": "fde429e6e97b9f81", "uuid": "480db91e-8bbf-4a1d-85f1-890eb1ec7265"}, "__new_primary_file_unique.pasture\|unique.pasture__": {"src": "hda", "id": "f408fc8f9300835d", "uuid": "10810240-3e47-4233-b28c-189c679d5571"}, "__new_primary_file_unique.pasture\|0.05.pasture__": {"src": "hda", "id": "93aeb4de827d6c47", "uuid": "bd646759-619e-4204-94c1-0432fc92542c"}, "logfile": {"src": "hda", "id": "f87690ae06d59048", "uuid": "27b54f17-ddd9-4c42-a15b-894f8a8a5ea3"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.oturep(list=otu.dat,label=unique-0.05-0.27-0.45,method=distance,col \rumn=dist.dat,name=nameOrCount.dat,group=group.dat,groups=forest-pasture,large=fa \rlse)\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\nunique\t96\n0.05\t78\n0.27\t12\n0.45\t2\n\nOutput File Names: \notu.unique.forest.rep.names\notu.unique.pasture.rep.names\notu.0.05.forest.rep.names\notu.0.05.pasture.rep.names\notu.0.27.forest.rep.names\notu.0.27.pasture.rep.names\notu.0.45.forest.rep.names\notu.0.45.pasture.rep.names\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1171.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1172.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1173.dat' nameOrCount.dat && ln -s 'None' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1174.dat' group.dat && echo 'get.oturep( list=otu.dat, label=unique-0.05-0.27-0.45, method=distance, column=dist.dat, name=nameOrCount.dat, group=group.dat, groups=forest-pasture, large=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:35:49.660708", "params": {"sorted": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method_condition": "{\"matrix_condition\": {\"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 1173}]}, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 1172}]}, \"__current_case__\": 0, \"matrix_format\": \"column\"}, \"large\": \"false\", \"__current_case__\": 0, \"pick\": {\"group\": {\"values\": [{\"src\": \"hda\", \"id\": 1174}]}, \"type\": \"yes\", \"groups\": [\"forest\", \"pasture\"], \"__current_case__\": 1}, \"fasta\": null, \"method_switch\": \"distance\"}", "dbkey": "\"hg17\"", "label": "[\"unique\", \"0.05\", \"0.27\", \"0.45\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19976", "id": "ffc368cd972b6cba", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_oturep.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"method_condition\|matrix_condition\|dist": {"src": "hda", "id": "958f42f7df38196a"}, "method_condition\|method_switch": "distance", "label": ["unique", "0.05", "0.27"], "method_condition\|matrix_condition\|matrix_format": "phylip", "method_condition\|matrix_condition\|nameOrCount": {"src": "hda", "id": "000295148157cfd1"}, "otu": {"src": "hda", "id": "373650fcf8f1288e"}}, "job": {"inputs": {"method_condition\|dist": {"src": "hda", "id": "958f42f7df38196a", "uuid": "400e1660-0d20-4d5c-830a-3772755a3393"}, "otu": {"src": "hda", "id": "373650fcf8f1288e", "uuid": "07cf7628-7743-4274-a93e-de87a21c1ccf"}, "method_condition\|nameOrCount": {"src": "hda", "id": "000295148157cfd1", "uuid": "fc4b5d83-a6f1-45de-b081-d489ab5d6fd3"}}, "update_time": "2018-02-08T17:36:19.731566", "tool_id": "mothur_get_oturep", "outputs": {"__new_primary_file_unique\|0.27__": {"src": "hda", "id": "333420e1d962f11c", "uuid": "4df77d09-1a1f-408d-b20e-042b1034ec40"}, "logfile": {"src": "hda", "id": "df814c1a97206794", "uuid": "4f24dc30-58c5-4090-b123-c1d740dda48e"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "0eb134575c8781c5", "uuid": "4e4a889b-eac7-456a-b098-c81ec17a6690"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "0f8c488416e0bcc6", "uuid": "4e9b21fb-c2f3-4e3f-99a3-ef7edc44b7a3"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.oturep(list=otu.dat,label=unique-0.05-0.27,method=distance,phylip=d \rist.dat,count=nameOrCount.dat,large=false)\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n********************************************************************\nunique\t96\n0.05\t78\n0.27\t12\n\nOutput File Names: \notu.unique.rep.count_table\notu.0.05.rep.count_table\notu.0.27.rep.count_table\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1184.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1185.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1186.dat' nameOrCount.dat && ln -s 'None' fasta.dat && echo 'get.oturep( list=otu.dat, label=unique-0.05-0.27, method=distance, phylip=dist.dat, count=nameOrCount.dat, large=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:36:16.372153", "params": {"sorted": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method_condition": "{\"matrix_condition\": {\"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 1186}]}, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 1185}]}, \"__current_case__\": 1, \"matrix_format\": \"phylip\"}, \"large\": \"false\", \"__current_case__\": 0, \"pick\": {\"type\": \"no\", \"__current_case__\": 0}, \"fasta\": null, \"method_switch\": \"distance\"}", "dbkey": "\"hg17\"", "label": "[\"unique\", \"0.05\", \"0.27\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20116", "id": "555065f5aff402d2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_oturep.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"method_condition\|method_switch": "abundance", "sorted": "name", "otu": {"src": "hda", "id": "d833ede7810d07eb"}, "method_condition\|nameOrCount": {"src": "hda", "id": "d98e0261251f3c05"}, "label": ["0.27", "unique"]}, "job": {"inputs": {"nameOrCount": {"src": "hda", "id": "d98e0261251f3c05", "uuid": "8ec5ddb4-55fd-4945-9e26-1b1a27ce00ca"}, "otu": {"src": "hda", "id": "d833ede7810d07eb", "uuid": "78a8119d-6cfb-4966-b6a8-e8a9bfd6d4c5"}}, "update_time": "2018-02-08T17:36:43.502738", "tool_id": "mothur_get_oturep", "outputs": {"__new_primary_file_unique\|0.27__": {"src": "hda", "id": "9323df72f1a4c803", "uuid": "8478ad40-7eff-4304-b99b-0f4f722801c5"}, "logfile": {"src": "hda", "id": "9e9b9c71a17f9730", "uuid": "8db390b1-489a-42db-90e1-b0f5c2534c60"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "5f798f9781df9c30", "uuid": "a377f0e3-2c9e-4de5-b1e9-cb6ef2872533"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.oturep(list=otu.dat,sorted=name,label=0.27-unique,method=abundance, \rcount=nameOrCount.dat)\nunique\t96\n0.27\t12\n\nOutput File Names: \notu.unique.rep.count_table\notu.0.27.rep.count_table\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1191.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1192.dat' nameOrCount.dat && echo 'get.oturep( list=otu.dat, sorted=name, label=0.27-unique, method=abundance, count=nameOrCount.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:36:40.304148", "params": {"sorted": "\"name\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method_condition": "{\"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 1192}]}, \"method_switch\": \"abundance\", \"__current_case__\": 1}", "dbkey": "\"hg17\"", "label": "[\"0.27\", \"unique\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20233", "id": "ea74846895a98ad3", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_oturep.test_tool_000005", "has_data": true}, {"data": {"status": "success", "inputs": {"accnos": {"src": "hda", "id": "a1bc33c7c6bf579d"}, "list": {"src": "hda", "id": "a2471179f56050c1"}}, "job": {"inputs": {"accnos": {"src": "hda", "id": "a1bc33c7c6bf579d", "uuid": "68ae3019-f0dc-4923-824d-edfddc8d9060"}, "list": {"src": "hda", "id": "a2471179f56050c1", "uuid": "34e8f19e-acf8-4c08-a1b1-c9ef0e042628"}}, "update_time": "2018-02-08T17:37:04.284293", "tool_id": "mothur_get_otus", "outputs": {"corraxes_out": {"src": "hda", "id": "981110199526228d", "uuid": "9cefca4b-082e-4454-bfc8-cd01cd83fd84"}, "list_out": {"src": "hda", "id": "2eb14780dee695c1", "uuid": "467173d6-22cb-4b24-bb51-8f26a5df802e"}, "otucorr_out": {"src": "hda", "id": "b45c9a5a1a91fef7", "uuid": "96768362-0f16-467e-a1f0-c16ac37103f2"}, "shared_out": {"src": "hda", "id": "e55896246ae83c97", "uuid": "aa3df8b6-e53a-4272-9b54-ad9ea1192d01"}, "logfile": {"src": "hda", "id": "6b2453e322eb9595", "uuid": "8616c117-8388-4dd3-b29c-05ff2a7ba0e0"}, "constaxonomy_out": {"src": "hda", "id": "91162ef60fa42a9a", "uuid": "4533757c-1612-4751-93a4-4493befbac61"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.otus(list=list.dat,accnos=accnos.dat)\nYou did not provide a label, I will use the first label in your inputfile.\nSelected 3 OTUs from your list file.\n\nOutput File Names: \nlist.unique.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1196.dat' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1197.dat' list.dat && echo 'get.otus( list=list.dat, accnos=accnos.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:37:00.894116", "params": {"corraxes": "null", "dbkey": "\"hg17\"", "otucorr": "null", "shared": "null", "labelsource": "{\"source\": \"list\", \"__current_case__\": 0, \"label\": null}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "constaxonomy": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20339", "id": "8ea35917f4649fec", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_otus.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"shared": {"src": "hda", "id": "76e195bd5a51c206"}, "labelsource\|source": "shared", "accnos": {"src": "hda", "id": "597e90101763a05b"}, "labelsource\|label": "0.03", "otucorr": {"src": "hda", "id": "7b95a997d2449dc0"}}, "job": {"inputs": {"shared": {"src": "hda", "id": "76e195bd5a51c206", "uuid": "89b37eef-3f9d-44e8-b962-d417da74c0d3"}, "accnos": {"src": "hda", "id": "597e90101763a05b", "uuid": "4d8dcce9-2afb-46b9-a0bf-d2f9fc7902a3"}, "otucorr": {"src": "hda", "id": "7b95a997d2449dc0", "uuid": "3ae2a72b-67e5-45c3-8539-c18b18baafaf"}}, "update_time": "2018-02-08T17:37:28.977887", "tool_id": "mothur_get_otus", "outputs": {"corraxes_out": {"src": "hda", "id": "9b61f34308fff2a9", "uuid": "f4b163d2-98cf-4b7e-8a3f-84e696308c4e"}, "list_out": {"src": "hda", "id": "51ff028a9c4e3d38", "uuid": "b0869f4c-8a97-4ea5-b3cb-b3a0f20cdf57"}, "otucorr_out": {"src": "hda", "id": "3f123558ac7162f4", "uuid": "39faed66-bef0-4e98-9a53-7e94365d63d8"}, "shared_out": {"src": "hda", "id": "c72e590e45abaffd", "uuid": "2cc58074-9cb0-44cd-b0d1-ea5b2b8ae892"}, "logfile": {"src": "hda", "id": "93c45a4fc85043cc", "uuid": "1cb7ccc9-5e1f-43b1-a078-fc434a62be91"}, "constaxonomy_out": {"src": "hda", "id": "5c870d3cd8d2cd2b", "uuid": "cb9391ce-9aa3-4410-b96c-b738f4a7f411"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.otus(shared=shared.dat,otucorr=otucorr.dat,accnos=accnos.dat,label= \r0.03)\nSelected 3 lines from your otu.corr file.\nSelected 3 OTUs from your shared file.\n\nOutput File Names: \notucorr.pick.dat\nshared.0.03.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1204.dat' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1205.dat' shared.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1206.dat' otucorr.dat && echo 'get.otus( shared=shared.dat, otucorr=otucorr.dat, accnos=accnos.dat ,label=0.03 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:37:25.632339", "params": {"list": "null", "corraxes": "null", "dbkey": "\"hg17\"", "labelsource": "{\"source\": \"shared\", \"__current_case__\": 1, \"label\": \"0.03\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "constaxonomy": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20469", "id": "86fc1a32b14d4612", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_otus.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "bfb8462f158178af"}, "label": ["0.03", "0.05"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "bfb8462f158178af", "uuid": "9e10e7f7-f01c-4af2-8418-74c67d0e372d"}}, "update_time": "2018-02-08T17:37:46.140219", "tool_id": "mothur_get_rabund", "outputs": {"rabund": {"src": "hda", "id": "14ea0e9326ca1861", "uuid": "f9b65b0c-d862-4482-8b97-9fcf8bdb3d34"}, "logfile": {"src": "hda", "id": "697f459f9324ea39", "uuid": "0903f896-82ca-499b-8cf4-eb4d3fa25238"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.rabund(label=0.03-0.05,sabund=otu.dat,sorted=false)\n0.03\n0.05\n\nOutput File Names: \notu.rabund\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1213.dat' otu.dat && echo 'get.rabund( label=0.03-0.05, sabund=otu.dat, sorted=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:37:43.011652", "params": {"count": "null", "sorted": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20564", "id": "c2096fa94981c9cc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_rabund.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "e852cf3dc3c7e42b"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "e852cf3dc3c7e42b", "uuid": "3b0701b3-41ab-4ddf-baaa-062ab5dcc4c4"}}, "update_time": "2018-02-08T17:38:03.722756", "tool_id": "mothur_get_rabund", "outputs": {"rabund": {"src": "hda", "id": "8bd0850a7e2f437b", "uuid": "9f88f7ab-3e6a-4d36-8fb7-b6d03ce3ef1a"}, "logfile": {"src": "hda", "id": "0d4414093f575fd4", "uuid": "5172947e-b101-420f-a161-b848fcbf0d4c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.rabund(list=otu.dat,sorted=false)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.rabund\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1216.dat' otu.dat && echo 'get.rabund( list=otu.dat, sorted=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:38:00.608880", "params": {"count": "null", "sorted": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20651", "id": "aa6cc630da5109fb", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_rabund.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "081df3333d4f9bbc"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "081df3333d4f9bbc", "uuid": "1b3a0577-d92e-424c-9c76-386b46161f6c"}}, "update_time": "2018-02-08T17:38:21.257992", "tool_id": "mothur_get_relabund", "outputs": {"logfile": {"src": "hda", "id": "782a500b6c6975dc", "uuid": "321e7030-ac8a-42cb-adb1-776f0c471f17"}, "relabund": {"src": "hda", "id": "a99a39c00943ef30", "uuid": "e959a3fd-2378-412e-9001-1150d4439ca4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.relabund(shared=otu.dat,scale=totalgroup)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.relabund\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1219.dat' otu.dat && echo 'get.relabund( shared=otu.dat, scale=totalgroup )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:38:18.141836", "params": {"scale": "\"totalgroup\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groups": "null", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20739", "id": "4c469a959b869c08", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_relabund.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "350367f7bcfdf2dd"}, "groups": "forest", "label": ["0.03", "0.05", "0.22"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "350367f7bcfdf2dd", "uuid": "5c37e7ee-4648-49dc-b771-adc2e70fe1cd"}}, "update_time": "2018-02-08T17:38:38.840628", "tool_id": "mothur_get_relabund", "outputs": {"logfile": {"src": "hda", "id": "3819ce922fdcf9e5", "uuid": "707f17eb-240b-45df-afe9-ce959eeaeeef"}, "relabund": {"src": "hda", "id": "41db60f4cf5f2831", "uuid": "07b85144-a45d-494e-a79f-071c71396902"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.relabund(shared=otu.dat,label=0.03-0.05-0.22,groups=forest,scale=to \rtalgroup)\n0.03\n0.05\n0.22\n\nOutput File Names: \notu.relabund\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1222.dat' otu.dat && echo 'get.relabund( shared=otu.dat, label=0.03-0.05-0.22, groups=forest, scale=totalgroup )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:38:35.746126", "params": {"scale": "\"totalgroup\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groups": "\"forest\"", "label": "[\"0.03\", \"0.05\", \"0.22\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20829", "id": "3d5f803521123c6e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_relabund.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "8a4ff393c0f15cf9"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "8a4ff393c0f15cf9", "uuid": "ec1c0799-83fe-4d5a-9068-6835c6412863"}}, "update_time": "2018-02-08T17:38:56.557586", "tool_id": "mothur_get_sabund", "outputs": {"logfile": {"src": "hda", "id": "d0f68e425dbbc775", "uuid": "ad4bd606-afc2-4016-9ce2-47640ddef2e0"}, "sabund": {"src": "hda", "id": "2fe4b83a9267275d", "uuid": "e734f708-7b0f-4796-b0ab-9a6890e53b30"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.sabund(rabund=otu.dat)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.sabund\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1225.dat' otu.dat && ln -s 'None' count.dat && echo 'get.sabund( rabund=otu.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:38:53.435236", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20916", "id": "ec0fb831200675f4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_sabund.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "a0a2ae0841f1568c"}, "label": ["0.03", "0.05"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "a0a2ae0841f1568c", "uuid": "7ed19e3e-c6bb-435f-bb82-90d8c7b36cdd"}}, "update_time": "2018-02-08T17:39:14.113078", "tool_id": "mothur_get_sabund", "outputs": {"logfile": {"src": "hda", "id": "24da0eeb3eec1daa", "uuid": "c1698ca0-1cde-4dd4-a1ca-fc3d5d5626a8"}, "sabund": {"src": "hda", "id": "3f9f964fe6121e92", "uuid": "8e27ffcb-96a8-490d-b26c-61861a529567"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.sabund(label=0.03-0.05,list=otu.dat)\n0.03\n0.05\n\nOutput File Names: \notu.sabund\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1228.dat' otu.dat && ln -s 'None' count.dat && echo 'get.sabund( label=0.03-0.05, list=otu.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:39:11.000346", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "21004", "id": "f1f75462f416e186", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_sabund.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"accnos": {"src": "hda", "id": "61d69f53aecda797"}, "fasta_in": {"src": "hda", "id": "c58efa153eba9565"}, "dups": false}, "job": {"inputs": {"accnos": {"src": "hda", "id": "61d69f53aecda797", "uuid": "ee95bfe3-7425-4e29-806a-84a726cab72c"}, "fasta_in": {"src": "hda", "id": "c58efa153eba9565", "uuid": "f541b4af-c928-4167-8bfd-84236cc32cb3"}}, "update_time": "2018-02-08T17:39:34.986176", "tool_id": "mothur_get_seqs", "outputs": {"logfile": {"src": "hda", "id": "5e3a9652455a7ed3", "uuid": "3b977c88-368c-44a6-940c-2d5b765bfe9e"}, "fasta_out": {"src": "hda", "id": "631e6f3f808d1daa", "uuid": "f7c805f9-9e85-41bb-b789-56c2b8e433b9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.seqs(accnos=accnos.dat,fasta=fasta_in.dat,dups=false)\nSelected 3 sequences from your fasta file.\n\nOutput File Names: \nfasta_in.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1231.dat' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1232.dat' fasta_in.dat && ln -s 'None' fastq_in.dat && ln -s 'None' count_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' taxonomy_in.dat && echo 'get.seqs( accnos=accnos.dat, fasta=fasta_in.dat, dups=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:39:31.864369", "params": {"fastq_in": "null", "dups": "\"false\"", "count_in": "null", "dbkey": "\"hg17\"", "group_in": "null", "taxonomy_in": "null", "alignreport_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "21125", "id": "f3e7443ed4070d7c", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fastq_in": {"src": "hda", "id": "011edc069103d7ec"}, "accnos": {"src": "hda", "id": "96df66444a6ec901"}}, "job": {"inputs": {"fastq_in": {"src": "hda", "id": "011edc069103d7ec", "uuid": "2a4e4303-b583-4bb7-8dc3-090ac8d784fb"}, "accnos": {"src": "hda", "id": "96df66444a6ec901", "uuid": "5f09f2d8-e815-481e-8319-680abfc1ee55"}}, "update_time": "2018-02-08T17:39:50.405005", "tool_id": "mothur_get_seqs", "outputs": {"logfile": {"src": "hda", "id": "11e2f427f678fd46", "uuid": "c8919f6f-d45e-476c-b870-02cd51988a1e"}, "fastq_out": {"src": "hda", "id": "aecf4c8180e80a4e", "uuid": "ebc254ae-cb1a-41b9-9b0d-dba079754227"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.seqs(accnos=accnos.dat,fastq=fastq_in.dat,dups=dups)\nSelected 3 sequences from your fastq file.\n\nOutput File Names: \nfastq_in.pick.dat\n\n[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1235.dat' accnos.dat && ln -s 'None' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1236.dat' fastq_in.dat && ln -s 'None' count_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' taxonomy_in.dat && echo 'get.seqs( accnos=accnos.dat, fastq=fastq_in.dat, dups=dups )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:39:47.449707", "params": {"dups": "\"true\"", "fasta_in": "null", "count_in": "null", "dbkey": "\"hg17\"", "group_in": "null", "taxonomy_in": "null", "alignreport_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "21248", "id": "a5170ff908b4401b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fastq_in": {"src": "hda", "id": "f34bcbdd0a72e0b4"}, "accnos": {"src": "hda", "id": "429998073c64a880"}, "fasta_in": {"src": "hda", "id": "ae159bf1c2125429"}, "dups": false}, "job": {"inputs": {"fastq_in": {"src": "hda", "id": "f34bcbdd0a72e0b4", "uuid": "d71804cd-863d-4cf8-9f8e-12a37d7ec74c"}, "fasta_in": {"src": "hda", "id": "ae159bf1c2125429", "uuid": "fd50d748-91bc-4253-b3a7-57b119542771"}, "accnos": {"src": "hda", "id": "429998073c64a880", "uuid": "ff206f5a-eecf-4f9d-9f49-88d2a2c7f8e8"}}, "update_time": "2018-02-08T17:40:10.037647", "tool_id": "mothur_get_seqs", "outputs": {"fasta_out": {"src": "hda", "id": "cc004dc337e74e6b", "uuid": "ec9de38c-7807-4109-aaac-4e2422131fd7"}, "logfile": {"src": "hda", "id": "38134c7758ca35f5", "uuid": "d334d6cc-a785-427d-b0e3-653a1cee3dc4"}, "fastq_out": {"src": "hda", "id": "a0e87d70eb117c6b", "uuid": "bb5beb8c-57ac-4fb0-8a64-98519ef3e355"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.seqs(accnos=accnos.dat,fasta=fasta_in.dat,fastq=fastq_in.dat,dups=f \ralse)\nSelected 3 sequences from your fasta file.\nSelected 3 sequences from your fastq file.\n\nOutput File Names: \nfasta_in.pick.dat\nfastq_in.pick.dat\n\n[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1239.dat' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1240.dat' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1241.dat' fastq_in.dat && ln -s 'None' count_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' taxonomy_in.dat && echo 'get.seqs( accnos=accnos.dat, fasta=fasta_in.dat, fastq=fastq_in.dat, dups=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:40:06.074352", "params": {"dups": "\"false\"", "count_in": "null", "dbkey": "\"hg17\"", "group_in": "null", "taxonomy_in": "null", "alignreport_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "21397", "id": "2b49763c55874680", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"accnos": {"src": "hda", "id": "2af669c98ffba1bc"}, "count_in": {"src": "hda", "id": "28ef132ecd41da41"}}, "job": {"inputs": {"accnos": {"src": "hda", "id": "2af669c98ffba1bc", "uuid": "495fec17-107e-4eee-8610-1c4e96f58a6d"}, "count_in": {"src": "hda", "id": "28ef132ecd41da41", "uuid": "f7cdf3dd-535d-4b35-883b-54caf42d9374"}}, "update_time": "2018-02-08T17:40:27.491400", "tool_id": "mothur_get_seqs", "outputs": {"logfile": {"src": "hda", "id": "7ccd0d003f1c770e", "uuid": "2b67b8c6-c764-4f46-ae9b-fe8bec450035"}, "count_out": {"src": "hda", "id": "0a69fafee8fab989", "uuid": "00faa3ff-4c97-424a-b5ef-5abf56f80208"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.seqs(accnos=accnos.dat,count=count_in.dat,dups=dups)\nSelected 8 sequences from your count file.\n\nOutput File Names: \ncount_in.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1245.dat' accnos.dat && ln -s 'None' fasta_in.dat && ln -s 'None' fastq_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1246.dat' count_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' taxonomy_in.dat && echo 'get.seqs( accnos=accnos.dat, count=count_in.dat, dups=dups )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:40:24.388969", "params": {"fastq_in": "null", "dups": "\"true\"", "fasta_in": "null", "dbkey": "\"hg17\"", "group_in": "null", "taxonomy_in": "null", "alignreport_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "21528", "id": "a5b8d21ac8fc30ea", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_seqs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"infile\|intype": "in_shared", "infile\|otu": {"src": "hda", "id": "8991ff1b69b89ded"}, "infile\|seqsfrom\|selection": "shared"}, "job": {"inputs": {"otu": {"src": "hda", "id": "8991ff1b69b89ded", "uuid": "872bf3b7-9f50-4f08-8cae-3392147d7120"}}, "update_time": "2018-02-08T17:40:42.546493", "tool_id": "mothur_get_sharedseqs", "outputs": {"__new_primary_file_0.55.unique.forest_pasture\|0.01.unique.forest_pasture__": {"src": "hda", "id": "fe96fd381a33cce5", "uuid": "6e62e8a0-9565-42a2-9211-7f4045d9802e"}, "__new_primary_file_0.55.unique.forest_pasture\|0.03.unique.forest_pasture__": {"src": "hda", "id": "abbd1960cbf160f9", "uuid": "03fd6ca0-4f2c-465a-8cb8-dbe825c563f1"}, "__new_primary_file_0.55.unique.forest_pasture\|0.12.unique.forest_pasture__": {"src": "hda", "id": "d07b459d41c7c945", "uuid": "03f90a30-0551-4910-97a7-dc0c226679fb"}, "__new_primary_file_0.55.unique.forest_pasture\|0.08.unique.forest_pasture__": {"src": "hda", "id": "0bb3941465c9f795", "uuid": "5c0613c1-f9a1-484d-a2b3-26a54e649ee9"}, "__new_primary_file_0.55.unique.forest_pasture\|0.36.unique.forest_pasture__": {"src": "hda", "id": "c785bef273d68b1e", "uuid": "1b0a9c63-56b9-4972-8b9f-02ba5c02c04f"}, "__new_primary_file_0.55.unique.forest_pasture\|0.33.unique.forest_pasture__": {"src": "hda", "id": "696fb5296f68042e", "uuid": "271c55c4-3601-4cfa-8890-aa71391cd4e4"}, "__new_primary_file_0.55.unique.forest_pasture\|0.23.unique.forest_pasture__": {"src": "hda", "id": "1705da10f105bf38", "uuid": "95d04c9c-0972-45cb-81b3-61f008596f88"}, "__new_primary_file_0.55.unique.forest_pasture\|0.32.unique.forest_pasture__": {"src": "hda", "id": "94b2b05bccf8c5b7", "uuid": "f0f831e2-5c81-40f5-af81-a6174cf1a4e5"}, "__new_primary_file_0.55.unique.forest_pasture\|0.06.unique.forest_pasture__": {"src": "hda", "id": "ee43e48dbb3db358", "uuid": "a4e1ae3d-6947-49bb-8b50-ab5d37eacbea"}, "__new_primary_file_0.55.unique.forest_pasture\|0.45.unique.forest_pasture__": {"src": "hda", "id": "e959a6a79feb9b78", "uuid": "860cb981-ff58-4f47-ba3f-7859fb678339"}, "__new_primary_file_0.55.unique.forest_pasture\|0.38.unique.forest_pasture__": {"src": "hda", "id": "af849d2a7341fcce", "uuid": "68ec2522-535a-423f-89de-ac8ee8073ae1"}, "__new_primary_file_0.55.unique.forest_pasture\|0.04.unique.forest_pasture__": {"src": "hda", "id": "e1caecba7fa68b40", "uuid": "038e3223-f87e-4d54-b647-e80c270d7fde"}, "__new_primary_file_0.55.unique.forest_pasture\|0.20.unique.forest_pasture__": {"src": "hda", "id": "93d3f7925ba4d071", "uuid": "b43ed593-75eb-4c3f-bfda-2a684feb05d9"}, "__new_primary_file_0.55.unique.forest_pasture\|0.26.unique.forest_pasture__": {"src": "hda", "id": "98949929b1176202", "uuid": "7b478ce3-2d42-4a2f-b821-11a03d939363"}, "__new_primary_file_0.55.unique.forest_pasture\|0.15.unique.forest_pasture__": {"src": "hda", "id": "c3ce2a80c0d89459", "uuid": "92173f88-ce59-4d94-96f8-4eb3b91721df"}, "__new_primary_file_0.55.unique.forest_pasture\|0.02.unique.forest_pasture__": {"src": "hda", "id": "2114951d23217870", "uuid": "30bbdd45-8509-476d-8500-7fb15c01fbfc"}, "__new_primary_file_0.55.unique.forest_pasture\|0.10.unique.forest_pasture__": {"src": "hda", "id": "5f161a30c8b2f408", "uuid": "9dc304f3-b581-4555-b2f0-4fcc85d063a6"}, "__new_primary_file_0.55.unique.forest_pasture\|0.17.unique.forest_pasture__": {"src": "hda", "id": "b9bb71cf44c7a0e7", "uuid": "cddaf8f8-e410-4633-aa7a-2bbec88cbc5c"}, "__new_primary_file_0.55.unique.forest_pasture\|0.29.unique.forest_pasture__": {"src": "hda", "id": "b4a250cf71b57d6e", "uuid": "06f5481a-e0b3-479a-8508-9a91fc743a7a"}, "__new_primary_file_0.55.unique.forest_pasture\|0.09.unique.forest_pasture__": {"src": "hda", "id": "22ee6ec8bba94753", "uuid": "7c493108-e4fa-4a7e-bb29-e20ede7859ab"}, "__new_primary_file_0.55.unique.forest_pasture\|0.22.unique.forest_pasture__": {"src": "hda", "id": "e79f5a70b4d84628", "uuid": "98be88e4-5708-41e8-ac3d-b8d99af0623f"}, "__new_primary_file_0.55.unique.forest_pasture\|0.16.unique.forest_pasture__": {"src": "hda", "id": "c0880ab75f60a05d", "uuid": "d1962c02-1150-42c4-a0b5-53f95b28f23b"}, "__new_primary_file_0.55.unique.forest_pasture\|0.14.unique.forest_pasture__": {"src": "hda", "id": "ae5dfc6c4ccf9fa5", "uuid": "440852d5-6a57-4390-beca-0da217e15cb3"}, "__new_primary_file_0.55.unique.forest_pasture\|0.05.unique.forest_pasture__": {"src": "hda", "id": "39ba608ca28de802", "uuid": "c5226c97-5550-4504-9368-9c34d154f7a0"}, "__new_primary_file_0.55.unique.forest_pasture\|0.19.unique.forest_pasture__": {"src": "hda", "id": "c8711b8e31575185", "uuid": "e388917c-c66e-4775-a573-6876087759ce"}, "__new_primary_file_0.55.unique.forest_pasture\|0.27.unique.forest_pasture__": {"src": "hda", "id": "a14db3cd22562c1c", "uuid": "facbec9c-ef23-4a49-832e-cb72d88e40c3"}, "__new_primary_file_0.55.unique.forest_pasture\|0.25.unique.forest_pasture__": {"src": "hda", "id": "fb26921841cf93b6", "uuid": "4a208dfa-fb3b-406b-a7ec-1ebd75312147"}, "__new_primary_file_0.55.unique.forest_pasture\|0.21.unique.forest_pasture__": {"src": "hda", "id": "a53b61a2057d1d37", "uuid": "2b481e20-a397-492d-8c8e-4ae5e926d273"}, "__new_primary_file_0.55.unique.forest_pasture\|0.11.unique.forest_pasture__": {"src": "hda", "id": "a2b4f906be8b27da", "uuid": "2d894fec-a661-443b-91f8-63eedcc74c30"}, "__new_primary_file_0.55.unique.forest_pasture\|0.41.unique.forest_pasture__": {"src": "hda", "id": "3c94cd72eddabd04", "uuid": "4b0ad5ec-65dc-4e5f-acb3-836c68d942dd"}, "__new_primary_file_0.55.unique.forest_pasture\|0.13.unique.forest_pasture__": {"src": "hda", "id": "81cefc9a8787c281", "uuid": "20a466e5-907c-40b2-97dc-aad52b3b7197"}, "__new_primary_file_0.55.unique.forest_pasture\|0.55.unique.forest_pasture__": {"src": "hda", "id": "f9dbbadeec4a7667", "uuid": "d64b8575-454c-4727-ad23-b5d8c6fe59ca"}, "logfile": {"src": "hda", "id": "97dddce84ce4448e", "uuid": "42368fb8-aa6a-44b7-9809-9ca33a75f9a0"}, "__new_primary_file_0.55.unique.forest_pasture\|0.24.unique.forest_pasture__": {"src": "hda", "id": "f4069f60e8f3e4ae", "uuid": "5a3e0161-4ff4-402f-9c1a-b5d52d8c353c"}, "__new_primary_file_0.55.unique.forest_pasture\|0.07.unique.forest_pasture__": {"src": "hda", "id": "18db42ecae15c51a", "uuid": "92fd9874-876c-4b24-9dad-7a4a10b4177a"}, "__new_primary_file_0.55.unique.forest_pasture\|0.18.unique.forest_pasture__": {"src": "hda", "id": "0bc713a3d3ce28f8", "uuid": "c8092fa4-b78d-4f24-acf5-7d3518cf5467"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.sharedseqs(shared=infile_otu.dat)\nunique\t0 - No otus shared by groups forest pasture.\n0.01\t1\n0.02\t1\n0.03\t2\n0.04\t4\n0.05\t7\n0.06\t9\n0.07\t9\n0.08\t9\n0.09\t9\n0.10\t8\n0.11\t8\n0.12\t8\n0.13\t8\n0.14\t9\n0.15\t9\n0.16\t9\n0.17\t10\n0.18\t10\n0.19\t11\n0.20\t10\n0.21\t9\n0.22\t9\n0.23\t8\n0.24\t7\n0.25\t7\n0.26\t7\n0.27\t6\n0.29\t4\n0.32\t3\n0.33\t2\n0.36\t2\n0.38\t2\n0.41\t1\n0.45\t1\n0.55\t1\n\nOutput File Names: \ninfile_otu.0.01.unique.forest_pasture.shared.seqs\ninfile_otu.0.02.unique.forest_pasture.shared.seqs\ninfile_otu.0.03.unique.forest_pasture.shared.seqs\ninfile_otu.0.04.unique.forest_pasture.shared.seqs\ninfile_otu.0.05.unique.forest_pasture.shared.seqs\ninfile_otu.0.06.unique.forest_pasture.shared.seqs\ninfile_otu.0.07.unique.forest_pasture.shared.seqs\ninfile_otu.0.08.unique.forest_pasture.shared.seqs\ninfile_otu.0.09.unique.forest_pasture.shared.seqs\ninfile_otu.0.10.unique.forest_pasture.shared.seqs\ninfile_otu.0.11.unique.forest_pasture.shared.seqs\ninfile_otu.0.12.unique.forest_pasture.shared.seqs\ninfile_otu.0.13.unique.forest_pasture.shared.seqs\ninfile_otu.0.14.unique.forest_pasture.shared.seqs\ninfile_otu.0.15.unique.forest_pasture.shared.seqs\ninfile_otu.0.16.unique.forest_pasture.shared.seqs\ninfile_otu.0.17.unique.forest_pasture.shared.seqs\ninfile_otu.0.18.unique.forest_pasture.shared.seqs\ninfile_otu.0.19.unique.forest_pasture.shared.seqs\ninfile_otu.0.20.unique.forest_pasture.shared.seqs\ninfile_otu.0.21.unique.forest_pasture.shared.seqs\ninfile_otu.0.22.unique.forest_pasture.shared.seqs\ninfile_otu.0.23.unique.forest_pasture.shared.seqs\ninfile_otu.0.24.unique.forest_pasture.shared.seqs\ninfile_otu.0.25.unique.forest_pasture.shared.seqs\ninfile_otu.0.26.unique.forest_pasture.shared.seqs\ninfile_otu.0.27.unique.forest_pasture.shared.seqs\ninfile_otu.0.29.unique.forest_pasture.shared.seqs\ninfile_otu.0.32.unique.forest_pasture.shared.seqs\ninfile_otu.0.33.unique.forest_pasture.shared.seqs\ninfile_otu.0.36.unique.forest_pasture.shared.seqs\ninfile_otu.0.38.unique.forest_pasture.shared.seqs\ninfile_otu.0.41.unique.forest_pasture.shared.seqs\ninfile_otu.0.45.unique.forest_pasture.shared.seqs\ninfile_otu.0.55.unique.forest_pasture.shared.seqs\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1249.dat' infile_otu.dat && echo 'get.sharedseqs( shared=infile_otu.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:40:37.022378", "params": {"output": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_shared\", \"seqsfrom\": {\"selection\": \"shared\", \"groups\": null, \"__current_case__\": 1}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1249}]}, \"__current_case__\": 0, \"label\": null}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "21699", "id": "84069f8e0a4c5a8e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_sharedseqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"infile\|intype": "in_listgroup", "infile\|otu": {"src": "hda", "id": "4b7d958e0a57cf76"}, "infile\|group": {"src": "hda", "id": "22e37d6ba86e2a2e"}}, "job": {"inputs": {"group": {"src": "hda", "id": "22e37d6ba86e2a2e", "uuid": "57e7e54e-4d04-466e-aee7-80aab3ddf238"}, "otu": {"src": "hda", "id": "4b7d958e0a57cf76", "uuid": "094a5b5c-cacc-4fa3-bb7d-4cdd0535c932"}}, "update_time": "2018-02-08T17:41:06.572855", "tool_id": "mothur_get_sharedseqs", "outputs": {"__new_primary_file_0.55.unique.forest_pasture\|0.01.unique.forest_pasture__": {"src": "hda", "id": "a6e53d78c2aa075a", "uuid": "30f325e4-4f11-4b7d-bde7-36f0f667cfa3"}, "__new_primary_file_0.55.unique.forest_pasture\|0.03.unique.forest_pasture__": {"src": "hda", "id": "e129f12cdcbea9f8", "uuid": "6bbf9fcb-96d3-4ae7-b4a5-ab6216cc6e48"}, "__new_primary_file_0.55.unique.forest_pasture\|0.12.unique.forest_pasture__": {"src": "hda", "id": "993d97a54f58371d", "uuid": "393135e9-fa41-4153-9aa3-2660c092c92c"}, "__new_primary_file_0.55.unique.forest_pasture\|0.08.unique.forest_pasture__": {"src": "hda", "id": "87221f8fb11b5cc8", "uuid": "9c6f73d1-4c93-40cb-8252-899acd0218a6"}, "__new_primary_file_0.55.unique.forest_pasture\|0.36.unique.forest_pasture__": {"src": "hda", "id": "983b943d65d6c7d7", "uuid": "e0b99c1d-e30f-4277-bf5c-f419f0638f89"}, "__new_primary_file_0.55.unique.forest_pasture\|0.33.unique.forest_pasture__": {"src": "hda", "id": "1c22c17396d9a02a", "uuid": "4196bbee-376f-4c74-b415-d84fb2253cea"}, "__new_primary_file_0.55.unique.forest_pasture\|0.23.unique.forest_pasture__": {"src": "hda", "id": "f39de65e2034ed3a", "uuid": "c79dcaf1-76cf-4441-981b-f6a2c2d1aef4"}, "__new_primary_file_0.55.unique.forest_pasture\|0.32.unique.forest_pasture__": {"src": "hda", "id": "c8f16105fabce55c", "uuid": "5dffad01-87c3-4695-a705-cf92f638cffb"}, "__new_primary_file_0.55.unique.forest_pasture\|0.06.unique.forest_pasture__": {"src": "hda", "id": "35de84ce53a9c828", "uuid": "4ba701d9-96ce-476d-9d70-091352681b8f"}, "__new_primary_file_0.55.unique.forest_pasture\|0.45.unique.forest_pasture__": {"src": "hda", "id": "9d80b37e646651a2", "uuid": "cca381a8-f0b1-451f-a0ca-4e21ff97a0ce"}, "__new_primary_file_0.55.unique.forest_pasture\|0.38.unique.forest_pasture__": {"src": "hda", "id": "1f5f52e2309ff559", "uuid": "d706fac0-066c-4140-a107-93c7a7dadc7b"}, "__new_primary_file_0.55.unique.forest_pasture\|0.04.unique.forest_pasture__": {"src": "hda", "id": "914cc9e62ef5365f", "uuid": "d748bcde-2616-4fe2-8ba0-70fc5002f414"}, "__new_primary_file_0.55.unique.forest_pasture\|0.20.unique.forest_pasture__": {"src": "hda", "id": "fad0ab3aea5cc191", "uuid": "23e411ec-733c-4172-b226-749c7bcc3a3b"}, "__new_primary_file_0.55.unique.forest_pasture\|0.26.unique.forest_pasture__": {"src": "hda", "id": "6b853ad1a5dc9670", "uuid": "d152f781-531f-4064-ac9e-77870a5fad59"}, "__new_primary_file_0.55.unique.forest_pasture\|0.15.unique.forest_pasture__": {"src": "hda", "id": "5b7a47d04f2ce92e", "uuid": "e272186f-af71-4f73-931c-caf7ff00bb2b"}, "__new_primary_file_0.55.unique.forest_pasture\|0.02.unique.forest_pasture__": {"src": "hda", "id": "fde35c4f1f75764c", "uuid": "21a7781c-a131-4cb1-9782-18fd7c7f2ae3"}, "__new_primary_file_0.55.unique.forest_pasture\|0.10.unique.forest_pasture__": {"src": "hda", "id": "c3e3c95393385769", "uuid": "8f838ca7-cb0a-49ed-92a0-7af2587aa95a"}, "__new_primary_file_0.55.unique.forest_pasture\|0.17.unique.forest_pasture__": {"src": "hda", "id": "bd17947ec32bf83e", "uuid": "cc13beef-971d-43d5-b420-278a82c15ab7"}, "__new_primary_file_0.55.unique.forest_pasture\|0.29.unique.forest_pasture__": {"src": "hda", "id": "89f023fa51ac47b1", "uuid": "e3ec40de-c3d1-4752-a9b1-eaa6a8c5df14"}, "__new_primary_file_0.55.unique.forest_pasture\|0.09.unique.forest_pasture__": {"src": "hda", "id": "e87af5eb583a6a0d", "uuid": "60bb585e-a501-4162-a97e-a817c7190865"}, "__new_primary_file_0.55.unique.forest_pasture\|0.22.unique.forest_pasture__": {"src": "hda", "id": "eef93538df20bc17", "uuid": "5a98686b-b17a-412a-8304-bcf4cb4d7a3d"}, "__new_primary_file_0.55.unique.forest_pasture\|0.16.unique.forest_pasture__": {"src": "hda", "id": "bdaadc18ac151cd2", "uuid": "4595f913-1a6d-402a-bc6e-db035606e6c5"}, "__new_primary_file_0.55.unique.forest_pasture\|0.14.unique.forest_pasture__": {"src": "hda", "id": "461683b0bc43792a", "uuid": "7c11441b-93c0-440a-bd46-3d9a53018f5a"}, "__new_primary_file_0.55.unique.forest_pasture\|0.05.unique.forest_pasture__": {"src": "hda", "id": "ad58d1ed1e353fc6", "uuid": "28520fde-77ab-44e6-a2b3-975f4aa7024d"}, "__new_primary_file_0.55.unique.forest_pasture\|0.19.unique.forest_pasture__": {"src": "hda", "id": "f8b18a16ce2a2213", "uuid": "26ed470f-185b-429e-8f93-f995c357df9d"}, "__new_primary_file_0.55.unique.forest_pasture\|0.27.unique.forest_pasture__": {"src": "hda", "id": "b45a8ae42a18587e", "uuid": "59e2a1d6-bb25-439e-9308-b5a96a05b7de"}, "__new_primary_file_0.55.unique.forest_pasture\|0.25.unique.forest_pasture__": {"src": "hda", "id": "0534db83ede63e64", "uuid": "be926160-a075-45d4-ad37-46cbf886ed43"}, "__new_primary_file_0.55.unique.forest_pasture\|0.21.unique.forest_pasture__": {"src": "hda", "id": "9a87b669ba9ab9db", "uuid": "d4f58cdd-b711-400e-a76e-0cda681abfd8"}, "__new_primary_file_0.55.unique.forest_pasture\|0.11.unique.forest_pasture__": {"src": "hda", "id": "e2e4c35d5ff4266b", "uuid": "12a6ac0f-1db6-4b96-875a-fcb7009814f4"}, "__new_primary_file_0.55.unique.forest_pasture\|0.41.unique.forest_pasture__": {"src": "hda", "id": "220fe64dce861a50", "uuid": "c057e845-b61a-4d4c-bb84-90eb7387d194"}, "__new_primary_file_0.55.unique.forest_pasture\|0.13.unique.forest_pasture__": {"src": "hda", "id": "64d82fdd6e113cc6", "uuid": "f10dd2e4-d8e1-4baa-9451-3d5d9bc74197"}, "__new_primary_file_0.55.unique.forest_pasture\|0.55.unique.forest_pasture__": {"src": "hda", "id": "cca4740627632b2c", "uuid": "7dd79344-3624-4f33-99e7-040a5fe90020"}, "logfile": {"src": "hda", "id": "76f3dabcdd118837", "uuid": "134d204a-412b-4b70-98a3-76345bf064c8"}, "__new_primary_file_0.55.unique.forest_pasture\|0.24.unique.forest_pasture__": {"src": "hda", "id": "eb651194166b0289", "uuid": "a6ed694b-7c67-4583-8274-10269dabae15"}, "__new_primary_file_0.55.unique.forest_pasture\|0.07.unique.forest_pasture__": {"src": "hda", "id": "a552f60ce7ee1aa3", "uuid": "799d8b21-d71e-4298-8675-6b790f0b7e06"}, "__new_primary_file_0.55.unique.forest_pasture\|0.18.unique.forest_pasture__": {"src": "hda", "id": "8c4aac77b9acb762", "uuid": "92b51647-e348-4bb0-988f-91020a0076da"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.sharedseqs(list=infile_otu.dat,group=infile.group.dat)\nunique\t0 - No otus shared by groups forest pasture.\n0.01\t1\n0.02\t1\n0.03\t2\n0.04\t4\n0.05\t7\n0.06\t9\n0.07\t9\n0.08\t9\n0.09\t9\n0.10\t8\n0.11\t8\n0.12\t8\n0.13\t8\n0.14\t9\n0.15\t9\n0.16\t9\n0.17\t10\n0.18\t10\n0.19\t11\n0.20\t10\n0.21\t9\n0.22\t9\n0.23\t8\n0.24\t7\n0.25\t7\n0.26\t7\n0.27\t6\n0.29\t4\n0.32\t3\n0.33\t2\n0.36\t2\n0.38\t2\n0.41\t1\n0.45\t1\n0.55\t1\n\nOutput File Names: \ninfile_otu.0.01.unique.forest_pasture.shared.seqs\ninfile_otu.0.02.unique.forest_pasture.shared.seqs\ninfile_otu.0.03.unique.forest_pasture.shared.seqs\ninfile_otu.0.04.unique.forest_pasture.shared.seqs\ninfile_otu.0.05.unique.forest_pasture.shared.seqs\ninfile_otu.0.06.unique.forest_pasture.shared.seqs\ninfile_otu.0.07.unique.forest_pasture.shared.seqs\ninfile_otu.0.08.unique.forest_pasture.shared.seqs\ninfile_otu.0.09.unique.forest_pasture.shared.seqs\ninfile_otu.0.10.unique.forest_pasture.shared.seqs\ninfile_otu.0.11.unique.forest_pasture.shared.seqs\ninfile_otu.0.12.unique.forest_pasture.shared.seqs\ninfile_otu.0.13.unique.forest_pasture.shared.seqs\ninfile_otu.0.14.unique.forest_pasture.shared.seqs\ninfile_otu.0.15.unique.forest_pasture.shared.seqs\ninfile_otu.0.16.unique.forest_pasture.shared.seqs\ninfile_otu.0.17.unique.forest_pasture.shared.seqs\ninfile_otu.0.18.unique.forest_pasture.shared.seqs\ninfile_otu.0.19.unique.forest_pasture.shared.seqs\ninfile_otu.0.20.unique.forest_pasture.shared.seqs\ninfile_otu.0.21.unique.forest_pasture.shared.seqs\ninfile_otu.0.22.unique.forest_pasture.shared.seqs\ninfile_otu.0.23.unique.forest_pasture.shared.seqs\ninfile_otu.0.24.unique.forest_pasture.shared.seqs\ninfile_otu.0.25.unique.forest_pasture.shared.seqs\ninfile_otu.0.26.unique.forest_pasture.shared.seqs\ninfile_otu.0.27.unique.forest_pasture.shared.seqs\ninfile_otu.0.29.unique.forest_pasture.shared.seqs\ninfile_otu.0.32.unique.forest_pasture.shared.seqs\ninfile_otu.0.33.unique.forest_pasture.shared.seqs\ninfile_otu.0.36.unique.forest_pasture.shared.seqs\ninfile_otu.0.38.unique.forest_pasture.shared.seqs\ninfile_otu.0.41.unique.forest_pasture.shared.seqs\ninfile_otu.0.45.unique.forest_pasture.shared.seqs\ninfile_otu.0.55.unique.forest_pasture.shared.seqs\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1286.dat' infile_otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1287.dat' infile.group.dat && ln -s 'None' infile_fasta.dat && ln -s 'None' count_in.dat && echo 'get.sharedseqs( list=infile_otu.dat ,group=infile.group.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:41:01.432445", "params": {"output": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"group\": {\"values\": [{\"src\": \"hda\", \"id\": 1287}]}, \"intype\": \"in_listgroup\", \"seqsfrom\": {\"selection\": \"all\", \"__current_case__\": 2}, \"count_in\": null, \"label\": null, \"__current_case__\": 1, \"fasta\": null, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1286}]}}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "21859", "id": "ec3c9d08d9062ead", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_sharedseqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"infile\|seqsfrom\|groups": ["forest", "pasture"], "infile\|intype": "in_shared", "infile\|otu": {"src": "hda", "id": "702df83b8d383f91"}, "infile\|seqsfrom\|selection": "shared", "infile\|label": ["0.03", "0.33", "0.41"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "702df83b8d383f91", "uuid": "5f1cc371-ef50-4a1b-a8c9-5f0ddde4d111"}}, "update_time": "2018-02-08T17:41:26.288697", "tool_id": "mothur_get_sharedseqs", "outputs": {"__new_primary_file_0.41.forest_pasture\|0.33.forest_pasture__": {"src": "hda", "id": "54f6c1e83cddf017", "uuid": "7fc3b6d7-cb7e-4156-a9a4-c6db5eee51a6"}, "logfile": {"src": "hda", "id": "4520cfd618792d79", "uuid": "83f35ee5-b93d-4d5c-ada4-b251a4b542b2"}, "__new_primary_file_0.41.forest_pasture\|0.41.forest_pasture__": {"src": "hda", "id": "a47f21eee894769a", "uuid": "a2ea857a-c68b-47fc-8e4f-5617cbf4906b"}, "__new_primary_file_0.41.forest_pasture\|0.03.forest_pasture__": {"src": "hda", "id": "edbb972fe95b9ac8", "uuid": "7ac4d017-b073-481c-bce7-ec153444bc1f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.sharedseqs(shared=infile_otu.dat,label=0.03-0.33-0.41,sharedgroups= \rforest-pasture)\n0.03\t2\n0.33\t2\n0.41\t1\n\nOutput File Names: \ninfile_otu.0.03.forest_pasture.shared.seqs\ninfile_otu.0.33.forest_pasture.shared.seqs\ninfile_otu.0.41.forest_pasture.shared.seqs\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1324.dat' infile_otu.dat && echo 'get.sharedseqs( shared=infile_otu.dat ,label=0.03-0.33-0.41 ,sharedgroups=forest-pasture )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:41:23.089850", "params": {"output": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_shared\", \"seqsfrom\": {\"selection\": \"shared\", \"groups\": [\"forest\", \"pasture\"], \"__current_case__\": 1}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1324}]}, \"__current_case__\": 0, \"label\": [\"0.03\", \"0.33\", \"0.41\"]}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "21958", "id": "802ffc5c50268813", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_sharedseqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"infile\|seqsfrom\|groups": "pasture", "infile\|otu": {"src": "hda", "id": "c8023bd8606946c1"}, "infile\|seqsfrom\|selection": "unique", "infile\|intype": "in_shared"}, "job": {"inputs": {"otu": {"src": "hda", "id": "c8023bd8606946c1", "uuid": "9333bd68-810e-4038-a81c-69f6b19fe400"}}, "update_time": "2018-02-08T17:41:45.507774", "tool_id": "mothur_get_sharedseqs", "outputs": {"__new_primary_file_unique.unique.pasture\|0.02.unique.pasture__": {"src": "hda", "id": "3f577f2345e462ae", "uuid": "389726b7-6e66-4f21-af77-918c4fa800ff"}, "__new_primary_file_unique.unique.pasture\|0.17.unique.pasture__": {"src": "hda", "id": "1051479745a019c3", "uuid": "b6f6e2d2-8d64-4423-8ba4-de195b2e4b06"}, "__new_primary_file_unique.unique.pasture\|0.13.unique.pasture__": {"src": "hda", "id": "d1a9e52845840800", "uuid": "e77a422a-81af-41a8-8cda-c47a4601f4c9"}, "__new_primary_file_unique.unique.pasture\|0.16.unique.pasture__": {"src": "hda", "id": "58bf1d0ea28ad39d", "uuid": "6b9687e9-7b07-46af-8b56-7f0575751939"}, "__new_primary_file_unique.unique.pasture\|0.07.unique.pasture__": {"src": "hda", "id": "547dde384e3b6a29", "uuid": "b1a80092-fc04-4452-8809-59ed8dbc52b7"}, "__new_primary_file_unique.unique.pasture\|0.06.unique.pasture__": {"src": "hda", "id": "fcd56e94d175000a", "uuid": "84b9cd98-591f-4e49-b863-e9077d4387d3"}, "__new_primary_file_unique.unique.pasture\|0.32.unique.pasture__": {"src": "hda", "id": "b1f82c5e1406130e", "uuid": "949a768c-0f8b-469b-9593-eb1561dee43a"}, "__new_primary_file_unique.unique.pasture\|0.20.unique.pasture__": {"src": "hda", "id": "2dabc8e196f33f11", "uuid": "a5c54946-b5e3-466c-9679-5c2ea79bd37f"}, "__new_primary_file_unique.unique.pasture\|0.09.unique.pasture__": {"src": "hda", "id": "c08963815c2b5a83", "uuid": "a01509e5-9712-46e0-befa-b910588c5905"}, "__new_primary_file_unique.unique.pasture\|0.22.unique.pasture__": {"src": "hda", "id": "94f70b574060c9d1", "uuid": "ba88e709-5a51-43e1-b653-a65f901202f2"}, "__new_primary_file_unique.unique.pasture\|0.18.unique.pasture__": {"src": "hda", "id": "9099f171c3563201", "uuid": "f6e48820-b9a6-4452-bc86-a31e6a55c681"}, "__new_primary_file_unique.unique.pasture\|0.41.unique.pasture__": {"src": "hda", "id": "544cc4ca9245289d", "uuid": "4cd8cee7-bd99-43ce-b79f-09a58f6cee55"}, "__new_primary_file_unique.unique.pasture\|0.14.unique.pasture__": {"src": "hda", "id": "6038958fffcae8aa", "uuid": "be2077b6-7958-4ca9-bcd2-f7a8f8e874fc"}, "__new_primary_file_unique.unique.pasture\|0.12.unique.pasture__": {"src": "hda", "id": "cdf7e255cbf9ad98", "uuid": "1fdca5fb-0bb8-4b2f-9874-4960f3b23105"}, "__new_primary_file_unique.unique.pasture\|0.23.unique.pasture__": {"src": "hda", "id": "50ee543b25a9233d", "uuid": "d19028de-2f78-42bb-bf30-69fe847e1718"}, "__new_primary_file_unique.unique.pasture\|0.36.unique.pasture__": {"src": "hda", "id": "c5a46b89f297f5cc", "uuid": "d5d615f3-7ef5-48df-93b5-39dcc2af1e5e"}, "__new_primary_file_unique.unique.pasture\|unique.unique.pasture__": {"src": "hda", "id": "7e2564a05bcc37a3", "uuid": "adbcacd7-f625-44e8-aff6-c182a725a54b"}, "__new_primary_file_unique.unique.pasture\|0.29.unique.pasture__": {"src": "hda", "id": "eb329b1ce8fe2773", "uuid": "8cf75325-c1aa-4857-b009-74a8f25c8851"}, "__new_primary_file_unique.unique.pasture\|0.27.unique.pasture__": {"src": "hda", "id": "011d5380a212a555", "uuid": "dda5a7f8-54ff-48df-af64-3ff6130a0023"}, "__new_primary_file_unique.unique.pasture\|0.19.unique.pasture__": {"src": "hda", "id": "a77423a55da368e3", "uuid": "f1239609-5743-4c9f-9243-76c541bdb9bb"}, "__new_primary_file_unique.unique.pasture\|0.26.unique.pasture__": {"src": "hda", "id": "6261490a58dd5bd4", "uuid": "baa0b45e-cb4c-4929-ad1c-ffba063ccb02"}, "__new_primary_file_unique.unique.pasture\|0.15.unique.pasture__": {"src": "hda", "id": "3fe313b443859214", "uuid": "570ab633-d41d-48d8-9cf7-e771d2c3cc2f"}, "__new_primary_file_unique.unique.pasture\|0.04.unique.pasture__": {"src": "hda", "id": "0f4fd06d624bc101", "uuid": "bf126e7c-1646-461b-bc1d-3d83eff9a600"}, "__new_primary_file_unique.unique.pasture\|0.08.unique.pasture__": {"src": "hda", "id": "85e8ecefb7a860ea", "uuid": "17fbd0f3-46e0-488b-9961-937fea3cba44"}, "__new_primary_file_unique.unique.pasture\|0.24.unique.pasture__": {"src": "hda", "id": "371b51682aba3c7b", "uuid": "302f844f-f79f-4a42-b4e7-890e4d85bd45"}, "__new_primary_file_unique.unique.pasture\|0.01.unique.pasture__": {"src": "hda", "id": "efb1b99b3edb7343", "uuid": "f449d3c5-8b9e-45df-971b-0d1e6fd4e853"}, "__new_primary_file_unique.unique.pasture\|0.10.unique.pasture__": {"src": "hda", "id": "06eac525c92ec5de", "uuid": "0d13a28c-8c50-4d7f-8ebe-079ef9ec2874"}, "__new_primary_file_unique.unique.pasture\|0.11.unique.pasture__": {"src": "hda", "id": "85d8593222a5f623", "uuid": "a2ba2714-ae96-436e-86b7-c67e97c34670"}, "__new_primary_file_unique.unique.pasture\|0.21.unique.pasture__": {"src": "hda", "id": "7e35c6c406c695d9", "uuid": "7bcb4870-2a34-4170-98df-b02bcaffa8e3"}, "__new_primary_file_unique.unique.pasture\|0.33.unique.pasture__": {"src": "hda", "id": "c3a0cd9a34f8c4f4", "uuid": "1f85a875-70d0-4a38-84b6-ee7cfed4b764"}, "logfile": {"src": "hda", "id": "035475ec449588b1", "uuid": "2240c935-ca06-45ff-838f-8f41eef1319d"}, "__new_primary_file_unique.unique.pasture\|0.03.unique.pasture__": {"src": "hda", "id": "f70fd0893b00e2ab", "uuid": "7cb952af-0619-4a0f-afc4-9d1eb18a232c"}, "__new_primary_file_unique.unique.pasture\|0.38.unique.pasture__": {"src": "hda", "id": "491bfe2fea6003a3", "uuid": "122cae7c-aa29-4832-8ce7-3c4ebc850373"}, "__new_primary_file_unique.unique.pasture\|0.05.unique.pasture__": {"src": "hda", "id": "35f0f6185017fb1f", "uuid": "d0439572-964a-48e3-8d3e-e74ee882c6c2"}, "__new_primary_file_unique.unique.pasture\|0.25.unique.pasture__": {"src": "hda", "id": "d9e7f0348948aedc", "uuid": "ff32829c-1011-488f-ad52-8432f3ec5913"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.sharedseqs(shared=infile_otu.dat,uniquegroups=pasture)\nunique\t48\n0.01\t46\n0.02\t43\n0.03\t42\n0.04\t39\n0.05\t35\n0.06\t30\n0.07\t28\n0.08\t23\n0.09\t23\n0.10\t22\n0.11\t19\n0.12\t17\n0.13\t16\n0.14\t13\n0.15\t12\n0.16\t11\n0.17\t10\n0.18\t9\n0.19\t8\n0.20\t7\n0.21\t7\n0.22\t6\n0.23\t6\n0.24\t4\n0.25\t3\n0.26\t2\n0.27\t2\n0.29\t2\n0.32\t1\n0.33\t1\n0.36\t1\n0.38\t1\n0.41\t1\n0.45\t0 - No otus shared by groups pasture.\n0.55\t0 - No otus shared by groups pasture.\n\nOutput File Names: \ninfile_otu.unique.unique.pasture.shared.seqs\ninfile_otu.0.01.unique.pasture.shared.seqs\ninfile_otu.0.02.unique.pasture.shared.seqs\ninfile_otu.0.03.unique.pasture.shared.seqs\ninfile_otu.0.04.unique.pasture.shared.seqs\ninfile_otu.0.05.unique.pasture.shared.seqs\ninfile_otu.0.06.unique.pasture.shared.seqs\ninfile_otu.0.07.unique.pasture.shared.seqs\ninfile_otu.0.08.unique.pasture.shared.seqs\ninfile_otu.0.09.unique.pasture.shared.seqs\ninfile_otu.0.10.unique.pasture.shared.seqs\ninfile_otu.0.11.unique.pasture.shared.seqs\ninfile_otu.0.12.unique.pasture.shared.seqs\ninfile_otu.0.13.unique.pasture.shared.seqs\ninfile_otu.0.14.unique.pasture.shared.seqs\ninfile_otu.0.15.unique.pasture.shared.seqs\ninfile_otu.0.16.unique.pasture.shared.seqs\ninfile_otu.0.17.unique.pasture.shared.seqs\ninfile_otu.0.18.unique.pasture.shared.seqs\ninfile_otu.0.19.unique.pasture.shared.seqs\ninfile_otu.0.20.unique.pasture.shared.seqs\ninfile_otu.0.21.unique.pasture.shared.seqs\ninfile_otu.0.22.unique.pasture.shared.seqs\ninfile_otu.0.23.unique.pasture.shared.seqs\ninfile_otu.0.24.unique.pasture.shared.seqs\ninfile_otu.0.25.unique.pasture.shared.seqs\ninfile_otu.0.26.unique.pasture.shared.seqs\ninfile_otu.0.27.unique.pasture.shared.seqs\ninfile_otu.0.29.unique.pasture.shared.seqs\ninfile_otu.0.32.unique.pasture.shared.seqs\ninfile_otu.0.33.unique.pasture.shared.seqs\ninfile_otu.0.36.unique.pasture.shared.seqs\ninfile_otu.0.38.unique.pasture.shared.seqs\ninfile_otu.0.41.unique.pasture.shared.seqs\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1329.dat' infile_otu.dat && echo 'get.sharedseqs( shared=infile_otu.dat ,uniquegroups=pasture )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:41:40.469435", "params": {"output": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_shared\", \"seqsfrom\": {\"selection\": \"unique\", \"groups\": \"pasture\", \"__current_case__\": 0}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1329}]}, \"__current_case__\": 0, \"label\": null}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "22093", "id": "6cc323ea174af743", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_sharedseqs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"infile\|intype": "in_shared", "infile\|otu": {"src": "hda", "id": "b411495052c9266d"}, "output": "accnos"}, "job": {"inputs": {"otu": {"src": "hda", "id": "b411495052c9266d", "uuid": "7c6eb3c4-6f8d-4d18-9537-c10cfa1e409d"}}, "update_time": "2018-02-08T17:42:06.077218", "tool_id": "mothur_get_sharedseqs", "outputs": {"__new_primary_file_0.55.unique.forest_pasture\|0.01.unique.forest_pasture__": {"src": "hda", "id": "9d500f70f1832c83", "uuid": "ac9d5a45-2acb-46d5-b1f9-5e003ed19514"}, "__new_primary_file_0.55.unique.forest_pasture\|0.03.unique.forest_pasture__": {"src": "hda", "id": "c1f59ad8186b7258", "uuid": "e7996e0e-6d7b-408b-856d-41452e493a71"}, "__new_primary_file_0.55.unique.forest_pasture\|0.12.unique.forest_pasture__": {"src": "hda", "id": "38ac28315a9c1e7b", "uuid": "b1741da4-5466-4887-83be-ad3bc92a2f29"}, "__new_primary_file_0.55.unique.forest_pasture\|0.08.unique.forest_pasture__": {"src": "hda", "id": "48cc0123b280b7cb", "uuid": "22a4a8fe-eff7-4452-8a4e-230423b1bf66"}, "__new_primary_file_0.55.unique.forest_pasture\|0.36.unique.forest_pasture__": {"src": "hda", "id": "c0a3fdb58381b5de", "uuid": "8c5f4133-31e3-4bf6-8fbc-47df79c017e0"}, "__new_primary_file_0.55.unique.forest_pasture\|0.33.unique.forest_pasture__": {"src": "hda", "id": "8616db7f86b8b1fb", "uuid": "c4da094f-0bfc-4e51-a648-16d96bad383e"}, "__new_primary_file_0.55.unique.forest_pasture\|0.23.unique.forest_pasture__": {"src": "hda", "id": "0426db8ff8502d52", "uuid": "3f614b76-8d01-41d3-8f0f-43d0654f09c1"}, "__new_primary_file_0.55.unique.forest_pasture\|0.32.unique.forest_pasture__": {"src": "hda", "id": "df800ebdaa3024a1", "uuid": "1c15724b-6716-4d9a-8181-a56a0a8edf5d"}, "__new_primary_file_0.55.unique.forest_pasture\|0.06.unique.forest_pasture__": {"src": "hda", "id": "7c8b5be6333b2d1a", "uuid": "1ef15538-f50f-4ab3-8b25-a8a105d4218e"}, "__new_primary_file_0.55.unique.forest_pasture\|0.45.unique.forest_pasture__": {"src": "hda", "id": "ad0acee00d55703d", "uuid": "4dc1095b-f3a7-42bc-8062-13c9429b332f"}, "__new_primary_file_0.55.unique.forest_pasture\|0.38.unique.forest_pasture__": {"src": "hda", "id": "e9a3b80d63e9de81", "uuid": "be08a878-a184-4bdf-9a94-36c570cf0c83"}, "__new_primary_file_0.55.unique.forest_pasture\|0.04.unique.forest_pasture__": {"src": "hda", "id": "eb160ab98cd3f367", "uuid": "ad491664-70d2-44b4-87b0-a6c8a8a8c3ce"}, "__new_primary_file_0.55.unique.forest_pasture\|0.20.unique.forest_pasture__": {"src": "hda", "id": "f41ba0754147b197", "uuid": "7ded26bf-5321-4726-958d-2e47645beb8d"}, "__new_primary_file_0.55.unique.forest_pasture\|0.26.unique.forest_pasture__": {"src": "hda", "id": "354372befa8340f4", "uuid": "b4bd2385-535a-47b6-9a64-11a0d1ef2871"}, "__new_primary_file_0.55.unique.forest_pasture\|0.15.unique.forest_pasture__": {"src": "hda", "id": "51ebda391f6af4df", "uuid": "74879c3a-0dd0-4396-b425-74c4f3dabde6"}, "__new_primary_file_0.55.unique.forest_pasture\|0.02.unique.forest_pasture__": {"src": "hda", "id": "46d062e2f01a1ecb", "uuid": "10358e21-ef57-425f-b57a-558c9887ed3f"}, "__new_primary_file_0.55.unique.forest_pasture\|0.10.unique.forest_pasture__": {"src": "hda", "id": "5f8360fb2204373b", "uuid": "5a37fb75-d0bd-46bb-9201-feab6e8dd465"}, "__new_primary_file_0.55.unique.forest_pasture\|0.17.unique.forest_pasture__": {"src": "hda", "id": "7e220261cc1c0de1", "uuid": "a9f9bf84-5ffb-4fd0-a213-69fd1ef62f66"}, "__new_primary_file_0.55.unique.forest_pasture\|0.29.unique.forest_pasture__": {"src": "hda", "id": "9d600998684d58e9", "uuid": "8383c705-f2ee-4916-b05a-387552913311"}, "__new_primary_file_0.55.unique.forest_pasture\|0.09.unique.forest_pasture__": {"src": "hda", "id": "70c41ebe9fe356e1", "uuid": "a0b9b8e4-2ead-4664-ab22-5a26d0e10b87"}, "__new_primary_file_0.55.unique.forest_pasture\|0.22.unique.forest_pasture__": {"src": "hda", "id": "32d143676e069a01", "uuid": "4f54818c-c01b-425d-b9b1-c35bfb348cba"}, "__new_primary_file_0.55.unique.forest_pasture\|0.16.unique.forest_pasture__": {"src": "hda", "id": "93f6fc8df710787a", "uuid": "3387ece6-c5f5-4515-9ec5-a9af2c72187f"}, "__new_primary_file_0.55.unique.forest_pasture\|0.14.unique.forest_pasture__": {"src": "hda", "id": "0cc0680429283dfc", "uuid": "5efa1f57-520b-4118-9352-c5d7eb89081c"}, "__new_primary_file_0.55.unique.forest_pasture\|0.05.unique.forest_pasture__": {"src": "hda", "id": "a57ebb089e76dd90", "uuid": "f9c6e61e-1668-4453-965e-bc29da5bd541"}, "__new_primary_file_0.55.unique.forest_pasture\|0.19.unique.forest_pasture__": {"src": "hda", "id": "b0b67d4068ae0475", "uuid": "37dca42d-d112-48a6-b47e-fd2935922124"}, "__new_primary_file_0.55.unique.forest_pasture\|0.27.unique.forest_pasture__": {"src": "hda", "id": "1071ff2ef49f04a3", "uuid": "c22998ee-cf2d-40cd-aa75-e5eb706b811f"}, "__new_primary_file_0.55.unique.forest_pasture\|0.25.unique.forest_pasture__": {"src": "hda", "id": "8c1fbe4c8d09a4f1", "uuid": "591cca04-40ce-440c-871c-a56201b4b2fe"}, "__new_primary_file_0.55.unique.forest_pasture\|0.21.unique.forest_pasture__": {"src": "hda", "id": "bb747ea2094b72f9", "uuid": "ccee3ad4-dade-45eb-b50c-f1e52a66a5ba"}, "__new_primary_file_0.55.unique.forest_pasture\|0.11.unique.forest_pasture__": {"src": "hda", "id": "96ad708bb449c3ab", "uuid": "14d7a1e1-dff2-4cc7-b6de-e126d0799ba7"}, "__new_primary_file_0.55.unique.forest_pasture\|0.41.unique.forest_pasture__": {"src": "hda", "id": "26447d823670d91d", "uuid": "fafdd585-9a02-47f0-b77d-924961aa608f"}, "__new_primary_file_0.55.unique.forest_pasture\|0.13.unique.forest_pasture__": {"src": "hda", "id": "e4017c53abb4d64e", "uuid": "3b1bb461-c82b-48b9-8244-6dbb7e580786"}, "__new_primary_file_0.55.unique.forest_pasture\|0.55.unique.forest_pasture__": {"src": "hda", "id": "461a1be07c3de467", "uuid": "4205bfbb-e0f6-4c3d-a99b-010ad75aa6a7"}, "logfile": {"src": "hda", "id": "c800ba3fbc6b74ec", "uuid": "be48e703-21fe-4856-ab8f-8ca6a45c7695"}, "__new_primary_file_0.55.unique.forest_pasture\|0.24.unique.forest_pasture__": {"src": "hda", "id": "d65b4a99cdfc8e57", "uuid": "60d7e552-e4e2-414d-8bc3-1a6c30e518c9"}, "__new_primary_file_0.55.unique.forest_pasture\|0.07.unique.forest_pasture__": {"src": "hda", "id": "fe0fc1f57508fe50", "uuid": "9b88c871-293e-4e8f-a1e7-1487e70e943e"}, "__new_primary_file_0.55.unique.forest_pasture\|0.18.unique.forest_pasture__": {"src": "hda", "id": "f74cebaa6e844ba8", "uuid": "48485671-082f-47e6-bff4-267b328a813c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.sharedseqs(shared=infile_otu.dat,output=accnos)\nunique\t0 - No otus shared by groups forest pasture.\n0.01\t1\n0.02\t1\n0.03\t2\n0.04\t4\n0.05\t7\n0.06\t9\n0.07\t9\n0.08\t9\n0.09\t9\n0.10\t8\n0.11\t8\n0.12\t8\n0.13\t8\n0.14\t9\n0.15\t9\n0.16\t9\n0.17\t10\n0.18\t10\n0.19\t11\n0.20\t10\n0.21\t9\n0.22\t9\n0.23\t8\n0.24\t7\n0.25\t7\n0.26\t7\n0.27\t6\n0.29\t4\n0.32\t3\n0.33\t2\n0.36\t2\n0.38\t2\n0.41\t1\n0.45\t1\n0.55\t1\n\nOutput File Names: \ninfile_otu.0.01.unique.forest_pasture.accnos\ninfile_otu.0.02.unique.forest_pasture.accnos\ninfile_otu.0.03.unique.forest_pasture.accnos\ninfile_otu.0.04.unique.forest_pasture.accnos\ninfile_otu.0.05.unique.forest_pasture.accnos\ninfile_otu.0.06.unique.forest_pasture.accnos\ninfile_otu.0.07.unique.forest_pasture.accnos\ninfile_otu.0.08.unique.forest_pasture.accnos\ninfile_otu.0.09.unique.forest_pasture.accnos\ninfile_otu.0.10.unique.forest_pasture.accnos\ninfile_otu.0.11.unique.forest_pasture.accnos\ninfile_otu.0.12.unique.forest_pasture.accnos\ninfile_otu.0.13.unique.forest_pasture.accnos\ninfile_otu.0.14.unique.forest_pasture.accnos\ninfile_otu.0.15.unique.forest_pasture.accnos\ninfile_otu.0.16.unique.forest_pasture.accnos\ninfile_otu.0.17.unique.forest_pasture.accnos\ninfile_otu.0.18.unique.forest_pasture.accnos\ninfile_otu.0.19.unique.forest_pasture.accnos\ninfile_otu.0.20.unique.forest_pasture.accnos\ninfile_otu.0.21.unique.forest_pasture.accnos\ninfile_otu.0.22.unique.forest_pasture.accnos\ninfile_otu.0.23.unique.forest_pasture.accnos\ninfile_otu.0.24.unique.forest_pasture.accnos\ninfile_otu.0.25.unique.forest_pasture.accnos\ninfile_otu.0.26.unique.forest_pasture.accnos\ninfile_otu.0.27.unique.forest_pasture.accnos\ninfile_otu.0.29.unique.forest_pasture.accnos\ninfile_otu.0.32.unique.forest_pasture.accnos\ninfile_otu.0.33.unique.forest_pasture.accnos\ninfile_otu.0.36.unique.forest_pasture.accnos\ninfile_otu.0.38.unique.forest_pasture.accnos\ninfile_otu.0.41.unique.forest_pasture.accnos\ninfile_otu.0.45.unique.forest_pasture.accnos\ninfile_otu.0.55.unique.forest_pasture.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1365.dat' infile_otu.dat && echo 'get.sharedseqs( shared=infile_otu.dat ,output=accnos )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:42:01.270327", "params": {"output": "\"accnos\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_shared\", \"seqsfrom\": {\"selection\": \"all\", \"__current_case__\": 2}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1365}]}, \"__current_case__\": 0, \"label\": null}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "22238", "id": "af2b33d2c4a65f6c", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_sharedseqs.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"infile\|intype": "in_listgroup", "infile\|otu": {"src": "hda", "id": "8d91fc817c607b8e"}, "infile\|fasta": {"src": "hda", "id": "a6f3a03f0bffe083"}, "infile\|group": {"src": "hda", "id": "52f04961369d0fd2"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "a6f3a03f0bffe083", "uuid": "2d9a27af-6077-4f21-9097-f6a9501d960c"}, "group": {"src": "hda", "id": "52f04961369d0fd2", "uuid": "fb77b6ff-8d4f-482a-87b1-bd2181197a17"}, "otu": {"src": "hda", "id": "8d91fc817c607b8e", "uuid": "76253355-c762-48e0-a725-f01d3acd4785"}}, "update_time": "2018-02-08T17:42:37.685956", "tool_id": "mothur_get_sharedseqs", "outputs": {"__new_primary_file_0.55.unique.forest_pasture\|0.01.unique.forest_pasture__": {"src": "hda", "id": "511e5219be7d6707", "uuid": "b75edb7a-a1a7-46fa-8bd9-5b6c7f94ad1f"}, "__new_primary_file_0.55.unique.forest_pasture\|0.03.unique.forest_pasture__": {"src": "hda", "id": "495f4784edb27bdf", "uuid": "0c2d0402-2f9a-43f9-ba87-40b8214ae564"}, "__new_primary_file_0.55.unique.forest_pasture\|0.12.unique.forest_pasture__": {"src": "hda", "id": "9591777882159fea", "uuid": "028d0537-b9ab-4a69-93fc-0c8c44a0b8bf"}, "__new_primary_file_0.55.unique.forest_pasture\|0.08.unique.forest_pasture__": {"src": "hda", "id": "6a717f18c0f373ef", "uuid": "16d90ea0-5922-4de6-a4d0-c81d4db1ad43"}, "__new_primary_file_0.55.unique.forest_pasture\|0.36.unique.forest_pasture__": {"src": "hda", "id": "b4da54e0b157a0e8", "uuid": "a3762dc8-b855-4b87-bdac-ea10ce2b12cd"}, "__new_primary_file_0.55.unique.forest_pasture\|0.33.unique.forest_pasture__": {"src": "hda", "id": "dbe0036ded1c1b07", "uuid": "79bbcc76-86f5-4afd-9e61-57fc3a8fb811"}, "__new_primary_file_0.55.unique.forest_pasture\|0.23.unique.forest_pasture__": {"src": "hda", "id": "f6c1555750ef1ba5", "uuid": "19f1c7c2-ec2f-46c7-93da-845760389a1f"}, "__new_primary_file_0.55.unique.forest_pasture\|0.32.unique.forest_pasture__": {"src": "hda", "id": "8701122ca649ef0e", "uuid": "fa3abfc6-e430-459f-b80b-45f289b43b73"}, "__new_primary_file_0.55.unique.forest_pasture\|0.06.unique.forest_pasture__": {"src": "hda", "id": "c1456ecfdc824977", "uuid": "16b1c6bc-df83-4831-acf1-bab966123e0c"}, "__new_primary_file_0.55.unique.forest_pasture\|0.45.unique.forest_pasture__": {"src": "hda", "id": "00a57718e499b089", "uuid": "34e53b49-a4f9-4760-8212-a8a75c95d923"}, "__new_primary_file_0.55.unique.forest_pasture\|0.38.unique.forest_pasture__": {"src": "hda", "id": "bbd0b9f57a884d99", "uuid": "447bac35-36b3-4950-aa8a-92281792870d"}, "__new_primary_file_0.55.unique.forest_pasture\|0.04.unique.forest_pasture__": {"src": "hda", "id": "db9feb02278bde1e", "uuid": "eff3a8da-9526-4a5c-9006-a4534adc087f"}, "__new_primary_file_0.55.unique.forest_pasture\|0.20.unique.forest_pasture__": {"src": "hda", "id": "a0b6b71fdb91e8d6", "uuid": "07d2fd80-4a5a-4b71-a109-418ada75f9b0"}, "__new_primary_file_0.55.unique.forest_pasture\|0.26.unique.forest_pasture__": {"src": "hda", "id": "fdc43dbaf89861e9", "uuid": "d9913622-9724-4e7a-a258-71e4b51d7e74"}, "__new_primary_file_0.55.unique.forest_pasture\|0.15.unique.forest_pasture__": {"src": "hda", "id": "818a1a9068d181a2", "uuid": "0e930c59-88a7-4170-9b62-baeb973ba3d2"}, "__new_primary_file_0.55.unique.forest_pasture\|0.02.unique.forest_pasture__": {"src": "hda", "id": "c192547d733b6f1c", "uuid": "1e0d0127-6b96-4f83-b731-a68c42755eb2"}, "__new_primary_file_0.55.unique.forest_pasture\|0.10.unique.forest_pasture__": {"src": "hda", "id": "68ce0d2a7fd661e7", "uuid": "3a586980-5f0e-4267-afcb-cdb1ff68ac90"}, "__new_primary_file_0.55.unique.forest_pasture\|0.17.unique.forest_pasture__": {"src": "hda", "id": "a4f459b907c399cc", "uuid": "81125254-4e5c-4a19-b1d9-ac782b94a317"}, "__new_primary_file_0.55.unique.forest_pasture\|0.29.unique.forest_pasture__": {"src": "hda", "id": "19ae04e79b51d442", "uuid": "8bf52cda-02f4-4749-b29f-a3487c96dc6b"}, "__new_primary_file_0.55.unique.forest_pasture\|0.09.unique.forest_pasture__": {"src": "hda", "id": "5d27d481e44c798e", "uuid": "3f7e8f14-2bf7-4ecc-92bb-38830620303a"}, "__new_primary_file_0.55.unique.forest_pasture\|0.22.unique.forest_pasture__": {"src": "hda", "id": "dea178949647e385", "uuid": "c2bb8d24-ef0e-4f4d-b41c-9ec355fb161c"}, "__new_primary_file_0.55.unique.forest_pasture\|0.16.unique.forest_pasture__": {"src": "hda", "id": "60abf49d2417a732", "uuid": "5ab2df46-7bf9-48cd-9f2a-8235c07b4ece"}, "__new_primary_file_0.55.unique.forest_pasture\|0.14.unique.forest_pasture__": {"src": "hda", "id": "df7b712664e24f20", "uuid": "57cdb709-5dc3-4c57-9f22-724485952ec1"}, "__new_primary_file_0.55.unique.forest_pasture\|0.05.unique.forest_pasture__": {"src": "hda", "id": "d4dc7f05ea35c530", "uuid": "511277c8-c696-4c57-9596-32ff3df816a5"}, "__new_primary_file_0.55.unique.forest_pasture\|0.19.unique.forest_pasture__": {"src": "hda", "id": "600dc09e02076335", "uuid": "0d6d7fc0-6d50-40ff-a8e1-0a416fe81103"}, "__new_primary_file_0.55.unique.forest_pasture\|0.27.unique.forest_pasture__": {"src": "hda", "id": "eec4effe5fe2e4fa", "uuid": "cc5bf893-19a5-4af9-a3b1-4d5be8a84477"}, "__new_primary_file_0.55.unique.forest_pasture\|0.25.unique.forest_pasture__": {"src": "hda", "id": "694ae81ce1930e68", "uuid": "b5e2809c-a837-4e87-b2f7-0a3f5068ac37"}, "__new_primary_file_0.55.unique.forest_pasture\|0.21.unique.forest_pasture__": {"src": "hda", "id": "7106c2d6deef3cfa", "uuid": "c3816365-54f1-46f7-b523-60785a851f05"}, "__new_primary_file_0.55.unique.forest_pasture\|0.11.unique.forest_pasture__": {"src": "hda", "id": "37d3583ea310e337", "uuid": "2df63967-e61b-4b07-bb20-49fa9aa30f17"}, "__new_primary_file_0.55.unique.forest_pasture\|0.41.unique.forest_pasture__": {"src": "hda", "id": "eafabd3a383ab29e", "uuid": "63045926-44cb-495f-b9fb-f5a3e2851045"}, "__new_primary_file_0.55.unique.forest_pasture\|0.13.unique.forest_pasture__": {"src": "hda", "id": "48b1ebf5a933ed38", "uuid": "90e6083a-29ca-49e2-b0c2-b0df7d244195"}, "__new_primary_file_0.55.unique.forest_pasture\|0.55.unique.forest_pasture__": {"src": "hda", "id": "cca6a764eaebccae", "uuid": "c04f97c4-be79-4d23-8380-e93ffe77f2a1"}, "logfile": {"src": "hda", "id": "739c965d51d75f3b", "uuid": "7863b87c-b2fe-429e-920d-4a3da20c400b"}, "__new_primary_file_0.55.unique.forest_pasture\|0.24.unique.forest_pasture__": {"src": "hda", "id": "d759666b93a781e8", "uuid": "1ac20ea6-2a85-40e0-a743-1046218a57e4"}, "__new_primary_file_0.55.unique.forest_pasture\|0.07.unique.forest_pasture__": {"src": "hda", "id": "e6e0520fd65a4854", "uuid": "d18d49ee-df35-44b8-be0e-d19c51c750e8"}, "__new_primary_file_0.55.unique.forest_pasture\|0.18.unique.forest_pasture__": {"src": "hda", "id": "e3d16ba9dbc1647b", "uuid": "6f753123-ea6c-4c27-8326-f26036a39360"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.sharedseqs(list=infile_otu.dat,group=infile.group.dat,fasta=infile_ \rfasta.dat)\nunique\t0 - No otus shared by groups forest pasture.\n0.01\t1\n0.02\t1\n0.03\t2\n0.04\t4\n0.05\t7\n0.06\t9\n0.07\t9\n0.08\t9\n0.09\t9\n0.10\t8\n0.11\t8\n0.12\t8\n0.13\t8\n0.14\t9\n0.15\t9\n0.16\t9\n0.17\t10\n0.18\t10\n0.19\t11\n0.20\t10\n0.21\t9\n0.22\t9\n0.23\t8\n0.24\t7\n0.25\t7\n0.26\t7\n0.27\t6\n0.29\t4\n0.32\t3\n0.33\t2\n0.36\t2\n0.38\t2\n0.41\t1\n0.45\t1\n0.55\t1\n\nOutput File Names: \ninfile_otu.0.01.unique.forest_pasture.shared.seqs\ninfile_fasta.0.01.unique.forest_pasture.shared.fasta\ninfile_otu.0.02.unique.forest_pasture.shared.seqs\ninfile_fasta.0.02.unique.forest_pasture.shared.fasta\ninfile_otu.0.03.unique.forest_pasture.shared.seqs\ninfile_fasta.0.03.unique.forest_pasture.shared.fasta\ninfile_otu.0.04.unique.forest_pasture.shared.seqs\ninfile_fasta.0.04.unique.forest_pasture.shared.fasta\ninfile_otu.0.05.unique.forest_pasture.shared.seqs\ninfile_fasta.0.05.unique.forest_pasture.shared.fasta\ninfile_otu.0.06.unique.forest_pasture.shared.seqs\ninfile_fasta.0.06.unique.forest_pasture.shared.fasta\ninfile_otu.0.07.unique.forest_pasture.shared.seqs\ninfile_fasta.0.07.unique.forest_pasture.shared.fasta\ninfile_otu.0.08.unique.forest_pasture.shared.seqs\ninfile_fasta.0.08.unique.forest_pasture.shared.fasta\ninfile_otu.0.09.unique.forest_pasture.shared.seqs\ninfile_fasta.0.09.unique.forest_pasture.shared.fasta\ninfile_otu.0.10.unique.forest_pasture.shared.seqs\ninfile_fasta.0.10.unique.forest_pasture.shared.fasta\ninfile_otu.0.11.unique.forest_pasture.shared.seqs\ninfile_fasta.0.11.unique.forest_pasture.shared.fasta\ninfile_otu.0.12.unique.forest_pasture.shared.seqs\ninfile_fasta.0.12.unique.forest_pasture.shared.fasta\ninfile_otu.0.13.unique.forest_pasture.shared.seqs\ninfile_fasta.0.13.unique.forest_pasture.shared.fasta\ninfile_otu.0.14.unique.forest_pasture.shared.seqs\ninfile_fasta.0.14.unique.forest_pasture.shared.fasta\ninfile_otu.0.15.unique.forest_pasture.shared.seqs\ninfile_fasta.0.15.unique.forest_pasture.shared.fasta\ninfile_otu.0.16.unique.forest_pasture.shared.seqs\ninfile_fasta.0.16.unique.forest_pasture.shared.fasta\ninfile_otu.0.17.unique.forest_pasture.shared.seqs\ninfile_fasta.0.17.unique.forest_pasture.shared.fasta\ninfile_otu.0.18.unique.forest_pasture.shared.seqs\ninfile_fasta.0.18.unique.forest_pasture.shared.fasta\ninfile_otu.0.19.unique.forest_pasture.shared.seqs\ninfile_fasta.0.19.unique.forest_pasture.shared.fasta\ninfile_otu.0.20.unique.forest_pasture.shared.seqs\ninfile_fasta.0.20.unique.forest_pasture.shared.fasta\ninfile_otu.0.21.unique.forest_pasture.shared.seqs\ninfile_fasta.0.21.unique.forest_pasture.shared.fasta\ninfile_otu.0.22.unique.forest_pasture.shared.seqs\ninfile_fasta.0.22.unique.forest_pasture.shared.fasta\ninfile_otu.0.23.unique.forest_pasture.shared.seqs\ninfile_fasta.0.23.unique.forest_pasture.shared.fasta\ninfile_otu.0.24.unique.forest_pasture.shared.seqs\ninfile_fasta.0.24.unique.forest_pasture.shared.fasta\ninfile_otu.0.25.unique.forest_pasture.shared.seqs\ninfile_fasta.0.25.unique.forest_pasture.shared.fasta\ninfile_otu.0.26.unique.forest_pasture.shared.seqs\ninfile_fasta.0.26.unique.forest_pasture.shared.fasta\ninfile_otu.0.27.unique.forest_pasture.shared.seqs\ninfile_fasta.0.27.unique.forest_pasture.shared.fasta\ninfile_otu.0.29.unique.forest_pasture.shared.seqs\ninfile_fasta.0.29.unique.forest_pasture.shared.fasta\ninfile_otu.0.32.unique.forest_pasture.shared.seqs\ninfile_fasta.0.32.unique.forest_pasture.shared.fasta\ninfile_otu.0.33.unique.forest_pasture.shared.seqs\ninfile_fasta.0.33.unique.forest_pasture.shared.fasta\ninfile_otu.0.36.unique.forest_pasture.shared.seqs\ninfile_fasta.0.36.unique.forest_pasture.shared.fasta\ninfile_otu.0.38.unique.forest_pasture.shared.seqs\ninfile_fasta.0.38.unique.forest_pasture.shared.fasta\ninfile_otu.0.41.unique.forest_pasture.shared.seqs\ninfile_fasta.0.41.unique.forest_pasture.shared.fasta\ninfile_otu.0.45.unique.forest_pasture.shared.seqs\ninfile_fasta.0.45.unique.forest_pasture.shared.fasta\ninfile_otu.0.55.unique.forest_pasture.shared.seqs\ninfile_fasta.0.55.unique.forest_pasture.shared.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1402.dat' infile_otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1403.dat' infile.group.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1404.dat' infile_fasta.dat && ln -s 'None' count_in.dat && echo 'get.sharedseqs( list=infile_otu.dat ,group=infile.group.dat ,fasta=infile_fasta.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:42:29.966838", "params": {"output": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"group\": {\"values\": [{\"src\": \"hda\", \"id\": 1403}]}, \"intype\": \"in_listgroup\", \"seqsfrom\": {\"selection\": \"all\", \"__current_case__\": 2}, \"count_in\": null, \"label\": null, \"__current_case__\": 1, \"fasta\": {\"values\": [{\"src\": \"hda\", \"id\": 1404}]}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1402}]}}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "22500", "id": "721a73f13e9921b7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_sharedseqs.test_tool_000005", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|has_groups": "no", "input\|otu": {"src": "hda", "id": "5aa4434a5de39ae3"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "5aa4434a5de39ae3", "uuid": "3fad1be5-92c7-499a-ad97-4df17029bb79"}}, "update_time": "2018-02-08T17:43:07.439864", "tool_id": "mothur_heatmap_bin", "outputs": {"__new_primary_file_unique.heatmap\|0.12.heatmap__": {"src": "hda", "id": "3736958d98c85038", "uuid": "a4133262-f568-437b-ae4f-0da9fcdc8592"}, "__new_primary_file_unique.heatmap\|0.16.heatmap__": {"src": "hda", "id": "1d7e16e67c25e161", "uuid": "fdd59c4f-5407-4ed2-8d14-3e1fac5c483a"}, "__new_primary_file_unique.heatmap\|0.19.heatmap__": {"src": "hda", "id": "8d3b08d9b3af5f9c", "uuid": "0936eae7-66f4-4c4d-9b32-6a9ecc1ceb1b"}, "__new_primary_file_unique.heatmap\|0.17.heatmap__": {"src": "hda", "id": "470eb1f9703ec6ce", "uuid": "ed2b8799-1815-42b9-996e-a99acc109c9a"}, "__new_primary_file_unique.heatmap\|0.15.heatmap__": {"src": "hda", "id": "f122c84b34480f3c", "uuid": "5b37b1a5-8639-4277-a8d7-e41cef4802b5"}, "__new_primary_file_unique.heatmap\|0.04.heatmap__": {"src": "hda", "id": "191aad2a235a14a2", "uuid": "1955e26c-38f5-4edb-9875-4bf51ee8342c"}, "__new_primary_file_unique.heatmap\|0.38.heatmap__": {"src": "hda", "id": "628d782395597178", "uuid": "cfa9705a-42a7-49f9-a6b8-eeda2fbf9a7d"}, "__new_primary_file_unique.heatmap\|0.08.heatmap__": {"src": "hda", "id": "366694fb7dd8b44f", "uuid": "b38393d5-0012-44bf-87e5-0aa6e0ebe15d"}, "__new_primary_file_unique.heatmap\|unique.heatmap__": {"src": "hda", "id": "8c18965d948ad2eb", "uuid": "60e0ce24-ffa5-4839-a210-6b1bf86df3f0"}, "__new_primary_file_unique.heatmap\|0.03.heatmap__": {"src": "hda", "id": "df6c40d10f33a9c4", "uuid": "2479c797-9034-4618-aa53-3c362bfb967b"}, "__new_primary_file_unique.heatmap\|0.05.heatmap__": {"src": "hda", "id": "fa1197388b314251", "uuid": "d249805c-a8b5-4ad7-94e5-6a31ed6955d9"}, "__new_primary_file_unique.heatmap\|0.33.heatmap__": {"src": "hda", "id": "567a86d1273a635a", "uuid": "49e3f568-909e-4cde-843e-76d6e45160eb"}, "__new_primary_file_unique.heatmap\|0.55.heatmap__": {"src": "hda", "id": "3dcdd65bc248798d", "uuid": "aa8e807a-e12a-4d81-ad9b-44d357fdf341"}, "__new_primary_file_unique.heatmap\|0.25.heatmap__": {"src": "hda", "id": "80a31c7cff5bc197", "uuid": "6a95e2a7-00ad-4cca-85fa-7b81c163a913"}, "__new_primary_file_unique.heatmap\|0.18.heatmap__": {"src": "hda", "id": "e2e89d7da5281839", "uuid": "d1514716-4259-4a64-b1dd-5c25fafd4840"}, "__new_primary_file_unique.heatmap\|0.09.heatmap__": {"src": "hda", "id": "2daeae546a05fdec", "uuid": "062f23d1-8d05-42f6-80b3-814a5becc446"}, "__new_primary_file_unique.heatmap\|0.22.heatmap__": {"src": "hda", "id": "b9010d0fbfd5e1f7", "uuid": "0eb1d487-49d3-4765-aede-99028c87eb25"}, "__new_primary_file_unique.heatmap\|0.45.heatmap__": {"src": "hda", "id": "0ff6ef528fac88f3", "uuid": "19750f5c-20b0-4b56-8c88-233ed11b9cb0"}, "__new_primary_file_unique.heatmap\|0.29.heatmap__": {"src": "hda", "id": "8b81c0162ce5557e", "uuid": "05a40fec-e894-49da-9985-93ef305650dd"}, "__new_primary_file_unique.heatmap\|0.06.heatmap__": {"src": "hda", "id": "349e07445c4e628f", "uuid": "de68102a-f9cc-444d-91a9-01493c828eb8"}, "__new_primary_file_unique.heatmap\|0.23.heatmap__": {"src": "hda", "id": "bdd6007a61f34fac", "uuid": "7596babd-1026-4a65-ba1a-686ee58ee90c"}, "__new_primary_file_unique.heatmap\|0.01.heatmap__": {"src": "hda", "id": "43f1006025db5fee", "uuid": "e30e539b-e9a3-4679-b312-b8a7d9cbf0ac"}, "__new_primary_file_unique.heatmap\|0.20.heatmap__": {"src": "hda", "id": "b47c5be399df737a", "uuid": "889338cc-898b-4c1b-9b56-7f4b8e8dfe4c"}, "__new_primary_file_unique.heatmap\|0.41.heatmap__": {"src": "hda", "id": "fdeb460c0475206a", "uuid": "0175d58e-1ff2-4bc5-bd9a-43ffde415d18"}, "__new_primary_file_unique.heatmap\|0.02.heatmap__": {"src": "hda", "id": "dd82c12810a978c9", "uuid": "0162abb7-41c1-4785-9bf5-a460d3c66373"}, "__new_primary_file_unique.heatmap\|0.13.heatmap__": {"src": "hda", "id": "012f7b1e3f7879e3", "uuid": "16ce423b-1008-4ec2-91ac-f045cb5a5abd"}, "__new_primary_file_unique.heatmap\|0.24.heatmap__": {"src": "hda", "id": "51e1e30118f27d1d", "uuid": "aa7d5d3a-c8e7-4637-9506-f5dc4713625d"}, "__new_primary_file_unique.heatmap\|0.26.heatmap__": {"src": "hda", "id": "46d5d629e90b7c88", "uuid": "c4d18a20-3db4-4990-b571-659cb5f67d2b"}, "__new_primary_file_unique.heatmap\|0.07.heatmap__": {"src": "hda", "id": "91a333426dbcec14", "uuid": "db8c22f8-2c63-45f5-bcf5-e8666607e632"}, "logfile": {"src": "hda", "id": "ef02fd8e80dbdfd0", "uuid": "aa179a93-b92f-4b4b-9123-4e1e6ab34654"}, "__new_primary_file_unique.heatmap\|0.36.heatmap__": {"src": "hda", "id": "54e503415a2c0682", "uuid": "d217e5c4-2c11-4de9-ac5e-3cf61b04e274"}, "__new_primary_file_unique.heatmap\|0.21.heatmap__": {"src": "hda", "id": "4900c210ae216634", "uuid": "84df347a-bca2-47af-8a5c-8dda81faf549"}, "__new_primary_file_unique.heatmap\|0.27.heatmap__": {"src": "hda", "id": "896ea37ce7a39150", "uuid": "53367c7d-546e-4f64-b0d8-d45f2cea1880"}, "__new_primary_file_unique.heatmap\|0.32.heatmap__": {"src": "hda", "id": "cf000b2b198e45cc", "uuid": "f69d2d62-be86-42bf-9de8-5485a3fa524d"}, "__new_primary_file_unique.heatmap\|0.10.heatmap__": {"src": "hda", "id": "4ab6b94dd0ff726f", "uuid": "b5e27a95-bea7-4c09-972c-0df95a595e53"}, "__new_primary_file_unique.heatmap\|0.11.heatmap__": {"src": "hda", "id": "c2eb533b1a115fca", "uuid": "09275784-5714-4597-9aac-4a47deffee64"}, "__new_primary_file_unique.heatmap\|0.14.heatmap__": {"src": "hda", "id": "f991b410e4f25497", "uuid": "6cf90f48-02ed-4ec4-aa8f-2ecb520549c0"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > heatmap.bin(list=input_otu.dat,scale=log10,sorted=shared,numotu=0,fonts \rize=24)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu.unique.heatmap.bin.svg\ninput_otu.0.01.heatmap.bin.svg\ninput_otu.0.02.heatmap.bin.svg\ninput_otu.0.03.heatmap.bin.svg\ninput_otu.0.04.heatmap.bin.svg\ninput_otu.0.05.heatmap.bin.svg\ninput_otu.0.06.heatmap.bin.svg\ninput_otu.0.07.heatmap.bin.svg\ninput_otu.0.08.heatmap.bin.svg\ninput_otu.0.09.heatmap.bin.svg\ninput_otu.0.10.heatmap.bin.svg\ninput_otu.0.11.heatmap.bin.svg\ninput_otu.0.12.heatmap.bin.svg\ninput_otu.0.13.heatmap.bin.svg\ninput_otu.0.14.heatmap.bin.svg\ninput_otu.0.15.heatmap.bin.svg\ninput_otu.0.16.heatmap.bin.svg\ninput_otu.0.17.heatmap.bin.svg\ninput_otu.0.18.heatmap.bin.svg\ninput_otu.0.19.heatmap.bin.svg\ninput_otu.0.20.heatmap.bin.svg\ninput_otu.0.21.heatmap.bin.svg\ninput_otu.0.22.heatmap.bin.svg\ninput_otu.0.23.heatmap.bin.svg\ninput_otu.0.24.heatmap.bin.svg\ninput_otu.0.25.heatmap.bin.svg\ninput_otu.0.26.heatmap.bin.svg\ninput_otu.0.27.heatmap.bin.svg\ninput_otu.0.29.heatmap.bin.svg\ninput_otu.0.32.heatmap.bin.svg\ninput_otu.0.33.heatmap.bin.svg\ninput_otu.0.36.heatmap.bin.svg\ninput_otu.0.38.heatmap.bin.svg\ninput_otu.0.41.heatmap.bin.svg\ninput_otu.0.45.heatmap.bin.svg\ninput_otu.0.55.heatmap.bin.svg\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1476.dat' input_otu.dat && echo 'heatmap.bin( list=input_otu.dat, scale=log10, sorted=shared, numotu=0, fontsize=24 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:43:02.760839", "params": {"scale": "\"log10\"", "numotu": "\"0\"", "dbkey": "\"hg17\"", "fontsize": "\"24\"", "input": "{\"label\": null, \"has_groups\": \"no\", \"__current_case__\": 0, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1476}]}}", "sorted": "\"shared\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "22663", "id": "943b175492f370d8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_heatmap_bin.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|label": "0.26", "input\|has_groups": "yes", "input\|groups": "forest", "input\|otu": {"src": "hda", "id": "1d330b92b21a7ce0"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "1d330b92b21a7ce0", "uuid": "69cae532-4ced-4046-9a3b-44ccc865523d"}}, "update_time": "2018-02-08T17:43:21.076293", "tool_id": "mothur_heatmap_bin", "outputs": {"__new_primary_file_0.26.heatmap\|0.26.heatmap__": {"src": "hda", "id": "f381faf65e5272fe", "uuid": "52ee9e76-a05d-4262-a98c-53120394753d"}, "logfile": {"src": "hda", "id": "f2f802538148d8ec", "uuid": "cafa5f29-4a43-4d35-8911-c2515cd598bc"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > heatmap.bin(relabund=input_otu.dat,groups=forest,label=0.26,scale=log10 \r,sorted=shared,numotu=0,fontsize=24)\n0.26\n\nOutput File Names: \ninput_otu.0.26.heatmap.bin.svg\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1514.dat' input_otu.dat && echo 'heatmap.bin( relabund=input_otu.dat, groups=forest, label=0.26, scale=log10, sorted=shared, numotu=0, fontsize=24 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:43:17.969781", "params": {"scale": "\"log10\"", "numotu": "\"0\"", "dbkey": "\"hg17\"", "fontsize": "\"24\"", "input": "{\"groups\": \"forest\", \"label\": \"0.26\", \"has_groups\": \"yes\", \"__current_case__\": 1, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1514}]}}", "sorted": "\"shared\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "22755", "id": "4b36d8f744e89cdc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_heatmap_bin.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"scale": "linear", "input\|groups": ["forest", "pasture"], "input\|label": ["0.03", "0.26", "0.55"], "input\|otu": {"src": "hda", "id": "838bdf0d25da8928"}, "fontsize": "100", "input\|has_groups": "yes", "sorted": "none"}, "job": {"inputs": {"otu": {"src": "hda", "id": "838bdf0d25da8928", "uuid": "a08df5d6-0bf7-453b-9dcd-797fff213c07"}}, "update_time": "2018-02-08T17:43:33.535279", "tool_id": "mothur_heatmap_bin", "outputs": {"__new_primary_file_0.55.heatmap\|0.03.heatmap__": {"src": "hda", "id": "b56e6f3aa0b63b69", "uuid": "cc96fe1f-0c4d-4359-8aea-36af82e05f9d"}, "__new_primary_file_0.55.heatmap\|0.55.heatmap__": {"src": "hda", "id": "b3785c43e2c86bb3", "uuid": "0f68e509-eec7-4eb9-94b3-8ba0fca3f4be"}, "logfile": {"src": "hda", "id": "662c759ed032ed85", "uuid": "75d94a1d-5eb2-4ac0-8a8b-9c392002d639"}, "__new_primary_file_0.55.heatmap\|0.26.heatmap__": {"src": "hda", "id": "50241e2b025a0fb6", "uuid": "cc33ffac-52bc-4567-a598-9fe45db09331"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > heatmap.bin(shared=input_otu.dat,groups=forest-pasture,label=0.03-0.26- \r0.55,scale=linear,sorted=none,numotu=0,fontsize=100)\n0.03\n0.26\n0.55\n\nOutput File Names: \ninput_otu.0.03.heatmap.bin.svg\ninput_otu.0.26.heatmap.bin.svg\ninput_otu.0.55.heatmap.bin.svg\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1517.dat' input_otu.dat && echo 'heatmap.bin( shared=input_otu.dat, groups=forest-pasture, label=0.03-0.26-0.55, scale=linear, sorted=none, numotu=0, fontsize=100 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:43:30.569021", "params": {"scale": "\"linear\"", "numotu": "\"0\"", "dbkey": "\"hg17\"", "fontsize": "\"100\"", "input": "{\"groups\": [\"forest\", \"pasture\"], \"label\": [\"0.03\", \"0.26\", \"0.55\"], \"has_groups\": \"yes\", \"__current_case__\": 1, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1517}]}}", "sorted": "\"none\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "22841", "id": "07fd1c8ec8f13176", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_heatmap_bin.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|dist": {"src": "hda", "id": "5580169e77bda3db"}, "input\|source": "phylip"}, "job": {"inputs": {"dist": {"src": "hda", "id": "5580169e77bda3db", "uuid": "d08e5ac9-6b04-43ac-b405-96b8cb95a1c6"}}, "update_time": "2018-02-08T17:43:45.725058", "tool_id": "mothur_heatmap_sim", "outputs": {"logfile": {"src": "hda", "id": "464746096d792407", "uuid": "bf43794a-d69f-457a-9fbc-23a419950c7c"}, "heatmap": {"src": "hda", "id": "22a2b448f3100bc3", "uuid": "dba5e528-d34f-43f6-baf2-cf6b0b10961e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > heatmap.sim(phylip=input_dist.dat,fontsize=24)\n\nOutput File Names: \ninput_dist.heatmap.sim.svg\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1522.dat' input_dist.dat && echo 'heatmap.sim( phylip=input_dist.dat, fontsize=24 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:43:42.621871", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "fontsize": "\"24\"", "dbkey": "\"hg17\"", "input": "{\"source\": \"phylip\", \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 1522}]}, \"__current_case__\": 2}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "22927", "id": "4b964545b41f57a8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_heatmap_sim.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|source": "shared", "input\|otu": {"src": "hda", "id": "4265beaf3ba354f1"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "4265beaf3ba354f1", "uuid": "93279366-4f83-443c-bc00-9fb96b1d2d0e"}}, "update_time": "2018-02-08T17:44:01.685558", "tool_id": "mothur_heatmap_sim", "outputs": {"__new_primary_file_unique.thetayc.heatmap\|0.15.thetayc.heatmap__": {"src": "hda", "id": "c4e4a5d9dc8d1120", "uuid": "a0adbef2-2d66-4920-9ce3-b64125941108"}, "__new_primary_file_unique.thetayc.heatmap\|0.29.jest.heatmap__": {"src": "hda", "id": "180af9b3f848a9ac", "uuid": "28b31770-b932-4ba5-8759-2b02de62ddcc"}, "__new_primary_file_unique.thetayc.heatmap\|0.04.thetayc.heatmap__": {"src": "hda", "id": "3586bb570babf8de", "uuid": "08bda45a-d895-4ed9-b2e3-f90932781ce8"}, "__new_primary_file_unique.thetayc.heatmap\|0.18.jest.heatmap__": {"src": "hda", "id": "d3c7d1db6565c99f", "uuid": "98069c1b-96d6-4058-9e74-3f9bd14f375c"}, "__new_primary_file_unique.thetayc.heatmap\|0.07.jest.heatmap__": {"src": "hda", "id": "51b118316409238c", "uuid": "2e5000b6-043f-4423-9843-c82800ca0689"}, "__new_primary_file_unique.thetayc.heatmap\|0.04.jest.heatmap__": {"src": "hda", "id": "ce40f08a4c5ff084", "uuid": "1ba3d221-c019-4df6-a23d-d0e3f2d94911"}, "__new_primary_file_unique.thetayc.heatmap\|0.02.jest.heatmap__": {"src": "hda", "id": "f6c11e10c580447f", "uuid": "186c5c11-8575-4bfa-88cc-91ea9233b3fb"}, "__new_primary_file_unique.thetayc.heatmap\|0.01.thetayc.heatmap__": {"src": "hda", "id": "2661a717f546e3b3", "uuid": "6d4d2020-863d-40a0-9901-d66a043f8e03"}, "__new_primary_file_unique.thetayc.heatmap\|0.22.thetayc.heatmap__": {"src": "hda", "id": "0f7d4a72d773ba0a", "uuid": "d652fc0c-36a6-4be2-b003-28cd245b0267"}, "__new_primary_file_unique.thetayc.heatmap\|0.13.thetayc.heatmap__": {"src": "hda", "id": "fe71c2db0b5692f4", "uuid": "e9fab26d-083a-4e40-9b6f-d107e995b550"}, "__new_primary_file_unique.thetayc.heatmap\|0.10.thetayc.heatmap__": {"src": "hda", "id": "97aa1ffb9ac3f2c4", "uuid": "e8f8906c-2aa3-44bc-b025-b31d0bbf7931"}, "__new_primary_file_unique.thetayc.heatmap\|0.41.jest.heatmap__": {"src": "hda", "id": "6a9f6d6282ff7ad7", "uuid": "e88dcba9-34bf-47d1-a188-90c9780d5cf9"}, "__new_primary_file_unique.thetayc.heatmap\|0.14.thetayc.heatmap__": {"src": "hda", "id": "30c58e9b8cdb761b", "uuid": "6ca1d288-f99b-4882-985f-3a1379038cd6"}, "__new_primary_file_unique.thetayc.heatmap\|0.06.jest.heatmap__": {"src": "hda", "id": "e1f6e4d686a02e1c", "uuid": "ade3c8ad-37ec-4a19-a9bc-104c80843136"}, "__new_primary_file_unique.thetayc.heatmap\|0.18.thetayc.heatmap__": {"src": "hda", "id": "f182b72ce68dba3b", "uuid": "621a6dc9-2f6c-4e7b-820a-bca58c7d0c44"}, "__new_primary_file_unique.thetayc.heatmap\|0.16.jest.heatmap__": {"src": "hda", "id": "7f3108983743f974", "uuid": "5eb1910e-dc13-43e4-abe7-8efbf333aa66"}, "__new_primary_file_unique.thetayc.heatmap\|0.02.thetayc.heatmap__": {"src": "hda", "id": "c1399bdeb7bb0b96", "uuid": "c1c8dc2a-b21e-4ef6-a1d1-4c62e1b866ba"}, "__new_primary_file_unique.thetayc.heatmap\|0.36.thetayc.heatmap__": {"src": "hda", "id": "b17dd69ce4a6c92a", "uuid": "9c460567-673b-434e-a1b0-9274d7c9b0c6"}, "__new_primary_file_unique.thetayc.heatmap\|0.03.jest.heatmap__": {"src": "hda", "id": "6f5f88291fc630a4", "uuid": "36dc39a0-9e0c-42d2-928b-d1e5e877589b"}, "__new_primary_file_unique.thetayc.heatmap\|0.11.thetayc.heatmap__": {"src": "hda", "id": "075a45415949b3d9", "uuid": "bda362ec-af8d-49a8-bbec-1c50741f87fb"}, "__new_primary_file_unique.thetayc.heatmap\|0.08.thetayc.heatmap__": {"src": "hda", "id": "3cafc91c25a578c3", "uuid": "9de9492a-332d-4c86-869e-a9079dd1be4a"}, "__new_primary_file_unique.thetayc.heatmap\|0.24.thetayc.heatmap__": {"src": "hda", "id": "d905a52c86490aa9", "uuid": "5bf0e476-bd75-4b22-a3dd-c54ed31b8201"}, "__new_primary_file_unique.thetayc.heatmap\|unique.jest.heatmap__": {"src": "hda", "id": "ecd1c6753e7f1590", "uuid": "75a2f6d5-53b9-45c8-ada4-f0854dfe978e"}, "__new_primary_file_unique.thetayc.heatmap\|0.10.jest.heatmap__": {"src": "hda", "id": "abf9c4ff55d20272", "uuid": "9a29811f-871b-46da-ac69-70ddf6c31821"}, "__new_primary_file_unique.thetayc.heatmap\|0.12.jest.heatmap__": {"src": "hda", "id": "87ffab3cd82b867a", "uuid": "fe8389cf-61fc-45e6-89f8-4b73e9bc94b3"}, "__new_primary_file_unique.thetayc.heatmap\|0.21.jest.heatmap__": {"src": "hda", "id": "399e6426f627a60f", "uuid": "2b4d2b38-7fad-498f-bc78-b503eb6e6ee7"}, "__new_primary_file_unique.thetayc.heatmap\|0.38.jest.heatmap__": {"src": "hda", "id": "a0417eda233d5437", "uuid": "6e3123a5-3b48-4adc-b7b4-0f35656af1d4"}, "__new_primary_file_unique.thetayc.heatmap\|0.05.thetayc.heatmap__": {"src": "hda", "id": "627ee27a222faba6", "uuid": "31938492-969e-488d-b50f-7048c7370452"}, "__new_primary_file_unique.thetayc.heatmap\|0.22.jest.heatmap__": {"src": "hda", "id": "d375c65bcca8b11f", "uuid": "6a623a0a-11ad-42a4-a970-41d30b77fe26"}, "__new_primary_file_unique.thetayc.heatmap\|0.06.thetayc.heatmap__": {"src": "hda", "id": "d81ddba20ea6fdac", "uuid": "a0bfcc9d-62c3-43ac-8696-5f24235a3cd9"}, "__new_primary_file_unique.thetayc.heatmap\|0.19.jest.heatmap__": {"src": "hda", "id": "ec382dfe788d855e", "uuid": "4a60e320-dfd2-4310-b73a-4b3784579401"}, "__new_primary_file_unique.thetayc.heatmap\|0.26.jest.heatmap__": {"src": "hda", "id": "d2d6386808d42c08", "uuid": "e9e104f7-2fa5-4368-9437-876c31907b8c"}, "__new_primary_file_unique.thetayc.heatmap\|0.26.thetayc.heatmap__": {"src": "hda", "id": "94434804054a7019", "uuid": "5cd804c7-9cd4-4ea7-9102-d79a93f3fa99"}, "__new_primary_file_unique.thetayc.heatmap\|0.16.thetayc.heatmap__": {"src": "hda", "id": "531de3de626c47cb", "uuid": "aa82c292-e3ac-46f9-8275-f9a86ddfa97f"}, "__new_primary_file_unique.thetayc.heatmap\|0.20.thetayc.heatmap__": {"src": "hda", "id": "36e7f5a8534de34e", "uuid": "7fafbb3e-40d8-4ded-a29f-a1e64ee93a99"}, "__new_primary_file_unique.thetayc.heatmap\|0.17.thetayc.heatmap__": {"src": "hda", "id": "74bf5c1117d594bb", "uuid": "9852c8b5-07f9-42fb-9cce-c63468dc8144"}, "__new_primary_file_unique.thetayc.heatmap\|0.24.jest.heatmap__": {"src": "hda", "id": "eb2f44379f3a257b", "uuid": "812f3ebb-f686-4191-b3b3-f3bf85026f06"}, "__new_primary_file_unique.thetayc.heatmap\|0.33.thetayc.heatmap__": {"src": "hda", "id": "319b443d728c0591", "uuid": "ef3d6bab-8234-47ef-9ec4-4a07149f80e8"}, "__new_primary_file_unique.thetayc.heatmap\|unique.thetayc.heatmap__": {"src": "hda", "id": "ecfd6f2be0aff1bc", "uuid": "11f15f0e-d5e4-49c2-a781-45cc3b11407e"}, "__new_primary_file_unique.thetayc.heatmap\|0.36.jest.heatmap__": {"src": "hda", "id": "d95e4d5581180ee4", "uuid": "254a54e9-6071-44f9-85be-f9f091ffd08b"}, "__new_primary_file_unique.thetayc.heatmap\|0.41.thetayc.heatmap__": {"src": "hda", "id": "e12283faed70e201", "uuid": "74b61069-dccc-4a7c-8f1f-efacb88d8e97"}, "__new_primary_file_unique.thetayc.heatmap\|0.14.jest.heatmap__": {"src": "hda", "id": "26a000ad4d0437be", "uuid": "d2ae8da6-5f0d-48a9-8b01-b6849b437b12"}, "__new_primary_file_unique.thetayc.heatmap\|0.17.jest.heatmap__": {"src": "hda", "id": "7fabedcd5eaa31af", "uuid": "25e5a63b-b36d-42ad-a667-40b0c32a897f"}, "__new_primary_file_unique.thetayc.heatmap\|0.12.thetayc.heatmap__": {"src": "hda", "id": "c7b7b54dddfe8542", "uuid": "bd5c54fa-644e-4d86-b2ea-302d6fadc74a"}, "__new_primary_file_unique.thetayc.heatmap\|0.38.thetayc.heatmap__": {"src": "hda", "id": "5a08e7f7c6972b7e", "uuid": "874e879f-02e7-44b6-b60e-8fc3a22c7c2f"}, "__new_primary_file_unique.thetayc.heatmap\|0.45.thetayc.heatmap__": {"src": "hda", "id": "0e13440bbe86b59c", "uuid": "c18e83fc-0fdf-4e8d-b628-eb0fb577709f"}, "__new_primary_file_unique.thetayc.heatmap\|0.27.thetayc.heatmap__": {"src": "hda", "id": "c4c4d05e3337f76a", "uuid": "58604af9-6807-4fc1-ad64-9c5a73cc1be8"}, "__new_primary_file_unique.thetayc.heatmap\|0.03.thetayc.heatmap__": {"src": "hda", "id": "d0a896fbe2eb1316", "uuid": "73f274be-9a72-487a-9ec1-9515984580c9"}, "__new_primary_file_unique.thetayc.heatmap\|0.55.jest.heatmap__": {"src": "hda", "id": "f5c809fe32817232", "uuid": "71ee4021-3a46-44be-89c3-485f098baded"}, "__new_primary_file_unique.thetayc.heatmap\|0.21.thetayc.heatmap__": {"src": "hda", "id": "b849d1f82032b54d", "uuid": "cb6ef9b7-9007-49c9-bed2-f577a0eef6ad"}, "__new_primary_file_unique.thetayc.heatmap\|0.15.jest.heatmap__": {"src": "hda", "id": "6f6c68569c74f67f", "uuid": "5f1b4fe1-ab23-46fe-8080-bd09fb414b87"}, "__new_primary_file_unique.thetayc.heatmap\|0.05.jest.heatmap__": {"src": "hda", "id": "229ad64670d8ad60", "uuid": "106e2022-e72e-4724-a9da-260389dbd7d8"}, "__new_primary_file_unique.thetayc.heatmap\|0.23.jest.heatmap__": {"src": "hda", "id": "8faba141af95bc64", "uuid": "2c390515-c7cc-44c3-9b52-a628af36839f"}, "logfile": {"src": "hda", "id": "c29ab6099fba2aa1", "uuid": "240da7a9-44f7-4803-8e59-393ea6a33af6"}, "__new_primary_file_unique.thetayc.heatmap\|0.19.thetayc.heatmap__": {"src": "hda", "id": "78b8885c8cacb5bb", "uuid": "09ec1cd6-4308-4f06-bd42-7a44624b77a7"}, "__new_primary_file_unique.thetayc.heatmap\|0.29.thetayc.heatmap__": {"src": "hda", "id": "057502b1b8032dfe", "uuid": "38e93f7b-35d5-4168-b52d-3c597989b303"}, "__new_primary_file_unique.thetayc.heatmap\|0.33.jest.heatmap__": {"src": "hda", "id": "7e27be0380c976f8", "uuid": "3489ff9b-0043-4a59-85e3-e369eeabf921"}, "__new_primary_file_unique.thetayc.heatmap\|0.55.thetayc.heatmap__": {"src": "hda", "id": "7287d543ad977f1e", "uuid": "a5e98bc5-f7a9-46a6-8026-319d79a1fb74"}, "__new_primary_file_unique.thetayc.heatmap\|0.09.jest.heatmap__": {"src": "hda", "id": "8374c09174fced28", "uuid": "da106ae4-db29-4183-940d-dbefead390ef"}, "__new_primary_file_unique.thetayc.heatmap\|0.45.jest.heatmap__": {"src": "hda", "id": "ec41825bcb3c7dfe", "uuid": "fc44c5be-793d-42f1-93da-3f2896c00154"}, "__new_primary_file_unique.thetayc.heatmap\|0.25.thetayc.heatmap__": {"src": "hda", "id": "f45962210a1c1b1c", "uuid": "d81d1a7e-2f35-45d3-b183-ef89b3ab9324"}, "__new_primary_file_unique.thetayc.heatmap\|0.25.jest.heatmap__": {"src": "hda", "id": "6c89a539eb5e59d3", "uuid": "384b0ded-431b-47ab-a0ab-3a725ee2f9f4"}, "__new_primary_file_unique.thetayc.heatmap\|0.01.jest.heatmap__": {"src": "hda", "id": "8e46a33d3b76a2b1", "uuid": "10a4cec1-dd2d-4efb-a23e-841104148bdf"}, "__new_primary_file_unique.thetayc.heatmap\|0.09.thetayc.heatmap__": {"src": "hda", "id": "904e4c855c1d3c13", "uuid": "74b7344d-0914-421c-b183-c2bcfbde9595"}, "__new_primary_file_unique.thetayc.heatmap\|0.32.thetayc.heatmap__": {"src": "hda", "id": "256cf1684db697f2", "uuid": "507108c1-fc03-4c9e-b50a-1c25fc53a6a8"}, "__new_primary_file_unique.thetayc.heatmap\|0.08.jest.heatmap__": {"src": "hda", "id": "54383a9e773e7ce7", "uuid": "fce7e350-6d03-4bca-b12d-dc85ee273db8"}, "__new_primary_file_unique.thetayc.heatmap\|0.32.jest.heatmap__": {"src": "hda", "id": "ad574be7e6b6aebd", "uuid": "088b8655-c52c-4952-9975-afe3eff2d474"}, "__new_primary_file_unique.thetayc.heatmap\|0.27.jest.heatmap__": {"src": "hda", "id": "0898b95704fa8260", "uuid": "736cbf06-4db0-4135-b3ab-710884ca9b58"}, "__new_primary_file_unique.thetayc.heatmap\|0.23.thetayc.heatmap__": {"src": "hda", "id": "02c68994751c0c6d", "uuid": "83a53fac-18f9-4dfa-bce8-3334153ba6c6"}, "__new_primary_file_unique.thetayc.heatmap\|0.20.jest.heatmap__": {"src": "hda", "id": "fc6d8959ec51886d", "uuid": "f51dcfdb-7c93-4b3f-9268-60a1ee921c67"}, "__new_primary_file_unique.thetayc.heatmap\|0.13.jest.heatmap__": {"src": "hda", "id": "310a57d95f681718", "uuid": "9c8edca0-2995-44b0-b007-b80dd1c7ad36"}, "__new_primary_file_unique.thetayc.heatmap\|0.11.jest.heatmap__": {"src": "hda", "id": "9551b524a295ab47", "uuid": "6baaca63-c25b-47f2-84ec-0bc9235a0d6f"}, "__new_primary_file_unique.thetayc.heatmap\|0.07.thetayc.heatmap__": {"src": "hda", "id": "5d0784c229354ea3", "uuid": "7d384e6e-a769-465a-a0be-0d79f1939c40"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > heatmap.sim(shared=input_otu.dat,calc=jest-thetayc,fontsize=24)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu.unique.jest.heatmap.sim.svg\ninput_otu.unique.thetayc.heatmap.sim.svg\ninput_otu.0.01.jest.heatmap.sim.svg\ninput_otu.0.01.thetayc.heatmap.sim.svg\ninput_otu.0.02.jest.heatmap.sim.svg\ninput_otu.0.02.thetayc.heatmap.sim.svg\ninput_otu.0.03.jest.heatmap.sim.svg\ninput_otu.0.03.thetayc.heatmap.sim.svg\ninput_otu.0.04.jest.heatmap.sim.svg\ninput_otu.0.04.thetayc.heatmap.sim.svg\ninput_otu.0.05.jest.heatmap.sim.svg\ninput_otu.0.05.thetayc.heatmap.sim.svg\ninput_otu.0.06.jest.heatmap.sim.svg\ninput_otu.0.06.thetayc.heatmap.sim.svg\ninput_otu.0.07.jest.heatmap.sim.svg\ninput_otu.0.07.thetayc.heatmap.sim.svg\ninput_otu.0.08.jest.heatmap.sim.svg\ninput_otu.0.08.thetayc.heatmap.sim.svg\ninput_otu.0.09.jest.heatmap.sim.svg\ninput_otu.0.09.thetayc.heatmap.sim.svg\ninput_otu.0.10.jest.heatmap.sim.svg\ninput_otu.0.10.thetayc.heatmap.sim.svg\ninput_otu.0.11.jest.heatmap.sim.svg\ninput_otu.0.11.thetayc.heatmap.sim.svg\ninput_otu.0.12.jest.heatmap.sim.svg\ninput_otu.0.12.thetayc.heatmap.sim.svg\ninput_otu.0.13.jest.heatmap.sim.svg\ninput_otu.0.13.thetayc.heatmap.sim.svg\ninput_otu.0.14.jest.heatmap.sim.svg\ninput_otu.0.14.thetayc.heatmap.sim.svg\ninput_otu.0.15.jest.heatmap.sim.svg\ninput_otu.0.15.thetayc.heatmap.sim.svg\ninput_otu.0.16.jest.heatmap.sim.svg\ninput_otu.0.16.thetayc.heatmap.sim.svg\ninput_otu.0.17.jest.heatmap.sim.svg\ninput_otu.0.17.thetayc.heatmap.sim.svg\ninput_otu.0.18.jest.heatmap.sim.svg\ninput_otu.0.18.thetayc.heatmap.sim.svg\ninput_otu.0.19.jest.heatmap.sim.svg\ninput_otu.0.19.thetayc.heatmap.sim.svg\ninput_otu.0.20.jest.heatmap.sim.svg\ninput_otu.0.20.thetayc.heatmap.sim.svg\ninput_otu.0.21.jest.heatmap.sim.svg\ninput_otu.0.21.thetayc.heatmap.sim.svg\ninput_otu.0.22.jest.heatmap.sim.svg\ninput_otu.0.22.thetayc.heatmap.sim.svg\ninput_otu.0.23.jest.heatmap.sim.svg\ninput_otu.0.23.thetayc.heatmap.sim.svg\ninput_otu.0.24.jest.heatmap.sim.svg\ninput_otu.0.24.thetayc.heatmap.sim.svg\ninput_otu.0.25.jest.heatmap.sim.svg\ninput_otu.0.25.thetayc.heatmap.sim.svg\ninput_otu.0.26.jest.heatmap.sim.svg\ninput_otu.0.26.thetayc.heatmap.sim.svg\ninput_otu.0.27.jest.heatmap.sim.svg\ninput_otu.0.27.thetayc.heatmap.sim.svg\ninput_otu.0.29.jest.heatmap.sim.svg\ninput_otu.0.29.thetayc.heatmap.sim.svg\ninput_otu.0.32.jest.heatmap.sim.svg\ninput_otu.0.32.thetayc.heatmap.sim.svg\ninput_otu.0.33.jest.heatmap.sim.svg\ninput_otu.0.33.thetayc.heatmap.sim.svg\ninput_otu.0.36.jest.heatmap.sim.svg\ninput_otu.0.36.thetayc.heatmap.sim.svg\ninput_otu.0.38.jest.heatmap.sim.svg\ninput_otu.0.38.thetayc.heatmap.sim.svg\ninput_otu.0.41.jest.heatmap.sim.svg\ninput_otu.0.41.thetayc.heatmap.sim.svg\ninput_otu.0.45.jest.heatmap.sim.svg\ninput_otu.0.45.thetayc.heatmap.sim.svg\ninput_otu.0.55.jest.heatmap.sim.svg\ninput_otu.0.55.thetayc.heatmap.sim.svg\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1525.dat' input_otu.dat && echo 'heatmap.sim( shared=input_otu.dat, calc=jest-thetayc, fontsize=24 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:43:55.214842", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "fontsize": "\"24\"", "dbkey": "\"hg17\"", "input": "{\"__current_case__\": 0, \"label\": null, \"source\": \"shared\", \"groups\": null, \"calc\": [\"jest\", \"thetayc\"], \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1525}]}}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23014", "id": "732b43bd12cd060f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_heatmap_sim.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|label": ["0.03", "0.26", "0.55"], "input\|source": "shared", "input\|groups": ["forest", "pasture"], "input\|calc": ["jclass", "jest", "sorclass", "sorest", "braycurtis", "jabund", "morisitahorn", "sorabund", "thetan", "thetayc"], "input\|otu": {"src": "hda", "id": "0e4b67279a0941db"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "0e4b67279a0941db", "uuid": "9f549eac-d1a5-4fde-b3e9-902bf0757f61"}}, "update_time": "2018-02-08T17:44:17.923624", "tool_id": "mothur_heatmap_sim", "outputs": {"__new_primary_file_0.55.thetayc.heatmap\|0.55.thetayc.heatmap__": {"src": "hda", "id": "97a1fd4764430d7d", "uuid": "126f6a6b-71ae-461c-8af1-bd714fd0f4ff"}, "__new_primary_file_0.55.thetayc.heatmap\|0.26.sorclass.heatmap__": {"src": "hda", "id": "440b08187b03ca78", "uuid": "2212efa2-29d8-48e5-9554-6f46f4d98ba0"}, "__new_primary_file_0.55.thetayc.heatmap\|0.26.morisitahorn.heatmap__": {"src": "hda", "id": "f7a22a56bf98efba", "uuid": "5f04e2bd-1506-469f-a5c8-b9a78e689794"}, "__new_primary_file_0.55.thetayc.heatmap\|0.26.jclass.heatmap__": {"src": "hda", "id": "fb48ee8a404d26a9", "uuid": "96252991-ed2c-4dc1-a35a-fac17f6d68c7"}, "__new_primary_file_0.55.thetayc.heatmap\|0.03.sorclass.heatmap__": {"src": "hda", "id": "6200b6b6e3e5d3c6", "uuid": "f61f9ef6-d00f-4e6c-ba5e-c0349ccbf8c3"}, "__new_primary_file_0.55.thetayc.heatmap\|0.26.jest.heatmap__": {"src": "hda", "id": "dfb5acc45c9e0393", "uuid": "32d7bbb8-b78c-4994-b5fd-f372bb4f1c54"}, "__new_primary_file_0.55.thetayc.heatmap\|0.55.jclass.heatmap__": {"src": "hda", "id": "4b0dcf789f89250e", "uuid": "c26de56e-5a88-454e-bd5f-851684f97089"}, "__new_primary_file_0.55.thetayc.heatmap\|0.55.sorabund.heatmap__": {"src": "hda", "id": "44753ae8c747323a", "uuid": "17bbbdb5-5e8a-493f-ac86-0f2a497e30d4"}, "__new_primary_file_0.55.thetayc.heatmap\|0.03.jclass.heatmap__": {"src": "hda", "id": "129ec904eaa7b025", "uuid": "e8f0c5ba-aa74-485c-8699-0643928426c4"}, "__new_primary_file_0.55.thetayc.heatmap\|0.26.sorest.heatmap__": {"src": "hda", "id": "ba44e50454176a40", "uuid": "1bd9af92-9e25-4124-9d7c-9fa25049917d"}, "__new_primary_file_0.55.thetayc.heatmap\|0.03.jest.heatmap__": {"src": "hda", "id": "3e552153c1355876", "uuid": "8ae431b0-596d-4231-8931-ef31e7a9ad93"}, "__new_primary_file_0.55.thetayc.heatmap\|0.03.thetayc.heatmap__": {"src": "hda", "id": "bf8f97fc9d2f53ad", "uuid": "78cda9a8-caff-4203-a1ef-63d0a5401087"}, "__new_primary_file_0.55.thetayc.heatmap\|0.26.braycurtis.heatmap__": {"src": "hda", "id": "52db18947e82628a", "uuid": "0dfee0e6-4d0d-4f37-b508-1adc585653c2"}, "__new_primary_file_0.55.thetayc.heatmap\|0.55.sorclass.heatmap__": {"src": "hda", "id": "6617d9e33373df14", "uuid": "a07948d5-4788-4678-ac13-cd8ada7bc7ef"}, "__new_primary_file_0.55.thetayc.heatmap\|0.26.sorabund.heatmap__": {"src": "hda", "id": "cadc96473f17a847", "uuid": "ec06c187-085e-46a5-be15-7fca21df5c1b"}, "__new_primary_file_0.55.thetayc.heatmap\|0.55.sorest.heatmap__": {"src": "hda", "id": "182f3c5e367f21ec", "uuid": "c76d1bf0-d70f-464a-90d8-ee4f478bf5d9"}, "__new_primary_file_0.55.thetayc.heatmap\|0.55.braycurtis.heatmap__": {"src": "hda", "id": "bfac8aa31a378884", "uuid": "c2d763e8-133a-466d-92eb-34c36f49daf5"}, "__new_primary_file_0.55.thetayc.heatmap\|0.55.jabund.heatmap__": {"src": "hda", "id": "be5c34656f56b1c8", "uuid": "bc8ea17e-e3fc-42f0-bc96-701c251b60d4"}, "__new_primary_file_0.55.thetayc.heatmap\|0.55.thetan.heatmap__": {"src": "hda", "id": "2c5c4a8381427e09", "uuid": "3e06e985-5947-4712-a497-833166777c18"}, "__new_primary_file_0.55.thetayc.heatmap\|0.03.morisitahorn.heatmap__": {"src": "hda", "id": "126bd5267c0c550c", "uuid": "52d36d37-f428-4e08-823f-9e7fd64a76f8"}, "__new_primary_file_0.55.thetayc.heatmap\|0.03.jabund.heatmap__": {"src": "hda", "id": "3adfe7a97cdc075a", "uuid": "2f4025aa-70f6-4987-9c60-cd38135a6eeb"}, "logfile": {"src": "hda", "id": "685dd60bfbef3aba", "uuid": "888d07e6-9a26-4129-8dcc-e6f10c65b9c1"}, "__new_primary_file_0.55.thetayc.heatmap\|0.55.jest.heatmap__": {"src": "hda", "id": "f8e11f8ada66d0f4", "uuid": "63b80517-8fd4-463a-906f-38c5fba20338"}, "__new_primary_file_0.55.thetayc.heatmap\|0.03.sorabund.heatmap__": {"src": "hda", "id": "1dc9e2614ae44c6f", "uuid": "10c8d90e-58dd-4bf2-837e-a9f3e6a08850"}, "__new_primary_file_0.55.thetayc.heatmap\|0.26.thetayc.heatmap__": {"src": "hda", "id": "9e4e9d5b1a0ea25c", "uuid": "b7db93e8-7e24-466b-a3cd-4c245586d39b"}, "__new_primary_file_0.55.thetayc.heatmap\|0.55.morisitahorn.heatmap__": {"src": "hda", "id": "1223008bb03781ea", "uuid": "d9e21b06-1794-4676-8d9f-ceb098994400"}, "__new_primary_file_0.55.thetayc.heatmap\|0.03.thetan.heatmap__": {"src": "hda", "id": "a3a1edb65ca58d52", "uuid": "f90d3ab8-422e-4aa5-b443-773503c56691"}, "__new_primary_file_0.55.thetayc.heatmap\|0.26.thetan.heatmap__": {"src": "hda", "id": "3d67993e78966025", "uuid": "dc62680a-b693-4256-a475-f78fb1a093cd"}, "__new_primary_file_0.55.thetayc.heatmap\|0.03.sorest.heatmap__": {"src": "hda", "id": "4e3fce0b8fcfe562", "uuid": "d7e5d7ec-d097-4d9e-9852-04dc3bb3739a"}, "__new_primary_file_0.55.thetayc.heatmap\|0.26.jabund.heatmap__": {"src": "hda", "id": "32fa0d439185428a", "uuid": "b55bd189-b583-4b1a-9325-399734daadcd"}, "__new_primary_file_0.55.thetayc.heatmap\|0.03.braycurtis.heatmap__": {"src": "hda", "id": "b46a645fa458e7c7", "uuid": "f8aa1f3c-bb6f-400c-905a-1ee7ff72a4b8"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > heatmap.sim(shared=input_otu.dat,label=0.03-0.26-0.55,groups=forest-pas \rture,calc=jclass-jest-sorclass-sorest-braycurtis-jabund-morisitahorn-sorabund-th \retan-thetayc,fontsize=24)\n0.03\n0.26\n0.55\n\nOutput File Names: \ninput_otu.0.03.jclass.heatmap.sim.svg\ninput_otu.0.03.jest.heatmap.sim.svg\ninput_otu.0.03.sorclass.heatmap.sim.svg\ninput_otu.0.03.sorest.heatmap.sim.svg\ninput_otu.0.03.braycurtis.heatmap.sim.svg\ninput_otu.0.03.jabund.heatmap.sim.svg\ninput_otu.0.03.morisitahorn.heatmap.sim.svg\ninput_otu.0.03.sorabund.heatmap.sim.svg\ninput_otu.0.03.thetan.heatmap.sim.svg\ninput_otu.0.03.thetayc.heatmap.sim.svg\ninput_otu.0.26.jclass.heatmap.sim.svg\ninput_otu.0.26.jest.heatmap.sim.svg\ninput_otu.0.26.sorclass.heatmap.sim.svg\ninput_otu.0.26.sorest.heatmap.sim.svg\ninput_otu.0.26.braycurtis.heatmap.sim.svg\ninput_otu.0.26.jabund.heatmap.sim.svg\ninput_otu.0.26.morisitahorn.heatmap.sim.svg\ninput_otu.0.26.sorabund.heatmap.sim.svg\ninput_otu.0.26.thetan.heatmap.sim.svg\ninput_otu.0.26.thetayc.heatmap.sim.svg\ninput_otu.0.55.jclass.heatmap.sim.svg\ninput_otu.0.55.jest.heatmap.sim.svg\ninput_otu.0.55.sorclass.heatmap.sim.svg\ninput_otu.0.55.sorest.heatmap.sim.svg\ninput_otu.0.55.braycurtis.heatmap.sim.svg\ninput_otu.0.55.jabund.heatmap.sim.svg\ninput_otu.0.55.morisitahorn.heatmap.sim.svg\ninput_otu.0.55.sorabund.heatmap.sim.svg\ninput_otu.0.55.thetan.heatmap.sim.svg\ninput_otu.0.55.thetayc.heatmap.sim.svg\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1599.dat' input_otu.dat && echo 'heatmap.sim( shared=input_otu.dat, label=0.03-0.26-0.55, groups=forest-pasture, calc=jclass-jest-sorclass-sorest-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc, fontsize=24 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:44:13.381299", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "fontsize": "\"24\"", "dbkey": "\"hg17\"", "input": "{\"__current_case__\": 0, \"label\": [\"0.03\", \"0.26\", \"0.55\"], \"source\": \"shared\", \"groups\": [\"forest\", \"pasture\"], \"calc\": [\"jclass\", \"jest\", \"sorclass\", \"sorest\", \"braycurtis\", \"jabund\", \"morisitahorn\", \"sorabund\", \"thetan\", \"thetayc\"], \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1599}]}}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23100", "id": "b7d5085eacaa6509", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_heatmap_sim.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"design": {"src": "hda", "id": "b75e6fd397636254"}, "dist": {"src": "hda", "id": "e781318b8db2a130"}}, "job": {"inputs": {"design": {"src": "hda", "id": "b75e6fd397636254", "uuid": "85c2ef82-3edd-4628-a8e1-83ee3078e9a2"}, "dist": {"src": "hda", "id": "e781318b8db2a130", "uuid": "6e3fccba-a0be-4020-9c3f-a1d7b22edff5"}}, "update_time": "2018-02-08T17:44:35.076991", "tool_id": "mothur_homova", "outputs": {"logfile": {"src": "hda", "id": "c27f325b0d5006b2", "uuid": "e59ee541-7405-47a1-a60c-100b5add88ed"}, "homova": {"src": "hda", "id": "05bd3a5145917735", "uuid": "90841dd8-01d4-4ef1-9c98-8705de5cc4d2"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > homova(phylip=dist.dat,design=design.dat,iters=1000,alpha=0.05)\nHOMOVA\tBValue\tP-value\tSSwithin/(Ni-1)_values\nA-B\t0.000158784\t0.983\t0.0491681\t0.0493482\nExperiment-wise error rate: 0.05\nIf you have borderline P-values, you should try increasing the number of iterations\n\nOutput File Names: \ndist.homova\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1631.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1632.dat' design.dat && echo 'homova( phylip=dist.dat, design=design.dat, iters=1000, alpha=0.05 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:44:31.897262", "params": {"iters": "\"1000\"", "alpha": "\"0.05\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "sets": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23208", "id": "7535296d23a37c60", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_homova.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"design": {"src": "hda", "id": "e3dee98f1c9649e3"}, "dist": {"src": "hda", "id": "633b54cb360cf9db"}, "sets": "A"}, "job": {"inputs": {"design": {"src": "hda", "id": "e3dee98f1c9649e3", "uuid": "908ca6b1-8c4c-4bea-a596-bdd91b839874"}, "dist": {"src": "hda", "id": "633b54cb360cf9db", "uuid": "deaecaee-ec95-4c03-b244-25f26b281919"}}, "update_time": "2018-02-08T17:44:55.739229", "tool_id": "mothur_homova", "outputs": {"logfile": {"src": "hda", "id": "c1fddc7a0d53eefd", "uuid": "e0ce6399-ff67-4c22-8cea-e623fe3b0216"}, "homova": {"src": "hda", "id": "d0a2e604f819e3c6", "uuid": "45572e52-1c5d-4123-a010-8850c8842c1f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > homova(phylip=dist.dat,design=design.dat,sets=A,iters=1000,alpha=0.05)\nHOMOVA\tBValue\tP-value\tSSwithin/(Ni-1)_values\nA\t-nan\t<0.001\t0.0491681\nExperiment-wise error rate: 0.05\nIf you have borderline P-values, you should try increasing the number of iterations\n\nOutput File Names: \ndist.homova\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1635.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1636.dat' design.dat && echo 'homova( phylip=dist.dat, design=design.dat, sets=A, iters=1000, alpha=0.05 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:44:52.539310", "params": {"iters": "\"1000\"", "alpha": "\"0.05\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "sets": "\"A\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23326", "id": "957dec9f2200cbe4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_homova.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"withdesign\|design": {"src": "hda", "id": "130add1cdbd710d8"}, "withdesign\|groups": ["tardis", "dalek"], "withdesign\|havedesign": "yes", "otu": {"src": "hda", "id": "71da8dd0f551f579"}, "label": "0.03"}, "job": {"inputs": {"design": {"src": "hda", "id": "130add1cdbd710d8", "uuid": "15911e5f-c171-4f42-9061-2f65d9e9a6e9"}, "otu": {"src": "hda", "id": "71da8dd0f551f579", "uuid": "4b9303dd-3e4b-4e6c-bf6d-33a8c6c28a87"}}, "update_time": "2018-02-08T17:45:16.789870", "tool_id": "mothur_indicator", "outputs": {"logfile": {"src": "hda", "id": "d3ae0c1d73470c9e", "uuid": "adfe74af-d747-4106-b553-74dfadcd5ede"}, "tree_out": {"src": "hda", "id": "b9f3ee2dd66df0a7", "uuid": "61fd6af0-ad22-457c-a4f2-00514ead459f"}, "summary": {"src": "hda", "id": "b84330ef16365123", "uuid": "747d571a-41a4-4dd5-b004-e17b52e62210"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > indicator(shared=otu.dat,label=0.03,groups=tardis-dalek,design=withdesi \rgn.design.dat,processors=1)\n\nUsing 1 processors.\n\nSpecies\tIndicator_Groups\tIndicatorValue\tpValue\n\n\nIt took 0 secs to find the indicator species.\n\nOutput File Names: \notu.indicator.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1639.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1640.dat' withdesign.design.dat && echo 'indicator( shared=otu.dat, label=0.03, groups=tardis-dalek, design=withdesign.design.dat, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:45:13.218298", "params": {"withdesign": "{\"design\": {\"values\": [{\"src\": \"hda\", \"id\": 1640}]}, \"havedesign\": \"yes\", \"tree\": null, \"groups\": [\"tardis\", \"dalek\"], \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "\"0.03\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23436", "id": "c809b2abaed97358", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_indicator.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"withdesign\|design": {"src": "hda", "id": "4d319bb7f31107cc"}, "withdesign\|groups": "tardis", "otu": {"src": "hda", "id": "f291c23df814c8b2"}, "withdesign\|havedesign": "yes"}, "job": {"inputs": {"design": {"src": "hda", "id": "4d319bb7f31107cc", "uuid": "f27eeb67-8afe-41c7-9c05-b619f5699688"}, "otu": {"src": "hda", "id": "f291c23df814c8b2", "uuid": "4b43aa5e-f1ee-497c-b108-5893d1f1a355"}}, "update_time": "2018-02-08T17:45:34.981694", "tool_id": "mothur_indicator", "outputs": {"logfile": {"src": "hda", "id": "0922d58fdca8782c", "uuid": "17ecbb2f-8aa3-4c45-9ee4-3148e749c893"}, "tree_out": {"src": "hda", "id": "358ee0efc1019ede", "uuid": "138af667-fb25-48f8-9b46-c4fe6b8c111c"}, "summary": {"src": "hda", "id": "b2b3ae4f6b3403ef", "uuid": "60c99c02-357b-44aa-98a6-e84288ae1b33"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > indicator(shared=otu.dat,groups=tardis,design=withdesign.design.dat,pro \rcessors=1)\nYou did not provide a label, I will use the first label in your inputfile.\n\nUsing 1 processors.\n\nSpecies\tIndicator_Groups\tIndicatorValue\tpValue\n\n\nIt took 0 secs to find the indicator species.\n\nOutput File Names: \notu.indicator.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1644.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1645.dat' withdesign.design.dat && echo 'indicator( shared=otu.dat, groups=tardis, design=withdesign.design.dat, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:45:31.778529", "params": {"withdesign": "{\"design\": {\"values\": [{\"src\": \"hda\", \"id\": 1645}]}, \"havedesign\": \"yes\", \"tree\": null, \"groups\": \"tardis\", \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23575", "id": "63f8201b30d2cadd", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_indicator.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"withdesign\|tree": {"src": "hda", "id": "cf368cb6bca06f2e"}, "withdesign\|groups": ["forest", "pasture"], "otu": {"src": "hda", "id": "34863713120b282b"}, "withdesign\|havedesign": "no"}, "job": {"inputs": {"tree": {"src": "hda", "id": "cf368cb6bca06f2e", "uuid": "fb91c6ca-5179-40d5-942b-9c0c41f565fe"}, "otu": {"src": "hda", "id": "34863713120b282b", "uuid": "a64db36f-188c-4ce3-aba8-b472e74488c1"}}, "update_time": "2018-02-08T17:45:51.764425", "tool_id": "mothur_indicator", "outputs": {"logfile": {"src": "hda", "id": "f90ecd13a46a1b7b", "uuid": "7c6a2d9d-ff55-4330-a2f1-353f525891a6"}, "tree_out": {"src": "hda", "id": "a7092c007b7a86a3", "uuid": "a828a14e-a4a1-4644-997f-34b2cd26c085"}, "summary": {"src": "hda", "id": "463c07f914921351", "uuid": "aed53623-3451-4cf4-8bdd-10ee5d8cc381"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > indicator(tree=withdesign.tree.dat,shared=otu.dat,groups=forest-pasture \r,processors=1)\nYou did not provide a label, I will use the first label in your inputfile.\n\nUsing 1 processors.\n\nNode\tSpecies\tIndicator_Groups\tIndicatorValue\tpValue\n\n\nIt took 0 secs to find the indicator species.\n\nOutput File Names: \notu.indicator.summary\nwithdesign.tree.indicator.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1649.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1650.dat' withdesign.tree.dat && echo 'indicator( tree=withdesign.tree.dat, shared=otu.dat, groups=forest-pasture, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:45:48.263076", "params": {"withdesign": "{\"havedesign\": \"no\", \"tree\": {\"values\": [{\"src\": \"hda\", \"id\": 1650}]}, \"groups\": [\"forest\", \"pasture\"], \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23689", "id": "9c8aa3de76c5f0c4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_indicator.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"withdesign\|tree": {"src": "hda", "id": "07756f5d8c72ca12"}, "withdesign\|groups": "forest", "otu": {"src": "hda", "id": "52ebed6720d1663f"}, "withdesign\|havedesign": "no"}, "job": {"inputs": {"tree": {"src": "hda", "id": "07756f5d8c72ca12", "uuid": "42c5f9ab-da25-4bd9-a714-f936b4738249"}, "otu": {"src": "hda", "id": "52ebed6720d1663f", "uuid": "77cd1cf9-2422-43c7-9e19-0030139b8dd6"}}, "update_time": "2018-02-08T17:46:10.011812", "tool_id": "mothur_indicator", "outputs": {"logfile": {"src": "hda", "id": "d5612dcbb5ce0366", "uuid": "fdb6bfce-1f1e-4b99-946a-998aa250c4eb"}, "tree_out": {"src": "hda", "id": "bf85d0c93ded3f21", "uuid": "4235f8b7-f464-457a-8eb2-54a0c6560517"}, "summary": {"src": "hda", "id": "84981bc5aab6e32e", "uuid": "604c93ea-ba6b-4c62-b777-8c1fbbd52fc7"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > indicator(tree=withdesign.tree.dat,shared=otu.dat,groups=forest,process \rors=1)\nYou did not provide a label, I will use the first label in your inputfile.\n\nUsing 1 processors.\n\nNode\tSpecies\tIndicator_Groups\tIndicatorValue\tpValue\n\n\nIt took 0 secs to find the indicator species.\n\nOutput File Names: \notu.indicator.summary\nwithdesign.tree.indicator.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1654.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1655.dat' withdesign.tree.dat && echo 'indicator( tree=withdesign.tree.dat, shared=otu.dat, groups=forest, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:46:06.809366", "params": {"withdesign": "{\"havedesign\": \"no\", \"tree\": {\"values\": [{\"src\": \"hda\", \"id\": 1655}]}, \"groups\": \"forest\", \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23799", "id": "3529226cbbc41f8d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_indicator.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"design": {"src": "hda", "id": "4c8788abad1b338d"}, "otu": {"src": "hda", "id": "ea73bab1c36fe6e9"}}, "job": {"inputs": {"design": {"src": "hda", "id": "4c8788abad1b338d", "uuid": "76ccc0a4-267f-42e0-8370-c8833609cf74"}, "otu": {"src": "hda", "id": "ea73bab1c36fe6e9", "uuid": "3ae7682f-ce62-4425-b388-004af01134e7"}}, "update_time": "2018-02-08T17:46:26.299101", "tool_id": "mothur_lefse", "outputs": {"logfile": {"src": "hda", "id": "db96ea5535812b22", "uuid": "c2965e21-4799-42a6-aca3-7a0095ede7cc"}, "summary": {"src": "hda", "id": "a62d77069d50a785", "uuid": "f4d010af-638e-4311-8a51-e32990abbb71"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > lefse(shared=shared.dat,design=design.dat,aalpha=0.05,walpha=0.05,lda=2 \r.0,iters=30,fboots=0.67,strict=0,minc=10,wilc=T,curv=F,norm=T)\n\nYou did not provide a class, using dpw.\n\n1\n\nNumber of significantly discriminative features: 0 ( 0 ) before internal wilcoxon.\nNo features with significant differences between the classes.\n\nOutput File Names: \nshared.1.lefse_summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1659.dat' shared.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1660.dat' design.dat && echo 'lefse( shared=shared.dat, design=design.dat, aalpha=0.05, walpha=0.05, lda=2.0, iters=30, fboots=0.67, strict=0, minc=10, wilc=T, curv=F, norm=T )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:46:23.249880", "params": {"curv": "\"false\"", "aalpha": "\"0.05\"", "lda": "\"2.0\"", "sclass": "\"\"", "iters": "\"30\"", "minc": "\"10\"", "dbkey": "\"hg17\"", "label": "null", "strict": "\"0\"", "fboots": "\"0.67\"", "walpha": "\"0.05\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "class": "\"\"", "norm": "\"true\"", "wilc": "\"true\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23913", "id": "c397987c596ee46a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_lefse.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"design": {"src": "hda", "id": "f2cb52eef4673733"}, "class": "dpw", "otu": {"src": "hda", "id": "e6bcd3f9b805457c"}, "label": "1"}, "job": {"inputs": {"design": {"src": "hda", "id": "f2cb52eef4673733", "uuid": "ce83be1e-e3f2-4832-9354-072e95c02005"}, "otu": {"src": "hda", "id": "e6bcd3f9b805457c", "uuid": "4a9e038b-4c1d-43ed-b0dc-956d4100cc25"}}, "update_time": "2018-02-08T17:46:47.849034", "tool_id": "mothur_lefse", "outputs": {"logfile": {"src": "hda", "id": "41697c66808448c5", "uuid": "0823ce30-2352-4a24-b35b-46a5ed46bc1e"}, "summary": {"src": "hda", "id": "cc3d3fc6d6226aa1", "uuid": "e66dff78-5bd6-43bb-b0ab-e1a54d06b08a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > lefse(shared=shared.dat,design=design.dat,class=dpw,label=1,aalpha=0.05 \r,walpha=0.05,lda=2.0,iters=30,fboots=0.67,strict=0,minc=10,wilc=T,curv=F,norm=T) \r\u001b[A\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[K)\n1\n\nNumber of significantly discriminative features: 0 ( 0 ) before internal wilcoxon.\nNo features with significant differences between the classes.\n\nOutput File Names: \nshared.1.lefse_summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1663.dat' shared.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1664.dat' design.dat && echo 'lefse( shared=shared.dat, design=design.dat, class=dpw, label=1, aalpha=0.05, walpha=0.05, lda=2.0, iters=30, fboots=0.67, strict=0, minc=10, wilc=T, curv=F, norm=T )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:46:44.723129", "params": {"curv": "\"false\"", "aalpha": "\"0.05\"", "lda": "\"2.0\"", "sclass": "\"\"", "iters": "\"30\"", "minc": "\"10\"", "dbkey": "\"hg17\"", "label": "\"1\"", "strict": "\"0\"", "fboots": "\"0.67\"", "walpha": "\"0.05\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "class": "\"dpw\"", "norm": "\"true\"", "wilc": "\"true\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24029", "id": "f5edea7d52e42cd6", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_lefse.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"group": {"src": "hda", "id": "0af819d9e24eaa3e"}, "dist": {"src": "hda", "id": "09113d1870481726"}}, "job": {"inputs": {"dist": {"src": "hda", "id": "09113d1870481726", "uuid": "5e9fd652-9864-48b9-a417-84a2afbcc375"}, "group": {"src": "hda", "id": "0af819d9e24eaa3e", "uuid": "2b23b0a7-96d9-4071-8c1a-a0d7c8e928ef"}}, "update_time": "2018-02-08T17:47:08.945526", "tool_id": "mothur_libshuff", "outputs": {"logfile": {"src": "hda", "id": "9a1d171d0e8eec98", "uuid": "28c0ee7e-69ee-48db-bda5-a8027c01c303"}, "coverage": {"src": "hda", "id": "cb463262cf10668c", "uuid": "91c4a6f2-c515-46c9-8348-65e34bc4d41f"}, "summary": {"src": "hda", "id": "ef6796f5d6fc008a", "uuid": "916bb2ff-845b-497b-a28e-9dfc1b69a58a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > libshuff(phylip=dist.dat,group=group.dat,sim=false,iters=10000)\n******************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n****************###########\nforest-pasture \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nComparison \tdCXYScore\tSignificance\n\nforest-pasture \t0.00500262\t0.0098\n\npasture-forest \t0.00289600\t0.0625\n\n\nOutput File Names: \ndist.libshuff.summary\ndist.libshuff.coverage\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1667.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1668.dat' group.dat && echo 'libshuff( phylip=dist.dat, group=group.dat, sim=false, iters=10000 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:47:05.439444", "params": {"form": "{\"form2\": \"integral\", \"__current_case__\": 0}", "iters": "\"10000\"", "dbkey": "\"hg17\"", "groups": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "sim": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24148", "id": "e6b222c9649e44d2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_libshuff.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"form\|form2": "discrete", "dist": {"src": "hda", "id": "1c7735ec1b73fbb8"}, "groups": ["forest", "pasture"], "group": {"src": "hda", "id": "1616a3130c86f35d"}, "form\|cutoff": "0.25", "form\|step": "0.25"}, "job": {"inputs": {"dist": {"src": "hda", "id": "1c7735ec1b73fbb8", "uuid": "46fd625d-9858-41ff-bdfa-5bc20ff40823"}, "group": {"src": "hda", "id": "1616a3130c86f35d", "uuid": "fbf06a31-6643-4fc8-bf56-ed4bd0ca8e3e"}}, "update_time": "2018-02-08T17:47:27.398142", "tool_id": "mothur_libshuff", "outputs": {"logfile": {"src": "hda", "id": "af6859f1d0663d97", "uuid": "1f3ac1e6-70fd-450e-8bf0-0513298e6b9d"}, "coverage": {"src": "hda", "id": "79fc5e356a32badd", "uuid": "0f4f377a-5ab6-471e-9623-c7bf16bab1cf"}, "summary": {"src": "hda", "id": "3161fe67334a087c", "uuid": "99b3061a-4061-46a7-935b-6151908ee0ad"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > libshuff(phylip=dist.dat,group=group.dat,groups=forest-pasture,sim=fals \re,step=0.25,cutoff=0.25,iters=10000)\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n****************###########\nforest-pasture \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n********************************************************************\n\nComparison \tdCXYScore\tSignificance\n\nforest-pasture \t0.00500262\t0.0086\n\npasture-forest \t0.00289600\t0.0615\n\n\nOutput File Names: \ndist.libshuff.summary\ndist.libshuff.coverage\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1672.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1673.dat' group.dat && echo 'libshuff( phylip=dist.dat, group=group.dat, groups=forest-pasture, sim=false, step=0.25, cutoff=0.25, iters=10000 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:47:23.914400", "params": {"form": "{\"form2\": \"discrete\", \"step\": \"0.25\", \"__current_case__\": 1, \"cutoff\": \"0.25\"}", "iters": "\"10000\"", "dbkey": "\"hg17\"", "groups": "[\"forest\", \"pasture\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "sim": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24259", "id": "6eb09fe0ca80e9ad", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_libshuff.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "03515b901bb7065c"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "03515b901bb7065c", "uuid": "7d8f0902-b27b-482b-b7b2-68062efece02"}}, "update_time": "2018-02-08T17:47:44.898090", "tool_id": "mothur_list_otulabels", "outputs": {"__new_primary_file_unique\|0.10__": {"src": "hda", "id": "1d124e18e52f63d6", "uuid": "43571c49-d01e-49dd-b357-784a688b67b7"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "e4eea0d00dd11fc1", "uuid": "3bc47209-507b-4bef-a09e-2a470838ddf3"}, "__new_primary_file_unique\|0.17__": {"src": "hda", "id": "0f127131f3eb2bfd", "uuid": "f479223f-8830-4086-adec-517a1bbe14cf"}, "__new_primary_file_unique\|0.02__": {"src": "hda", "id": "e98378c72dd331ce", "uuid": "c303d2bf-1895-46f0-aa12-a075667eacd8"}, "__new_primary_file_unique\|0.21__": {"src": "hda", "id": "102e4f978a39c67b", "uuid": "c57020f8-a106-4414-84b1-8c90cddfe6fb"}, "__new_primary_file_unique\|0.16__": {"src": "hda", "id": "511779d6bc9751e8", "uuid": "b545984e-ffbb-4573-8967-34a02064b17c"}, "__new_primary_file_unique\|0.45__": {"src": "hda", "id": "da0dba679b1ff231", "uuid": "09097db4-4139-4801-b08f-9eaf37d6ebce"}, "__new_primary_file_unique\|0.03__": {"src": "hda", "id": "dfc4bdd80e844267", "uuid": "d976179c-5b00-45e2-849b-be48d3768b0f"}, "__new_primary_file_unique\|0.15__": {"src": "hda", "id": "29e2d6771c60c803", "uuid": "39c4051b-8b46-453e-84d7-f3bc7779c936"}, "__new_primary_file_unique\|0.08__": {"src": "hda", "id": "1f6c0bf0abda3a36", "uuid": "5f97d8d5-7362-4f87-b5fb-3755e0f8e3b7"}, "__new_primary_file_unique\|0.14__": {"src": "hda", "id": "046c583ea67d56fe", "uuid": "fc632040-56b9-47b0-8cff-625533d47792"}, "__new_primary_file_unique\|0.13__": {"src": "hda", "id": "6d3f04dcd4f83b40", "uuid": "dfaffc5e-216d-4867-91a6-25370405386f"}, "__new_primary_file_unique\|0.09__": {"src": "hda", "id": "bac292913e61351f", "uuid": "703444c0-9ba6-4550-b52b-3b20d36cd2cb"}, "__new_primary_file_unique\|0.12__": {"src": "hda", "id": "6c240f6767045bc7", "uuid": "7923dc0a-8dc7-4e53-aaf9-007771a94681"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "5d51f2eb28447d68", "uuid": "ff23e7fb-20d5-4922-8750-a01fe8aaa1a3"}, "__new_primary_file_unique\|0.11__": {"src": "hda", "id": "9efd53024480d419", "uuid": "18440ce6-14b8-4ba0-9a30-bc4897ee117f"}, "__new_primary_file_unique\|0.41__": {"src": "hda", "id": "5cee183d473e5065", "uuid": "fb9b3b63-f9fa-4dff-b85c-c2073fc04577"}, "__new_primary_file_unique\|0.06__": {"src": "hda", "id": "8ae7d654d115358b", "uuid": "0bdbe523-7a38-4898-bf1d-7b6ea5a81f9c"}, "__new_primary_file_unique\|0.25__": {"src": "hda", "id": "071905bbb8e343b5", "uuid": "8bddde77-2e1a-48c3-8194-396b5ab2af56"}, "__new_primary_file_unique\|0.22__": {"src": "hda", "id": "3e4dfa0ba4528210", "uuid": "89788c08-81a1-44d7-894f-cf9117672a38"}, "__new_primary_file_unique\|0.36__": {"src": "hda", "id": "207deb3ab3773d6e", "uuid": "032b2031-ad18-4990-b85a-2f7a69664241"}, "__new_primary_file_unique\|0.04__": {"src": "hda", "id": "4d7e2d7680b0f930", "uuid": "45702390-3a68-43d6-8611-7fa08fceab0c"}, "__new_primary_file_unique\|0.23__": {"src": "hda", "id": "ee5577484782be17", "uuid": "f6d7b004-22f6-4c71-973b-59a4b9d42703"}, "__new_primary_file_unique\|0.33__": {"src": "hda", "id": "9f1be559dcee58e4", "uuid": "338d2719-bd3a-4314-823e-fc375345a4cf"}, "logfile": {"src": "hda", "id": "eabc8b40ba5517ea", "uuid": "52bd6bf7-6519-4db6-90d9-2e94bd5cebea"}, "__new_primary_file_unique\|0.20__": {"src": "hda", "id": "84978e4e99593596", "uuid": "7159457d-d852-4043-a553-f6203c785eb6"}, "__new_primary_file_unique\|0.29__": {"src": "hda", "id": "791caff901bcced2", "uuid": "5d5663aa-90f1-4dd1-bcc3-7d75f5f1d512"}, "__new_primary_file_unique\|0.38__": {"src": "hda", "id": "a254ed162f2c861f", "uuid": "5449536b-602f-4cb2-b7f4-962f6ef68935"}, "__new_primary_file_unique\|0.55__": {"src": "hda", "id": "da52058ee935cacf", "uuid": "0510615d-706e-4a59-941a-42f81914f237"}, "__new_primary_file_unique\|0.07__": {"src": "hda", "id": "e42a943db0671336", "uuid": "e5f093e3-26e9-41eb-8a2f-b498242c876f"}, "__new_primary_file_unique\|0.26__": {"src": "hda", "id": "0f9af512d4e9c186", "uuid": "c8c56ede-3e49-41dc-a259-dafffc9cec14"}, "__new_primary_file_unique\|0.32__": {"src": "hda", "id": "9dd182eaaac31990", "uuid": "20386d9f-3bf1-4fb6-852f-8ff182f333df"}, "__new_primary_file_unique\|0.27__": {"src": "hda", "id": "566a42aa096b25c3", "uuid": "27d523b1-85da-4fc9-afa6-1dbbe5aec3f7"}, "__new_primary_file_unique\|0.19__": {"src": "hda", "id": "98d05f669e70824c", "uuid": "107b9482-ee08-47a5-83f0-4f1dc6429926"}, "__new_primary_file_unique\|0.01__": {"src": "hda", "id": "5d7f51f61764264a", "uuid": "9f25bddf-d98f-4a32-84c9-49bd1cb35377"}, "__new_primary_file_unique\|0.24__": {"src": "hda", "id": "94c8505ae27068a3", "uuid": "6d194638-4392-4ff1-a076-62bd7235a064"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "fdb3c5bd15bc0651", "uuid": "780b8b1b-3593-4a03-acf9-b0b75bd52b24"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > list.otulabels(list=otu.dat)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.unique.otulabels\notu.0.01.otulabels\notu.0.02.otulabels\notu.0.03.otulabels\notu.0.04.otulabels\notu.0.05.otulabels\notu.0.06.otulabels\notu.0.07.otulabels\notu.0.08.otulabels\notu.0.09.otulabels\notu.0.10.otulabels\notu.0.11.otulabels\notu.0.12.otulabels\notu.0.13.otulabels\notu.0.14.otulabels\notu.0.15.otulabels\notu.0.16.otulabels\notu.0.17.otulabels\notu.0.18.otulabels\notu.0.19.otulabels\notu.0.20.otulabels\notu.0.21.otulabels\notu.0.22.otulabels\notu.0.23.otulabels\notu.0.24.otulabels\notu.0.25.otulabels\notu.0.26.otulabels\notu.0.27.otulabels\notu.0.29.otulabels\notu.0.32.otulabels\notu.0.33.otulabels\notu.0.36.otulabels\notu.0.38.otulabels\notu.0.41.otulabels\notu.0.45.otulabels\notu.0.55.otulabels\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1677.dat' otu.dat && echo 'list.otulabels( list=otu.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:47:40.035318", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groups": "null", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24355", "id": "09dbeac489d85549", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_list_otulabels.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "7ce5ee5ae5d96148"}, "groups": "forest"}, "job": {"inputs": {"otu": {"src": "hda", "id": "7ce5ee5ae5d96148", "uuid": "629a26cb-120d-42bb-a917-3507c7a35418"}}, "update_time": "2018-02-08T17:48:11.584139", "tool_id": "mothur_list_otulabels", "outputs": {"__new_primary_file_unique\|0.10__": {"src": "hda", "id": "c77fbb66c7668cd4", "uuid": "e3a05278-a424-4f20-b031-29fa9a7fa9f8"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "717b2cf20a54ded4", "uuid": "4b2b6afc-25c4-4653-a862-79631562fb61"}, "__new_primary_file_unique\|0.17__": {"src": "hda", "id": "d2ce13293faca460", "uuid": "b6e06792-d467-48c8-b40b-51b038ab70ad"}, "__new_primary_file_unique\|0.02__": {"src": "hda", "id": "f0912769592a4e8c", "uuid": "e545aa5a-7692-42fb-b8d9-61ea22fe33a1"}, "__new_primary_file_unique\|0.21__": {"src": "hda", "id": "f0fe4746ca4a5cb1", "uuid": "dae9e7f3-2427-4449-90b8-17276da76712"}, "__new_primary_file_unique\|0.16__": {"src": "hda", "id": "5828ffd76b6255d8", "uuid": "3a2848ec-f49a-49a7-bdea-50917937318c"}, "__new_primary_file_unique\|0.45__": {"src": "hda", "id": "13115f036dcfbd13", "uuid": "eddceaf9-34d4-4a66-b453-ad1e42fb8dc1"}, "__new_primary_file_unique\|0.03__": {"src": "hda", "id": "e10a735ff6c491f5", "uuid": "2d058ae9-31bd-49b6-94ac-77b47d0246ee"}, "__new_primary_file_unique\|0.15__": {"src": "hda", "id": "09e374ba6c9df1b6", "uuid": "f90bc0fb-0b7e-44cf-b816-a72b1ed30834"}, "__new_primary_file_unique\|0.08__": {"src": "hda", "id": "aa1c99020c7a5496", "uuid": "746158e2-fa91-4263-8728-7bfbce770538"}, "__new_primary_file_unique\|0.14__": {"src": "hda", "id": "2ce508ad7dc7ffe8", "uuid": "2f412f03-52b6-4026-9667-a25b2be652be"}, "__new_primary_file_unique\|0.13__": {"src": "hda", "id": "96df058c67bf3756", "uuid": "b6f88151-19b5-441e-b4a4-29ba406a55de"}, "__new_primary_file_unique\|0.09__": {"src": "hda", "id": "1e1097535bca43f6", "uuid": "096f9562-7a76-42d3-ba5b-1d8004fbe29a"}, "__new_primary_file_unique\|0.12__": {"src": "hda", "id": "d9c53c113024c2ff", "uuid": "95f38409-54a2-458d-9c73-637d017ce72f"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "ae08f308b8be372c", "uuid": "644ef164-ef54-4991-b6e3-c14bf7306b09"}, "__new_primary_file_unique\|0.11__": {"src": "hda", "id": "b6c238a14dcfd0b8", "uuid": "33420052-8afa-4719-ac1c-c1821c4f9bf4"}, "__new_primary_file_unique\|0.41__": {"src": "hda", "id": "306338cd3056de25", "uuid": "3e5974d8-4c08-4504-b4b7-4b42af41f9a0"}, "__new_primary_file_unique\|0.06__": {"src": "hda", "id": "0ceb1b0e1e46c312", "uuid": "5a36fae3-2fa1-46f0-917f-76de86e29a70"}, "__new_primary_file_unique\|0.25__": {"src": "hda", "id": "330f23492086f076", "uuid": "b22bb044-989b-495e-be17-366d614a309a"}, "__new_primary_file_unique\|0.22__": {"src": "hda", "id": "861415528bc25cb7", "uuid": "f6afa0f8-20e6-4d0a-9a1c-1ae169842bfc"}, "__new_primary_file_unique\|0.36__": {"src": "hda", "id": "938c47791fccd58a", "uuid": "d4f17b45-c40e-4a6c-94f8-b631ec5d925c"}, "__new_primary_file_unique\|0.04__": {"src": "hda", "id": "035ac92f40b8d8a9", "uuid": "0b125a96-5b32-4501-b360-b982ce27236e"}, "__new_primary_file_unique\|0.23__": {"src": "hda", "id": "2ba6ff9c01b5db74", "uuid": "b4acf26a-f6b5-40c6-b960-ecec9fe811b6"}, "__new_primary_file_unique\|0.33__": {"src": "hda", "id": "79c26bac844e1a03", "uuid": "637026ef-b3ed-4e17-b0f9-8ca825ee950d"}, "logfile": {"src": "hda", "id": "2df65164c2a87bdc", "uuid": "56e7ab14-244b-4ee0-b40e-6215c9c539fa"}, "__new_primary_file_unique\|0.20__": {"src": "hda", "id": "aa19462bf237ee74", "uuid": "cad5634f-3445-42ec-bb8f-ee3141eb3459"}, "__new_primary_file_unique\|0.29__": {"src": "hda", "id": "bd16ccfcb6f28f4b", "uuid": "2a3390f4-a79b-40e4-a074-06c1b585f817"}, "__new_primary_file_unique\|0.38__": {"src": "hda", "id": "8cada7d471147894", "uuid": "f0021787-d9ed-44fc-aeb7-e5ca738fa31f"}, "__new_primary_file_unique\|0.55__": {"src": "hda", "id": "4618478724b1d128", "uuid": "35b26fef-9160-4e42-bffc-7a9a2c2acd41"}, "__new_primary_file_unique\|0.07__": {"src": "hda", "id": "00a9b8f80d5c35db", "uuid": "9ff0b0f4-e24b-4a5b-a9ef-3c99aaa43615"}, "__new_primary_file_unique\|0.26__": {"src": "hda", "id": "e699037a579b0cad", "uuid": "298b1cee-f6b6-42fb-b5bd-bbb7b4057061"}, "__new_primary_file_unique\|0.32__": {"src": "hda", "id": "0f4cd4de4fddb960", "uuid": "ba0f8840-ec46-40dd-9346-2daf3d11a964"}, "__new_primary_file_unique\|0.27__": {"src": "hda", "id": "be56adfd92e0d058", "uuid": "f63c2a9e-b301-45a4-8689-b0dfe4216641"}, "__new_primary_file_unique\|0.19__": {"src": "hda", "id": "4502c5e78b18d95e", "uuid": "1b2321ce-5b3f-4ec2-aee6-5463412c94a3"}, "__new_primary_file_unique\|0.01__": {"src": "hda", "id": "710278472322a44f", "uuid": "57996085-931a-4897-87e3-a3ba1dc7a451"}, "__new_primary_file_unique\|0.24__": {"src": "hda", "id": "6a9e5657586fa330", "uuid": "218dd813-729e-4edb-a210-9efd78a05d10"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "5f438a17e0a96676", "uuid": "9c0a9e33-9cbd-4a88-8105-46a2d7a26145"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > list.otulabels(shared=otu.dat,groups=forest)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.unique.otulabels\notu.0.01.otulabels\notu.0.02.otulabels\notu.0.03.otulabels\notu.0.04.otulabels\notu.0.05.otulabels\notu.0.06.otulabels\notu.0.07.otulabels\notu.0.08.otulabels\notu.0.09.otulabels\notu.0.10.otulabels\notu.0.11.otulabels\notu.0.12.otulabels\notu.0.13.otulabels\notu.0.14.otulabels\notu.0.15.otulabels\notu.0.16.otulabels\notu.0.17.otulabels\notu.0.18.otulabels\notu.0.19.otulabels\notu.0.20.otulabels\notu.0.21.otulabels\notu.0.22.otulabels\notu.0.23.otulabels\notu.0.24.otulabels\notu.0.25.otulabels\notu.0.26.otulabels\notu.0.27.otulabels\notu.0.29.otulabels\notu.0.32.otulabels\notu.0.33.otulabels\notu.0.36.otulabels\notu.0.38.otulabels\notu.0.41.otulabels\notu.0.45.otulabels\notu.0.55.otulabels\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1715.dat' otu.dat && echo 'list.otulabels( shared=otu.dat ,groups=forest )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:48:06.700381", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groups": "\"forest\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24441", "id": "3a07e8fa101f66c3", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_list_otulabels.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"search\|input": {"src": "hda", "id": "bddc530082ef8a20"}, "search\|intype": "fasta"}, "job": {"inputs": {"input": {"src": "hda", "id": "bddc530082ef8a20", "uuid": "949ae96f-0362-4b67-92e8-be705e219275"}}, "update_time": "2018-02-08T17:48:30.417744", "tool_id": "mothur_list_seqs", "outputs": {"logfile": {"src": "hda", "id": "37b4fa647e89d65b", "uuid": "363b76a4-71ba-472d-b2af-a9993410eb84"}, "accnos": {"src": "hda", "id": "cc03cfa56ce85621", "uuid": "853392dc-4c63-478b-85cc-5f4a20fc9f9a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > list.seqs(fasta=search.input.dat)\n\nOutput File Names: \nsearch.input.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1753.dat' search.input.dat && echo 'list.seqs( fasta=search.input.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:48:27.251930", "params": {"search": "{\"input\": {\"values\": [{\"src\": \"hda\", \"id\": 1753}]}, \"intype\": \"fasta\", \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24527", "id": "a8b7bad9a0464ba9", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_list_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"search\|input": {"src": "hda", "id": "8fd9b8ef17ae00b1"}, "search\|intype": "count"}, "job": {"inputs": {"input": {"src": "hda", "id": "8fd9b8ef17ae00b1", "uuid": "71a0a345-5ef4-451a-81d5-830ab3ad315c"}}, "update_time": "2018-02-08T17:48:47.846109", "tool_id": "mothur_list_seqs", "outputs": {"logfile": {"src": "hda", "id": "14a780cce250e27d", "uuid": "d3f0444f-4f52-44ad-ad38-44a9bca04a96"}, "accnos": {"src": "hda", "id": "812d58a31cb0e2dc", "uuid": "048efb02-e858-49f5-959c-8a122946fa2f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > list.seqs(count=search.input.dat)\n\nOutput File Names: \nsearch.input.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1756.dat' search.input.dat && echo 'list.seqs( count=search.input.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:48:44.763422", "params": {"search": "{\"input\": {\"values\": [{\"src\": \"hda\", \"id\": 1756}]}, \"intype\": \"count\", \"__current_case__\": 7}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24617", "id": "7b32cfe10869d24e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_list_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "bfae85c1836289e5"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "bfae85c1836289e5", "uuid": "0f8f79f6-42d3-4908-9e5e-9fa7368630da"}}, "update_time": "2018-02-08T17:49:07.085680", "tool_id": "mothur_make_biom", "outputs": {"__new_primary_file_unique\|0.10__": {"src": "hda", "id": "0915854899960126", "uuid": "d64654a5-1a30-430a-ac1a-005c525a06b9"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "1b9599242429ea82", "uuid": "f55ce27e-c13d-493c-9d7f-c4444c538749"}, "__new_primary_file_unique\|0.17__": {"src": "hda", "id": "6a2c7b5090ae2641", "uuid": "2b0f00ed-c062-419e-929e-cb19c1e9cbc7"}, "__new_primary_file_unique\|0.02__": {"src": "hda", "id": "d8977dbfd5fe2600", "uuid": "016a6cad-0a69-4239-8e19-012adb3b3e06"}, "__new_primary_file_unique\|0.21__": {"src": "hda", "id": "1198cc8050ddcaae", "uuid": "6f6cae48-5375-443b-b28f-28d5ccfae448"}, "__new_primary_file_unique\|0.16__": {"src": "hda", "id": "4b2729dfe19d84de", "uuid": "8319c5c2-6b30-48d4-86a9-6bcfe0da2c84"}, "__new_primary_file_unique\|0.45__": {"src": "hda", "id": "7027bb045e039323", "uuid": "62102e99-f3ec-4cee-bde5-baa2ef469b14"}, "__new_primary_file_unique\|0.03__": {"src": "hda", "id": "5608a3ee5cd775a6", "uuid": "5855cbdf-9ef8-4e03-9e39-6b08f909ad14"}, "__new_primary_file_unique\|0.15__": {"src": "hda", "id": "fec153023f9b1d9e", "uuid": "77cb4dc6-b006-421b-a1de-07a50fc52ada"}, "__new_primary_file_unique\|0.08__": {"src": "hda", "id": "003c8452d769ee89", "uuid": "8fc0f9e9-8437-48e0-97a4-48819ad9d079"}, "__new_primary_file_unique\|0.14__": {"src": "hda", "id": "8163ea9a30f0397d", "uuid": "4661216f-bea5-40ce-ad43-7ec3be0de710"}, "__new_primary_file_unique\|0.13__": {"src": "hda", "id": "8f46422d2f09daf7", "uuid": "2824087a-7d29-4de4-bc5b-1e5d570c097f"}, "__new_primary_file_unique\|0.09__": {"src": "hda", "id": "a5a9105172fdd91a", "uuid": "c4b734f4-24d7-4db9-94d7-65c624345fb8"}, "__new_primary_file_unique\|0.12__": {"src": "hda", "id": "64eef14501ccd4ab", "uuid": "52662d8c-6207-41b7-b89e-efc9fb8ffd10"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "de02e3e208bf1269", "uuid": "c0b2f1ff-287f-42ff-91ac-b66d2c20b76c"}, "__new_primary_file_unique\|0.11__": {"src": "hda", "id": "e3f5b81c3cbfdcdf", "uuid": "4f669977-d70b-4bf9-ac7d-b151cd0519e9"}, "__new_primary_file_unique\|0.41__": {"src": "hda", "id": "11a4cfd609b30231", "uuid": "2a9fb9af-2e93-40c6-a070-1ddd29d71233"}, "__new_primary_file_unique\|0.06__": {"src": "hda", "id": "39f31be0d2a47263", "uuid": "c5860154-e79a-4168-92ad-b5cfa370c6c6"}, "__new_primary_file_unique\|0.25__": {"src": "hda", "id": "167e0067a671882a", "uuid": "d9b9dc3d-f24e-413d-9435-02b84aadc3b0"}, "__new_primary_file_unique\|0.22__": {"src": "hda", "id": "d19d640fc3be2602", "uuid": "0e8f323c-3c29-4dfb-8da4-6e5256b824b9"}, "__new_primary_file_unique\|0.36__": {"src": "hda", "id": "1530f791843ef8a6", "uuid": "a0444193-49e6-4494-91c9-f54559c5b2dd"}, "__new_primary_file_unique\|0.04__": {"src": "hda", "id": "3dc5251947e7e28a", "uuid": "77a5052b-e9d0-427d-a791-6a87225a01cc"}, "__new_primary_file_unique\|0.23__": {"src": "hda", "id": "eb8ff02f919a6d53", "uuid": "63062340-9cb6-428d-a49a-8279ece828a5"}, "__new_primary_file_unique\|0.33__": {"src": "hda", "id": "0dc27fbedcc45ffc", "uuid": "de5d6db7-b33f-485b-939e-273ff9ec3430"}, "logfile": {"src": "hda", "id": "15a27f85b655084f", "uuid": "26755b2e-9832-4f7d-acb2-9d1d847c2b51"}, "__new_primary_file_unique\|0.20__": {"src": "hda", "id": "e14d9e71cf2baa46", "uuid": "4c3dd9a9-86f0-4518-ba22-e93881251f9d"}, "__new_primary_file_unique\|0.29__": {"src": "hda", "id": "aae81213b7398bbb", "uuid": "d0a16ace-ab73-4d26-93c3-0724b3887a6d"}, "__new_primary_file_unique\|0.38__": {"src": "hda", "id": "8730f173539a4bd2", "uuid": "b9342ef9-4afa-4a3e-a1c5-5175e0fe0da8"}, "__new_primary_file_unique\|0.55__": {"src": "hda", "id": "5bd80237c4b2a4d2", "uuid": "2ae4018d-6c82-40ea-a836-e45678ec92c7"}, "__new_primary_file_unique\|0.07__": {"src": "hda", "id": "3e009a540553e32f", "uuid": "52b0efc8-143b-49a5-94a7-9c0e0cf686ba"}, "__new_primary_file_unique\|0.26__": {"src": "hda", "id": "bd8570a9749b756e", "uuid": "2629c96b-cff5-4116-8545-b1349908a6c9"}, "__new_primary_file_unique\|0.32__": {"src": "hda", "id": "cfc1466e3cee5ffe", "uuid": "3ad83ef3-d941-4dfe-ba65-2faebc5c943e"}, "__new_primary_file_unique\|0.27__": {"src": "hda", "id": "90655b23123ebb49", "uuid": "06c79f68-a6b2-486b-9256-d2a202109b22"}, "__new_primary_file_unique\|0.19__": {"src": "hda", "id": "4df3a051f1ec097e", "uuid": "3c9f80b5-e238-47da-87b7-e809ad9650d2"}, "__new_primary_file_unique\|0.01__": {"src": "hda", "id": "5ac9d236a72d89c9", "uuid": "dc1a9140-6481-4007-80d2-082030ded364"}, "__new_primary_file_unique\|0.24__": {"src": "hda", "id": "71ecf7184a915076", "uuid": "c8c31def-b63e-4562-97d7-b33efb01d479"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "faecacf595ac39e2", "uuid": "2afa052a-b65f-4497-8a1d-a0ac9586133e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.biom(shared=otu.dat,matrixtype=sparse)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.unique.biom\notu.0.01.biom\notu.0.02.biom\notu.0.03.biom\notu.0.04.biom\notu.0.05.biom\notu.0.06.biom\notu.0.07.biom\notu.0.08.biom\notu.0.09.biom\notu.0.10.biom\notu.0.11.biom\notu.0.12.biom\notu.0.13.biom\notu.0.14.biom\notu.0.15.biom\notu.0.16.biom\notu.0.17.biom\notu.0.18.biom\notu.0.19.biom\notu.0.20.biom\notu.0.21.biom\notu.0.22.biom\notu.0.23.biom\notu.0.24.biom\notu.0.25.biom\notu.0.26.biom\notu.0.27.biom\notu.0.29.biom\notu.0.32.biom\notu.0.33.biom\notu.0.36.biom\notu.0.38.biom\notu.0.41.biom\notu.0.45.biom\notu.0.55.biom\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1759.dat' otu.dat && ln -s 'None' constaxonomy.dat && ln -s 'None' metadata.dat && echo 'make.biom( shared=otu.dat, matrixtype=sparse )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:49:02.186797", "params": {"matrixtype": "\"sparse\"", "picrustc": "{\"use\": \"no\", \"__current_case__\": 1}", "dbkey": "\"hg17\"", "label": "null", "groups": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "constaxonomy": "null", "metadata": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24703", "id": "3fc9b5ca07992501", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_biom.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "9f85b398b863e225"}, "groups": "forest", "label": ["0.36", "0.38", "0.41"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "9f85b398b863e225", "uuid": "60bfcab3-d3b9-44ff-aca3-32717277d27a"}}, "update_time": "2018-02-08T17:49:25.911998", "tool_id": "mothur_make_biom", "outputs": {"__new_primary_file_0.41\|0.38__": {"src": "hda", "id": "6124a241728fed7b", "uuid": "b762f29a-2704-443f-b4d3-bbea479d086b"}, "logfile": {"src": "hda", "id": "101d321fbee7d3a2", "uuid": "83c2a1a4-92e5-4f94-83e5-cc2bb65c66bf"}, "__new_primary_file_0.41\|0.36__": {"src": "hda", "id": "39279bb4f32c9cd5", "uuid": "0fef610e-5bb0-4a7f-90c3-a32bcb82e1cf"}, "__new_primary_file_0.41\|0.41__": {"src": "hda", "id": "bcc6ea767bb5f894", "uuid": "8ad1e0bb-4ec2-4c11-8a8b-748de9043914"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.biom(shared=otu.dat,label=0.36-0.38-0.41,groups=forest,matrixtype= \rsparse)\n0.36\n0.38\n0.41\n\nOutput File Names: \notu.0.36.biom\notu.0.38.biom\notu.0.41.biom\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1797.dat' otu.dat && ln -s 'None' constaxonomy.dat && ln -s 'None' metadata.dat && echo 'make.biom( shared=otu.dat, label=0.36-0.38-0.41, groups=forest, matrixtype=sparse )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:49:22.733946", "params": {"matrixtype": "\"sparse\"", "picrustc": "{\"use\": \"no\", \"__current_case__\": 1}", "dbkey": "\"hg17\"", "label": "[\"0.36\", \"0.38\", \"0.41\"]", "groups": "\"forest\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "constaxonomy": "null", "metadata": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24791", "id": "6c12052addbdbf10", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_biom.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "45a7e4eec17b01cd"}, "constaxonomy": {"src": "hda", "id": "bf5dc6d85ce11a2a"}, "metadata": {"src": "hda", "id": "68fe6c8323c3e617"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "45a7e4eec17b01cd", "uuid": "c7c39dbf-9d32-4c75-aa2b-72d738c2356d"}, "constaxonomy": {"src": "hda", "id": "bf5dc6d85ce11a2a", "uuid": "2182557c-bb36-4e43-9f24-6026f34e8869"}, "metadata": {"src": "hda", "id": "68fe6c8323c3e617", "uuid": "b1eab905-87df-40e4-aaf2-697205e2c2ab"}}, "update_time": "2018-02-08T17:49:45.406914", "tool_id": "mothur_make_biom", "outputs": {"logfile": {"src": "hda", "id": "a54f199e2763d2d1", "uuid": "76e1e856-efb0-4095-9f38-8cb64dd2847e"}, "__new_primary_file_1\|1__": {"src": "hda", "id": "7fc77adef3161147", "uuid": "56d5e4b4-b16b-44d9-9a30-7af0343c66cb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.biom(shared=otu.dat,constaxonomy=constaxonomy.dat,metadata=metadat \ra.dat,matrixtype=sparse)\n1\n\nOutput File Names: \notu.1.biom\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1802.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1803.dat' constaxonomy.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1804.dat' metadata.dat && echo 'make.biom( shared=otu.dat, constaxonomy=constaxonomy.dat, metadata=metadata.dat, matrixtype=sparse )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:49:42.311244", "params": {"matrixtype": "\"sparse\"", "picrustc": "{\"use\": \"no\", \"__current_case__\": 1}", "dbkey": "\"hg17\"", "label": "null", "groups": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24934", "id": "3cb3ad12c0574547", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_biom.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"input_type\|forward_fastq": {"src": "hda", "id": "40b793aeee43e4b6"}, "input_type\|reverse_fastq": {"src": "hda", "id": "8da9ebed1ea03269"}, "input_type\|type": "regular"}, "job": {"inputs": {"forward_fastq": {"src": "hda", "id": "40b793aeee43e4b6", "uuid": "d177e8df-000a-438c-866c-8da4fb15a7e8"}, "reverse_fastq": {"src": "hda", "id": "8da9ebed1ea03269", "uuid": "4183434a-6517-4bf4-8aef-45298a77e00e"}}, "update_time": "2018-02-08T17:50:06.290005", "tool_id": "mothur_make_contigs", "outputs": {"scrapqual": {"src": "hda", "id": "bb84ff5118ea4500", "uuid": "6a187a01-8e75-4077-aba6-27cf1b2efc0c"}, "scrapfasta": {"src": "hda", "id": "609fed3f705180b0", "uuid": "40ef29cd-1760-461e-837c-fb9cf9ef54fc"}, "qual": {"src": "hda", "id": "e106c55583a975c8", "uuid": "f8b1c8aa-4338-4084-9e20-156d7b490568"}, "report": {"src": "hda", "id": "9356319465a4ba53", "uuid": "1a949e57-40e4-4dfe-8baf-2eb21796226f"}, "fasta": {"src": "hda", "id": "a4b7a61fc28685f4", "uuid": "c618030d-ef87-4a9b-af99-137e62eaa53d"}, "logfile": {"src": "hda", "id": "67a1201bdc0a51a0", "uuid": "f83d1e2d-870d-42fe-9107-b5be8f0ddd26"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.contigs(ffastq=ffastq.dat,rfastq=rfastq.dat,align=needleman,match= \r1,mismatch=-1,gapopen=-2,gapextend=-1,processors=1)\n\nUsing 1 processors.\nMaking contigs...\n25\nDone.\nIt took 0 secs to process 25 sequences.\n\n\nOutput File Names: \nffastq.trim.contigs.fasta\nffastq.scrap.contigs.fasta\nffastq.trim.contigs.qual\nffastq.scrap.contigs.qual\nffastq.contigs.report\n\n[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1807.dat' ffastq.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1808.dat' rfastq.dat && echo 'make.contigs( ffastq=ffastq.dat, rfastq=rfastq.dat, align=needleman, match=1, mismatch=-1, gapopen=-2, gapextend=-1, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:50:02.824847", "params": {"oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "input_type": "{\"forward_fastq\": {\"values\": [{\"src\": \"hda\", \"id\": 1807}]}, \"reverse_fastq\": {\"values\": [{\"src\": \"hda\", \"id\": 1808}]}, \"type\": \"regular\", \"__current_case__\": 0}", "align": "\"needleman\"", "gapopen": "\"-2\"", "mismatch": "\"-1\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "gapextend": "\"-1\"", "match": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25043", "id": "032dc790b013bafc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_contigs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input_type\|type": "simple_collection", "input_type\|paired_collection": {"src": "hdca", "id": "b323ca264f40001e"}}, "job": {"inputs": {"paired_collection1": {"src": "hda", "id": "0e34f88fe3f1ff0f", "uuid": "c4b8cf08-3eaa-4a06-b0ce-2cfb892f5b33"}, "paired_collection2": {"src": "hda", "id": "f1d296c611fd20af", "uuid": "4980d4b2-7b82-452f-b610-85ef365a1cc6"}}, "update_time": "2018-02-08T17:50:39.239356", "tool_id": "mothur_make_contigs", "outputs": {"scrapqual": {"src": "hda", "id": "1c4bd19fb1ecc433", "uuid": "7b96413f-88d9-4095-8e81-41daaaf25b5b"}, "scrapfasta": {"src": "hda", "id": "5f1708e38b3558fc", "uuid": "50c50c4c-681f-4366-800b-0650b3179bcd"}, "qual": {"src": "hda", "id": "1bd9d366bb876da0", "uuid": "76592125-34b1-404a-bae8-e434bc0ecb57"}, "report": {"src": "hda", "id": "38241bcf61ff4dc4", "uuid": "e4407411-a51e-4918-be13-cae227dafa01"}, "fasta": {"src": "hda", "id": "0cf22b7aa65fb1a8", "uuid": "cec921c2-641b-47f7-b989-4a16060eb8bb"}, "logfile": {"src": "hda", "id": "2437f8b06af7836c", "uuid": "4998833e-6620-4888-8ebd-4427df633478"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.contigs(ffastq=ffastq.dat,rfastq=rfastq.dat,align=needleman,match= \r1,mismatch=-1,gapopen=-2,gapextend=-1,processors=1)\n\nUsing 1 processors.\nMaking contigs...\n25\nDone.\nIt took 0 secs to process 25 sequences.\n\n\nOutput File Names: \nffastq.trim.contigs.fasta\nffastq.scrap.contigs.fasta\nffastq.trim.contigs.qual\nffastq.scrap.contigs.qual\nffastq.contigs.report\n\n[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1815.dat' ffastq.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1816.dat' rfastq.dat && echo 'make.contigs( ffastq=ffastq.dat, rfastq=rfastq.dat, align=needleman, match=1, mismatch=-1, gapopen=-2, gapextend=-1, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:50:35.719002", "params": {"oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "input_type": "{\"paired_collection\": {\"values\": [{\"src\": \"hdca\", \"id\": 70}]}, \"type\": \"simple_collection\", \"__current_case__\": 1}", "align": "\"needleman\"", "gapopen": "\"-2\"", "mismatch": "\"-1\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "gapextend": "\"-1\"", "match": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25159", "id": "4a03c449ab1f345a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_contigs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input_type\|type": "simple_collection", "input_type\|paired_collection": {"src": "hdca", "id": "08fbf3fbfe908f7c"}, "align": "gotoh", "gapopen": "-3", "mismatch": "-2", "gapextend": "-2", "match": "2"}, "job": {"inputs": {"paired_collection1": {"src": "hda", "id": "91ae388b1da266fc", "uuid": "0b67f0e7-1839-4bf7-a7b6-7e9b43f66848"}, "paired_collection2": {"src": "hda", "id": "b97b38fe046d6cc3", "uuid": "86c5e085-9f4a-4f4c-9ae5-b8cfc143dd03"}}, "update_time": "2018-02-08T17:51:09.729195", "tool_id": "mothur_make_contigs", "outputs": {"scrapqual": {"src": "hda", "id": "d9efe2ab3f0b324f", "uuid": "b3333766-777b-4e7e-9ab5-93a62a99364f"}, "scrapfasta": {"src": "hda", "id": "8b7d704c8dec53b3", "uuid": "2ce03472-3cd8-484d-a1f2-740e8bd6573d"}, "qual": {"src": "hda", "id": "bd6616cdad8b15de", "uuid": "aa923b33-96f3-476e-8f3d-9c1698a89575"}, "report": {"src": "hda", "id": "9529b46206034a2c", "uuid": "ed4518c1-1549-4607-aa5d-0d416351c12c"}, "fasta": {"src": "hda", "id": "bde0ddf414dac721", "uuid": "04370737-4778-4385-9606-195aff41b2ac"}, "logfile": {"src": "hda", "id": "4c02de16bce2c9b2", "uuid": "7348bc0c-b9db-4660-81c0-f0822b689e9b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.contigs(ffastq=ffastq.dat,rfastq=rfastq.dat,align=gotoh,match=2,mi \rsmatch=-2,gapopen=-3,gapextend=-2,processors=1)\n\nUsing 1 processors.\nMaking contigs...\n25\nDone.\nIt took 1 secs to process 25 sequences.\n\n\nOutput File Names: \nffastq.trim.contigs.fasta\nffastq.scrap.contigs.fasta\nffastq.trim.contigs.qual\nffastq.scrap.contigs.qual\nffastq.contigs.report\n\n[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1823.dat' ffastq.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1824.dat' rfastq.dat && echo 'make.contigs( ffastq=ffastq.dat, rfastq=rfastq.dat, align=gotoh, match=2, mismatch=-2, gapopen=-3, gapextend=-2, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:51:06.412196", "params": {"oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "input_type": "{\"paired_collection\": {\"values\": [{\"src\": \"hdca\", \"id\": 71}]}, \"type\": \"simple_collection\", \"__current_case__\": 1}", "align": "\"gotoh\"", "gapopen": "\"-3\"", "mismatch": "\"-2\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "gapextend": "\"-2\"", "match": "\"2\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25275", "id": "2afa7a4578b8f4fd", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_contigs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"input_type\|type": "list_collection", "input_type\|list_paired_collection": {"src": "hdca", "id": "ca4ebafec84c6506"}}, "job": {"inputs": {"list_paired_collection4": {"src": "hda", "id": "99e29abee4bbbed4", "uuid": "a78035ab-1253-4bb6-a4ca-3dc8352d355a"}, "list_paired_collection2": {"src": "hda", "id": "e655594793c63949", "uuid": "17cbba95-5854-4048-b01a-ae8523a58668"}, "list_paired_collection3": {"src": "hda", "id": "d5278219f70ebcfa", "uuid": "d2403292-9ed0-42fd-ae7c-07fee2f5166e"}, "list_paired_collection1": {"src": "hda", "id": "374d576ea0abb1c1", "uuid": "658855be-1bc8-4e8f-8016-92a344cb7f32"}}, "update_time": "2018-02-08T17:51:47.835378", "tool_id": "mothur_make_contigs", "outputs": {"scrapqual": {"src": "hda", "id": "6ccb9232700adf3a", "uuid": "e60c1270-4bfa-43d0-9b2c-5283f50341c8"}, "group": {"src": "hda", "id": "7843946a99274b74", "uuid": "bcc33c04-5751-496d-8025-9ffd9c43579b"}, "scrapfasta": {"src": "hda", "id": "6149d2026be5ab0e", "uuid": "3748da5e-abcc-4af1-9add-34059b824fb5"}, "qual": {"src": "hda", "id": "a5ab925c30b3f870", "uuid": "775aeca4-234d-449e-bdf2-f0313c2f18d3"}, "report": {"src": "hda", "id": "77ac7afdfe20d572", "uuid": "16a48568-2560-4d63-abf6-55dfa871ad94"}, "fasta": {"src": "hda", "id": "712f958ac1325a99", "uuid": "2c779df1-4ec7-466e-9fc5-c43a09076140"}, "logfile": {"src": "hda", "id": "7f39cb8d0fec48fe", "uuid": "f44c09a3-d08f-4a8c-9938-d7a117de4e71"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.contigs(file=combo_fastq.dat,align=needleman,match=1,mismatch=-1,g \rapopen=-2,gapextend=-1,processors=1)\n\nUsing 1 processors.\n\n>>>>>\tProcessing file pair dataset_1831.dat - dataset_1832.dat (files 1 of 2)\t<<<<<\nMaking contigs...\n25\nDone.\n\nIt took 0 secs to assemble 25 reads.\n\n\n>>>>>\tProcessing file pair dataset_1833.dat - dataset_1834.dat (files 2 of 2)\t<<<<<\nMaking contigs...\n5\nDone.\n\nIt took 0 secs to assemble 5 reads.\n\nIt took 0 secs to process 30 sequences.\n\nGroup count: \nPair1\t25\nPair2\t5\n\nTotal of all groups is 30\n\nOutput File Names: \ncombo_fastq.trim.contigs.fasta\ncombo_fastq.trim.contigs.qual\ncombo_fastq.contigs.report\ncombo_fastq.scrap.contigs.fasta\ncombo_fastq.scrap.contigs.qual\ncombo_fastq.contigs.groups\n\n[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s /tmp/saskia/tmpKSDp0p/files/001/dataset_1831.dat `basename /tmp/saskia/tmpKSDp0p/files/001/dataset_1831.dat` && ln -s /tmp/saskia/tmpKSDp0p/files/001/dataset_1832.dat `basename /tmp/saskia/tmpKSDp0p/files/001/dataset_1832.dat` && echo -e \"Pair1\\t`basename /tmp/saskia/tmpKSDp0p/files/001/dataset_1831.dat`\\t`basename /tmp/saskia/tmpKSDp0p/files/001/dataset_1832.dat`\" >> combo_fastq.dat && ln -s /tmp/saskia/tmpKSDp0p/files/001/dataset_1833.dat `basename /tmp/saskia/tmpKSDp0p/files/001/dataset_1833.dat` && ln -s /tmp/saskia/tmpKSDp0p/files/001/dataset_1834.dat `basename /tmp/saskia/tmpKSDp0p/files/001/dataset_1834.dat` && echo -e \"Pair2\\t`basename /tmp/saskia/tmpKSDp0p/files/001/dataset_1833.dat`\\t`basename /tmp/saskia/tmpKSDp0p/files/001/dataset_1834.dat`\" >> combo_fastq.dat && echo 'make.contigs( file=combo_fastq.dat, align=needleman, match=1, mismatch=-1, gapopen=-2, gapextend=-1, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:51:43.455820", "params": {"oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "input_type": "{\"type\": \"list_collection\", \"list_paired_collection\": {\"values\": [{\"src\": \"hdca\", \"id\": 72}]}, \"__current_case__\": 2}", "align": "\"needleman\"", "gapopen": "\"-2\"", "mismatch": "\"-1\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "gapextend": "\"-1\"", "match": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25436", "id": "5c0379f640540f7d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_contigs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"groupings_0\|name": "tardis", "source": {"src": "hda", "id": "c0114fb85356a3fb"}, "groupings_1\|name": "dalek", "groupings_0\|groups": ["forest", "pasture"], "groupings_1\|groups": "pasture"}, "job": {"inputs": {"source": {"src": "hda", "id": "c0114fb85356a3fb", "uuid": "59f866f6-6861-4466-9249-f035d655cb8b"}}, "update_time": "2018-02-08T17:52:23.285242", "tool_id": "mothur_make_design", "outputs": {"design": {"src": "hda", "id": "7c99b6a4ddb58575", "uuid": "2039e3c1-2b85-4d57-a319-396e9b39b9b3"}}, "stdout": "", "command_line": "set -o pipefail; echo -e \"forest\\ttardis\" >> /tmp/saskia/tmpKSDp0p/files/001/dataset_1843.dat; echo -e \"pasture\\ttardis\" >> /tmp/saskia/tmpKSDp0p/files/001/dataset_1843.dat; echo -e \"pasture\\tdalek\" >> /tmp/saskia/tmpKSDp0p/files/001/dataset_1843.dat;", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:52:20.357728", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groupings": "[{\"__index__\": 0, \"name\": \"tardis\", \"groups\": [\"forest\", \"pasture\"]}, {\"__index__\": 1, \"name\": \"dalek\", \"groups\": \"pasture\"}]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25542", "id": "2b215f192af96e2f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_design.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "4511ff07d3afd311"}, "qfile": {"src": "hda", "id": "ad82eee45b640977"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "4511ff07d3afd311", "uuid": "42033d28-15c3-43ee-8a75-a6338adcc78f"}, "qfile": {"src": "hda", "id": "ad82eee45b640977", "uuid": "b886b19e-0ebd-4723-b577-366f90f330eb"}}, "update_time": "2018-02-08T17:52:38.863124", "tool_id": "mothur_make_fastq", "outputs": {"fastq": {"src": "hda", "id": "41a06d54c9c9cb7c", "uuid": "ce1591c1-60c3-4e28-a73a-f8c98803cacd"}, "logfile": {"src": "hda", "id": "11da7bf4b3931f2a", "uuid": "057b847c-f6fe-4962-b476-b3b3cd574689"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.fastq(fasta=fasta.dat,qfile=qfile.dat)\n\nOutput File Names: \nfasta.fastq\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1844.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1845.dat' qfile.dat && echo 'make.fastq( fasta=fasta.dat, qfile=qfile.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:52:35.794214", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "chooseformat": "{\"use\": \"no\", \"__current_case__\": 1}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25644", "id": "ab313dd72b645b75", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_fastq.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "8e1caf8a5e3462d0"}, "chooseformat\|use": "yes", "chooseformat\|format": "illumina", "qfile": {"src": "hda", "id": "c6e05146e8b0a21e"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "8e1caf8a5e3462d0", "uuid": "e8632eb7-681b-4c70-898c-072215cc6faa"}, "qfile": {"src": "hda", "id": "c6e05146e8b0a21e", "uuid": "6eca077a-507f-4610-8455-e4bfecb1301c"}}, "update_time": "2018-02-08T17:52:59.564809", "tool_id": "mothur_make_fastq", "outputs": {"fastq": {"src": "hda", "id": "45c59e8d24947c4c", "uuid": "f306145c-649a-40d9-ba28-8f2bb5c8e5bf"}, "logfile": {"src": "hda", "id": "4855098d5a3d8633", "uuid": "a1bba381-c9dc-4f6f-95e4-bbe022811c74"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.fastq(fasta=fasta.dat,qfile=qfile.dat,format=illumina)\n\nOutput File Names: \nfasta.fastq\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1848.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1849.dat' qfile.dat && echo 'make.fastq( fasta=fasta.dat, qfile=qfile.dat ,format=illumina )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:52:56.419955", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "chooseformat": "{\"use\": \"yes\", \"__current_case__\": 0, \"format\": \"illumina\"}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25753", "id": "11fff4f70c354168", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_fastq.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"method\|inputs_0\|fasta": {"src": "hda", "id": "5690f3eca16a24c2"}, "method\|inputs_1\|group": "testgroup2", "method\|inputs_0\|group": "testgroup", "method\|inputs_1\|fasta": {"src": "hda", "id": "5690f3eca16a24c2"}, "method\|how": "manually"}, "job": {"inputs": {"method\|inputs_0\|fasta": {"src": "hda", "id": "5690f3eca16a24c2", "uuid": "2e0c4243-034b-441f-b3b2-19e0a041de32"}, "method\|inputs_1\|fasta": {"src": "hda", "id": "5690f3eca16a24c2", "uuid": "2e0c4243-034b-441f-b3b2-19e0a041de32"}}, "update_time": "2018-02-08T17:53:21.184357", "tool_id": "mothur_make_group", "outputs": {"output": {"src": "hda", "id": "c2fd07bff4c5634d", "uuid": "c35e4cc0-bb7f-4b33-ad23-c8394419b96a"}, "logfile": {"src": "hda", "id": "3c09fc160c7c949a", "uuid": "8413a64d-b800-4ce9-9ef9-628ede96cdd6"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.group(fasta=fasta_0.dat-fasta_1.dat,groups=testgroup-testgroup2)\n\nOutput File Names: fasta_0.fasta_1.groups\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1853.dat' fasta_0.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1853.dat' fasta_1.dat && echo 'make.group( fasta=fasta_0.dat-fasta_1.dat, groups=testgroup-testgroup2 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:53:17.417101", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "{\"how\": \"manually\", \"__current_case__\": 1, \"inputs\": [{\"__index__\": 0, \"fasta\": {\"values\": [{\"src\": \"hda\", \"id\": 1853}]}, \"group\": \"testgroup\"}, {\"__index__\": 1, \"fasta\": {\"values\": [{\"src\": \"hda\", \"id\": 1853}]}, \"group\": \"testgroup2\"}]}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25879", "id": "cf6f5650773911ff", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_group.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"method\|how": "collection", "method\|fasta_collection": {"src": "hdca", "id": "b31f4d82ada5e956"}}, "job": {"inputs": {"fasta_collection2": {"src": "hda", "id": "ead8b19bd4100f06", "uuid": "9810929b-444b-47dd-aeb1-435bb19e9440"}, "fasta_collection1": {"src": "hda", "id": "ead8b19bd4100f06", "uuid": "9810929b-444b-47dd-aeb1-435bb19e9440"}}, "update_time": "2018-02-08T17:53:41.867928", "tool_id": "mothur_make_group", "outputs": {"output": {"src": "hda", "id": "1048ce0425f8cb59", "uuid": "11a01df2-365b-4ca7-8be2-27bc18e495c0"}, "logfile": {"src": "hda", "id": "8d7a576c822a8355", "uuid": "4b3ba1ce-f095-47d5-b798-fc7c8f5821d7"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.group(fasta=fasta_testgroup.dat-fasta_testgroup2.dat,groups=testgr \roup-testgroup2)\n\nOutput File Names: fasta_testgroup.fasta_testgroup2.groups\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1857.dat' fasta_testgroup.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1857.dat' fasta_testgroup2.dat && echo 'make.group( fasta=fasta_testgroup.dat-fasta_testgroup2.dat, groups=testgroup-testgroup2 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:53:38.125674", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "{\"how\": \"collection\", \"fasta_collection\": {\"values\": [{\"src\": \"hdca\", \"id\": 73}]}, \"__current_case__\": 0}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25990", "id": "6e055b0f6b730971", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_group.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "ecf48c02251dfb67"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "ecf48c02251dfb67", "uuid": "a1e67bd3-07a2-4356-a5c9-ddaf5aa4e700"}}, "update_time": "2018-02-08T17:53:56.373528", "tool_id": "mothur_make_lefse", "outputs": {"lefse_out": {"src": "hda", "id": "c30adaf179fc5aaa", "uuid": "02e1aead-76bc-4cc9-ba9e-9bcd1221ba6e"}, "logfile": {"src": "hda", "id": "388d1db82fb077e8", "uuid": "16207fbb-8b4a-4a67-8d62-dcf39553f42c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.lefse(shared=otu.dat,scale=totalgroup)\nYou did not provide a label, I will use the first label in your inputfile.\n\nOutput File Names: \notu.unique.lefse\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1860.dat' otu.dat && ln -s 'None' design.dat && ln -s 'None' constaxonomy.dat && echo 'make.lefse( shared=otu.dat, scale=totalgroup )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:53:53.261854", "params": {"scale": "\"totalgroup\"", "dbkey": "\"hg17\"", "label": "null", "design": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "constaxonomy": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "26077", "id": "cc61617d359bbeb4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_lefse.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"design": {"src": "hda", "id": "2472375c89218954"}, "otu": {"src": "hda", "id": "4f48e12496476004"}, "label": "0.18"}, "job": {"inputs": {"design": {"src": "hda", "id": "2472375c89218954", "uuid": "40876580-3afb-4f31-8f7b-bab66411eed3"}, "otu": {"src": "hda", "id": "4f48e12496476004", "uuid": "e90c477f-8e02-4657-84ab-4900b982a6fc"}}, "update_time": "2018-02-08T17:54:18.037929", "tool_id": "mothur_make_lefse", "outputs": {"lefse_out": {"src": "hda", "id": "a5002b1773fb3add", "uuid": "b145b155-24a6-4ed1-9769-8142168681db"}, "logfile": {"src": "hda", "id": "293a2e724ad85605", "uuid": "66059d43-b491-40a9-be2c-d4d1f7b5a047"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.lefse(relabund=otu.dat,design=design.dat,label=0.18,scale=totalgro \rup)\n\nOutput File Names: \notu.0.18.lefse\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1863.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1864.dat' design.dat && ln -s 'None' constaxonomy.dat && echo 'make.lefse( relabund=otu.dat, design=design.dat, label=0.18, scale=totalgroup )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:54:14.907485", "params": {"scale": "\"totalgroup\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "constaxonomy": "null", "dbkey": "\"hg17\"", "label": "\"0.18\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "26188", "id": "8617c587cd9e4e77", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_lefse.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"reference\|template": {"src": "hda", "id": "5383cf1b3b9fd9bd"}, "reference\|source": "hist", "flow": {"src": "hda", "id": "dd4a25701e5bf03c"}, "error": {"src": "hda", "id": "ddb7b6e6b5a5748d"}}, "job": {"inputs": {"flow": {"src": "hda", "id": "dd4a25701e5bf03c", "uuid": "224fce87-9cc8-4912-bca5-c86096fedae9"}, "template": {"src": "hda", "id": "5383cf1b3b9fd9bd", "uuid": "60e32d13-d224-4951-89f2-827a0db4d984"}, "error": {"src": "hda", "id": "ddb7b6e6b5a5748d", "uuid": "05ddcf44-ecd1-45e4-989d-6ba2198d0fb5"}}, "update_time": "2018-02-08T17:54:42.911228", "tool_id": "mothur_make_lookup", "outputs": {"logfile": {"src": "hda", "id": "9695ced70a424d8b", "uuid": "0a0bb69d-b81a-4c73-988c-c32e3257d345"}, "lookup_out": {"src": "hda", "id": "7c234923b0122c52", "uuid": "e8efa2fc-1a1f-4ee8-acaf-f4a7f65a8999"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.lookup(reference=reference.template.dat,flow=flow.dat,error=error. \rdat,order=A,barcode=AACCGTGTC,key=TCAG,threshold=10000)\nGQY1XT001A8C6I != M00967_43_000000000-A3JHG_1_1101_11148_6457\nGQY1XT001BPRBN != M00967_43_000000000-A3JHG_1_1101_7079_6722\n\nData for homopolymer lengths of 0 and longer were imputed for this analysis\n\n\nOutput File Names: \nflow.lookup\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1867.dat' reference.template.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1868.dat' flow.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1869.dat' error.dat && echo 'make.lookup( reference=reference.template.dat, flow=flow.dat, error=error.dat, order=A, barcode=AACCGTGTC, key=TCAG, threshold=10000 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:54:39.698392", "params": {"reference": "{\"source\": \"hist\", \"template\": {\"values\": [{\"src\": \"hda\", \"id\": 1867}]}, \"__current_case__\": 1}", "barcode": "\"AACCGTGTC\"", "dbkey": "\"hg17\"", "key": "\"TCAG\"", "threshold": "\"10000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "order": "\"A\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "26384", "id": "fc6a9ef5f7630e87", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_lookup.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"reference\|template": {"src": "hda", "id": "3989eef2a0b46a62"}, "barcode": "XAXAXCXCXGXTXGXTXC", "flow": {"src": "hda", "id": "af2e40921cfe1b21"}, "reference\|source": "hist", "key": "XTXCXAXGX", "error": {"src": "hda", "id": "7a7dcacb06603266"}}, "job": {"inputs": {"flow": {"src": "hda", "id": "af2e40921cfe1b21", "uuid": "c96ef4ba-fb78-4d80-9013-40185fe043db"}, "template": {"src": "hda", "id": "3989eef2a0b46a62", "uuid": "01d49cac-26ff-4b61-82c2-6d0f8f04a9c0"}, "error": {"src": "hda", "id": "7a7dcacb06603266", "uuid": "a4fd69ea-45f1-4bbb-ab55-5e84c6aa4e30"}}, "update_time": "2018-02-08T17:55:06.797669", "tool_id": "mothur_make_lookup", "outputs": {"logfile": {"src": "hda", "id": "a2907571b551cae9", "uuid": "f842ac50-4067-4e7a-9e11-39cad5e7a7d7"}, "lookup_out": {"src": "hda", "id": "54704a1dcf64f2e8", "uuid": "7696d203-cf2b-46c7-b147-001e0dc86df5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.lookup(reference=reference.template.dat,flow=flow.dat,error=error. \rdat,order=A,barcode=AACCGTGTC,key=TCAG,threshold=10000)\nGQY1XT001A8C6I != M00967_43_000000000-A3JHG_1_1101_11148_6457\nGQY1XT001BPRBN != M00967_43_000000000-A3JHG_1_1101_7079_6722\n\nData for homopolymer lengths of 0 and longer were imputed for this analysis\n\n\nOutput File Names: \nflow.lookup\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1872.dat' reference.template.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1873.dat' flow.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1874.dat' error.dat && echo 'make.lookup( reference=reference.template.dat, flow=flow.dat, error=error.dat, order=A, barcode=AACCGTGTC, key=TCAG, threshold=10000 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:55:03.580091", "params": {"reference": "{\"source\": \"hist\", \"template\": {\"values\": [{\"src\": \"hda\", \"id\": 1872}]}, \"__current_case__\": 1}", "barcode": "\"XAXAXCXCXGXTXGXTXC\"", "dbkey": "\"hg17\"", "key": "\"XTXCXAXGX\"", "threshold": "\"10000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "order": "\"A\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "26513", "id": "dd28ab0e62f6c657", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_lookup.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"intype\|infile": "biom", "intype\|otu": {"src": "hda", "id": "9f7864eb5fec163b"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "9f7864eb5fec163b", "uuid": "dd47f7cd-9004-4ed5-bd85-1c25d74c261c"}}, "update_time": "2018-02-08T17:55:24.413838", "tool_id": "mothur_make_shared", "outputs": {"shared": {"src": "hda", "id": "fd1c56392329a112", "uuid": "6784c2f8-881c-4339-84f6-d79007188b0b"}, "logfile": {"src": "hda", "id": "f78fa183df45cc17", "uuid": "90f3f7f2-1148-4fae-b6eb-3be63593972a"}, "groupout": {"src": "hda", "id": "e6696f8460301cd8", "uuid": "bb629e4d-c6ee-4f53-bb9c-a82ca1454555"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.shared(biom=intype_otu.dat)\n\nuserLabel\n\nOutput File Names: \nintype_otu.shared\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1877.dat' intype_otu.dat && echo 'make.shared( biom=intype_otu.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv mothur..logfile \"/tmp/saskia/tmpKSDp0p/files/001/dataset_1878.dat\" && mv intype_otu.shared \"/tmp/saskia/tmpKSDp0p/files/001/dataset_1879.dat\"", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:55:21.200554", "params": {"intype": "{\"infile\": \"biom\", \"__current_case__\": 1, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1877}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "26602", "id": "4dfde39352bb574f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_shared.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"intype\|infile": "otulist", "intype\|group": {"src": "hda", "id": "7f99cfb1de31b6f4"}, "intype\|otu": {"src": "hda", "id": "d4490cd22d2e91a2"}}, "job": {"inputs": {"group": {"src": "hda", "id": "7f99cfb1de31b6f4", "uuid": "6d5585d0-a1f5-46f0-b357-325d6b02b5a2"}, "otu": {"src": "hda", "id": "d4490cd22d2e91a2", "uuid": "b85240a3-aaec-45f8-bf25-008930ce7ae9"}}, "update_time": "2018-02-08T17:55:45.993342", "tool_id": "mothur_make_shared", "outputs": {"shared": {"src": "hda", "id": "7967c060fcc2b0c3", "uuid": "65a75bf7-90f6-45d6-8be1-01d3a2cb6092"}, "logfile": {"src": "hda", "id": "d911dc399b1b3959", "uuid": "ae0a8ddf-438e-4ca9-b113-5bf60e2578b1"}, "groupout": {"src": "hda", "id": "a6619ad3bbdc2f3d", "uuid": "83193b9b-370e-4845-b426-943fc8a35c9f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.shared(group=intype_group.dat,list=intype_otu.dat)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \nintype_otu.shared\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1881.dat' intype_otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1882.dat' intype_group.dat && echo 'make.shared( group=intype_group.dat, list=intype_otu.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv mothur..logfile \"/tmp/saskia/tmpKSDp0p/files/001/dataset_1883.dat\" && mv intype_otu.shared \"/tmp/saskia/tmpKSDp0p/files/001/dataset_1884.dat\"", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:55:42.150192", "params": {"intype": "{\"group\": {\"values\": [{\"src\": \"hda\", \"id\": 1882}]}, \"__current_case__\": 0, \"label\": null, \"groups\": null, \"infile\": \"otulist\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1881}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "26721", "id": "f060dd6bec0b0c91", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_shared.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"intype\|infile": "otulist", "intype\|group": {"src": "hda", "id": "11cbcf7169f85c4f"}, "intype\|otu": {"src": "hda", "id": "3ac08cc66e07c165"}, "intype\|groups": ["forest", "pasture"], "intype\|label": ["0.03", "0.05", "0.22"]}, "job": {"inputs": {"group": {"src": "hda", "id": "11cbcf7169f85c4f", "uuid": "24f0a7f3-acf4-48e6-a19b-701ae5977f5b"}, "otu": {"src": "hda", "id": "3ac08cc66e07c165", "uuid": "b2fb6d6f-d5c1-4e8c-ba17-afa3ccf9791a"}}, "update_time": "2018-02-08T17:56:10.243068", "tool_id": "mothur_make_shared", "outputs": {"groupout": {"src": "hda", "id": "ca3baaede20d3608", "uuid": "187fa39c-3715-445d-b050-6e8e9df82e58"}, "__new_primary_file_0.22\|0.22__": {"src": "hda", "id": "65fc46f73aabdfda", "uuid": "4d84238e-343f-48a4-9a0d-6ba323b6bbf8"}, "__new_primary_file_0.22\|0.05__": {"src": "hda", "id": "16eec28fa6281f7f", "uuid": "5652e0e4-810d-45e7-8ea9-fb1a38d404d8"}, "shared": {"src": "hda", "id": "1bab9e4fed59ebfb", "uuid": "4dd2c469-e1db-4a00-b840-1e880cd3e460"}, "logfile": {"src": "hda", "id": "0d9db12bc460aef9", "uuid": "42cb6d93-e1a3-40a6-a678-c6c1c4d5d9b3"}, "__new_primary_file_0.22\|0.03__": {"src": "hda", "id": "b042b0cfab22e670", "uuid": "6843b9dc-09d3-4a7c-b42e-ecbc82632993"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.shared(group=intype_group.dat,label=0.03-0.05-0.22,groups=forest-p \rasture,list=intype_otu.dat)\n0.03\n0.05\n0.22\n\nOutput File Names: \nintype_otu.forest.pasture.groups\nintype_otu.0.03.shared\nintype_otu.0.05.shared\nintype_otu.0.22.shared\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1886.dat' intype_otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1887.dat' intype_group.dat && echo 'make.shared( group=intype_group.dat, label=0.03-0.05-0.22, groups=forest-pasture, list=intype_otu.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv mothur..logfile \"/tmp/saskia/tmpKSDp0p/files/001/dataset_1888.dat\" && mv intype_otu.groups \"/tmp/saskia/tmpKSDp0p/files/001/dataset_1890.dat\"", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:56:06.575770", "params": {"intype": "{\"group\": {\"values\": [{\"src\": \"hda\", \"id\": 1887}]}, \"__current_case__\": 0, \"label\": [\"0.03\", \"0.05\", \"0.22\"], \"groups\": [\"forest\", \"pasture\"], \"infile\": \"otulist\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1886}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n/tmp/saskia/tmpKSDp0p/job_working_directory/000/488/galaxy_488.sh: line 40: [: too many arguments\n", "job_metrics": [], "model_class": "Job", "external_id": "26831", "id": "d13b0aeade1f3b9f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_shared.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"project": {"src": "hda", "id": "55d802277995b0ed"}, "sff": {"src": "hda", "id": "9adfeb8ffc5068e4"}, "mimark": {"src": "hda", "id": "6124c38139ecb629"}, "oligos": {"src": "hda", "id": "14500b6333a1070c"}}, "job": {"inputs": {"project": {"src": "hda", "id": "55d802277995b0ed", "uuid": "bac32361-557f-42dc-8ca5-4cb8c17348a9"}, "oligos": {"src": "hda", "id": "14500b6333a1070c", "uuid": "a25517e0-bfdc-4afe-a916-8caaafb04375"}, "sff": {"src": "hda", "id": "9adfeb8ffc5068e4", "uuid": "4051a32d-cd21-4c47-b718-55969c1da954"}, "mimark": {"src": "hda", "id": "6124c38139ecb629", "uuid": "704c7182-88d1-43e6-a8dc-7133cba88d86"}}, "update_time": "2018-02-08T17:56:46.294658", "tool_id": "mothur_make_sra", "outputs": {"submission_xml": {"src": "hda", "id": "4f9964cac71ceae2", "uuid": "25e41557-5ee7-452d-8456-eea7543d75c7"}, "flow_out": {"src": "hda", "id": "a625551c8e7496b4", "uuid": "8e7b6655-e359-470c-9fc3-4e101bbf3b67"}, "qual_out": {"src": "hda", "id": "0d7bfb86ba13c2bf", "uuid": "3505c479-7e32-4834-aa0d-fd4583bfa61b"}, "fasta_out": {"src": "hda", "id": "269645e76dd38019", "uuid": "fa9e3c7a-4f42-4d4e-a835-df97df662e48"}, "scrap_sff": {"src": "hda", "id": "4f070c1374b9df0b", "uuid": "7b4ae88a-44a5-46c6-9bdc-118a5aa48166"}, "logfile": {"src": "hda", "id": "6d9db605bb466f8a", "uuid": "c25b3e9e-1b70-4be5-9b9f-eaeaf6c32309"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.sra(project=project.dat,sff=sff.dat,oligos=oligos.dat,mimark=mimar \rk.dat,bdiffs=0,pdiffs=0,tdiffs=0,ldiffs=0,sdiffs=0,checkorient=false,orientation \r=forward,platform=_LS454,instrument=454_GS,libstrategy=AMPLICON,libselection=PCR \r,libsource=METAGENOMIC,datatype=METAGENOME,trim=True,includescrap=True)\n\n/***************************************/\nRunning command: sffinfo(sff=sff.dat, oligos=oligos.dat, trim=True)\nExtracting info from sff.dat ...\n10\nIt took 0 secs to extract 10.\n\nOutput File Names: \nsff.fasta\nsff.qual\nsff.flow\nsff.scrap.sff\n\n/**************************************/\n\nOutput File Names: \nsff.fasta\nsff.qual\nsff.flow\nsff.scrap.sff\nsubmission.xml\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1894.dat' project.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1895.dat' sff.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1896.dat' oligos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1897.dat' mimark.dat && ln -s 'None' fastq.dat && echo 'make.sra( project=project.dat, sff=sff.dat, oligos=oligos.dat, mimark=mimark.dat, bdiffs=0, pdiffs=0, tdiffs=0, ldiffs=0, sdiffs=0, checkorient=false, orientation=forward, platform=_LS454, instrument=454_GS, libstrategy=AMPLICON, libselection=PCR, libsource=METAGENOMIC, datatype=METAGENOME, trim=True, includescrap=True )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:56:41.999131", "params": {"bdiffs": "\"0\"", "trim": "\"true\"", "sdiffs": "\"0\"", "libselection": "\"PCR\"", "ldiffs": "\"0\"", "libsource": "\"METAGENOMIC\"", "checkorient": "\"false\"", "fastq": "null", "pdiffs": "\"0\"", "dbkey": "\"hg17\"", "includescrap": "\"true\"", "instrument": "\"454_GS\"", "datatype": "\"METAGENOME\"", "orientation": "\"forward\"", "platform": "\"_LS454\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "libstrategy": "\"AMPLICON\"", "tdiffs": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "26993", "id": "4c17a0c0b24f3d2a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_sra.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"dist": {"src": "hda", "id": "72ec7f16ae254bf0"}, "dist2": {"src": "hda", "id": "96c8304a26dfa89d"}}, "job": {"inputs": {"dist": {"src": "hda", "id": "72ec7f16ae254bf0", "uuid": "69e3357c-572a-4248-ba48-1ae412fb9be5"}, "dist2": {"src": "hda", "id": "96c8304a26dfa89d", "uuid": "a043bab0-8e7d-4047-9d55-f3184fba1218"}}, "update_time": "2018-02-08T17:57:29.492577", "tool_id": "mothur_mantel", "outputs": {"logfile": {"src": "hda", "id": "0750df27179eb44a", "uuid": "0c3d1424-d5a6-4a69-b0fb-e01c603c2749"}, "mantel": {"src": "hda", "id": "a0d6fe44ad497cef", "uuid": "42af4d39-71bc-4850-90d1-5986cfc8e4a5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > mantel(phylip1=dist.dat,phylip2=dist2.dat,method=pearson,iters=1000)\n\nmantel = 0.304745\tpValue = 0.000000\n\nOutput File Names: \ndist.mantel\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1904.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1905.dat' dist2.dat && echo 'mantel( phylip1=dist.dat, phylip2=dist2.dat, method=pearson, iters=1000 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:57:26.139913", "params": {"iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"pearson\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "27140", "id": "2c905c266975a822", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_mantel.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"merge\|type": "fasta", "merge\|inputs": [{"src": "hda", "id": "de3e1eb0e9cadbab"}, {"src": "hda", "id": "417510e0ae171d2e"}, {"src": "hda", "id": "6e2b9e3a5eac2ec6"}]}, "job": {"inputs": {"inputs2": {"src": "hda", "id": "417510e0ae171d2e", "uuid": "9467c807-a9f3-4740-8c68-3ff70ccdcc9f"}, "inputs": {"src": "hda", "id": "de3e1eb0e9cadbab", "uuid": "0de05468-1a0f-4cf1-b8af-474e0cc3cf31"}, "inputs1": {"src": "hda", "id": "de3e1eb0e9cadbab", "uuid": "0de05468-1a0f-4cf1-b8af-474e0cc3cf31"}, "inputs3": {"src": "hda", "id": "6e2b9e3a5eac2ec6", "uuid": "354c013c-439a-4dcb-87a8-f5716c2cfec2"}}, "update_time": "2018-02-08T17:57:56.177705", "tool_id": "mothur_merge_files", "outputs": {"output": {"src": "hda", "id": "0fb2e145d63428e3", "uuid": "d1a7062b-9bce-4396-a7b8-2a276cefc398"}, "logfile": {"src": "hda", "id": "b8e3f2c4e0441645", "uuid": "88fa2ee1-a971-4a14-9fde-78c8e4124b17"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > merge.files(input=input0.dat-input1.dat-input2.dat,output=/tmp/saskia/t \rmpKSDp0p/files/001/dataset_1912.dat)\n\nOutput File Names: \n/tmp/saskia/tmpKSDp0p/files/001/dataset_1912.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1908.dat' input0.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1909.dat' input1.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1910.dat' input2.dat && echo 'merge.files( input=input0.dat-input1.dat-input2.dat-, output=/tmp/saskia/tmpKSDp0p/files/001/dataset_1912.dat )' \| sed 's/ //g' \| sed 's/-,/,/g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:57:53.020816", "params": {"merge": "{\"inputs\": {\"values\": [{\"src\": \"hda\", \"id\": 1908}, {\"src\": \"hda\", \"id\": 1909}, {\"src\": \"hda\", \"id\": 1910}]}, \"type\": \"fasta\", \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "27277", "id": "5932136d963c1318", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_merge_files.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"design\|source": "hist", "design\|design_dataset": {"src": "hda", "id": "32a578a19336cfbe"}, "otu": {"src": "hda", "id": "78f9790ceb9e760a"}}, "job": {"inputs": {"design_dataset": {"src": "hda", "id": "32a578a19336cfbe", "uuid": "53411ffe-5c48-4de5-914e-2143f57be4fe"}, "otu": {"src": "hda", "id": "78f9790ceb9e760a", "uuid": "b01887a3-f0fe-408f-9ae7-e2a382c4c9f9"}}, "update_time": "2018-02-08T17:58:17.037551", "tool_id": "mothur_merge_groups", "outputs": {"merged_shared": {"src": "hda", "id": "46591abe7f08ccf9", "uuid": "036b9366-aeeb-4334-b1bc-28eba7afbf33"}, "logfile": {"src": "hda", "id": "b0f3daede2de0400", "uuid": "1f85c9aa-1a03-4684-96e1-6bc38e54b5ed"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > merge.groups(design=design_dataset.dat,shared=otu.dat,method=sum)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.merge.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1913.dat' otu.dat && ln -s 'None' group.dat && ln -s 'None' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1914.dat' design_dataset.dat && echo 'merge.groups( design=design_dataset.dat ,shared=otu.dat ,method=sum )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:58:13.874471", "params": {"group": "null", "dbkey": "\"hg17\"", "label": "null", "design": "{\"source\": \"hist\", \"design_dataset\": {\"values\": [{\"src\": \"hda\", \"id\": 1914}]}, \"__current_case__\": 0}", "groups": "null", "fasta": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"sum\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "27386", "id": "b7c449f860774475", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_merge_groups.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"design\|source": "hist", "design\|design_dataset": {"src": "hda", "id": "41e5dce11cc91f7a"}, "otu": {"src": "hda", "id": "d36489c18c908bb1"}, "groups": ["forest", "pasture"], "label": ["0.05", "0.22", "0.38"]}, "job": {"inputs": {"design_dataset": {"src": "hda", "id": "41e5dce11cc91f7a", "uuid": "587ebff1-49e7-47f6-bd51-d7b2e4b3521a"}, "otu": {"src": "hda", "id": "d36489c18c908bb1", "uuid": "23cfb8bb-56fa-4193-84db-7d4adf3f91f1"}}, "update_time": "2018-02-08T17:58:38.787975", "tool_id": "mothur_merge_groups", "outputs": {"merged_shared": {"src": "hda", "id": "ab07adc211b2df50", "uuid": "bf4c1384-c484-4f17-a982-c58fbd809afd"}, "logfile": {"src": "hda", "id": "6b8aa44b4322962a", "uuid": "c5f34277-320d-489a-9e08-74a73979c558"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > merge.groups(design=design_dataset.dat,shared=otu.dat,groups=forest-pas \rture,label=0.05-0.22-0.38,method=sum)\n0.05\n0.22\n0.38\n\nOutput File Names: \notu.merge.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1917.dat' otu.dat && ln -s 'None' group.dat && ln -s 'None' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1918.dat' design_dataset.dat && echo 'merge.groups( design=design_dataset.dat ,shared=otu.dat ,groups=forest-pasture ,label=0.05-0.22-0.38 ,method=sum )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:58:35.565687", "params": {"group": "null", "dbkey": "\"hg17\"", "label": "[\"0.05\", \"0.22\", \"0.38\"]", "design": "{\"source\": \"hist\", \"design_dataset\": {\"values\": [{\"src\": \"hda\", \"id\": 1918}]}, \"__current_case__\": 0}", "groups": "[\"forest\", \"pasture\"]", "fasta": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"sum\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "27513", "id": "5300091d026f85af", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_merge_groups.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"design\|design_dataset": {"src": "hda", "id": "e4b594eefb7aada3"}, "design\|source": "hist", "group": {"src": "hda", "id": "b81396351716a7ed"}}, "job": {"inputs": {"group": {"src": "hda", "id": "b81396351716a7ed", "uuid": "3b9b1091-7209-4254-88c3-d8ade7e87586"}, "design_dataset": {"src": "hda", "id": "e4b594eefb7aada3", "uuid": "9cb733df-b949-4852-ac5b-76459cd4cdac"}}, "update_time": "2018-02-08T17:58:59.407641", "tool_id": "mothur_merge_groups", "outputs": {"merged_group": {"src": "hda", "id": "58a81f0c48a42115", "uuid": "a1a56d3a-ac4a-4557-96a8-201b4e48ecd8"}, "logfile": {"src": "hda", "id": "d7ea930ce32eed6a", "uuid": "f3c9e925-f54a-4def-99c8-724daed3eeda"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > merge.groups(design=design_dataset.dat,group=group.dat,method=sum)\n\nOutput File Names: \ngroup.merge.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s 'None' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1921.dat' group.dat && ln -s 'None' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1922.dat' design_dataset.dat && echo 'merge.groups( design=design_dataset.dat ,group=group.dat ,method=sum )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:58:56.393115", "params": {"dbkey": "\"hg17\"", "label": "null", "design": "{\"source\": \"hist\", \"design_dataset\": {\"values\": [{\"src\": \"hda\", \"id\": 1922}]}, \"__current_case__\": 0}", "groups": "null", "fasta": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"sum\"", "otu": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "27627", "id": "3808e741d551ae79", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_merge_groups.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"design\|design_dataset": {"src": "hda", "id": "7e1cf2195f01e827"}, "fasta": {"src": "hda", "id": "8f85c19787d8d333"}, "design\|source": "hist", "method": "median", "group": {"src": "hda", "id": "983faa3420093487"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "8f85c19787d8d333", "uuid": "621a07be-1a42-4c72-9e04-2f089737f369"}, "group": {"src": "hda", "id": "983faa3420093487", "uuid": "e36ee2d6-ce27-4d5d-ab87-3b6dea9473de"}, "design_dataset": {"src": "hda", "id": "7e1cf2195f01e827", "uuid": "7f20534c-ce2e-4dde-985b-6fbf6eaff13b"}}, "update_time": "2018-02-08T17:59:24.175570", "tool_id": "mothur_merge_groups", "outputs": {"merged_group": {"src": "hda", "id": "930b92102bb55843", "uuid": "821f7ea2-87d4-4404-a237-0e409f05737c"}, "logfile": {"src": "hda", "id": "c8e74883aba54288", "uuid": "8c385a77-3e61-47d5-89a0-0c42618d1bcc"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > merge.groups(design=design_dataset.dat,count=group.dat,fasta=fasta.dat, \rmethod=median)\n\nOutput File Names: \ngroup.merge.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s 'None' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1925.dat' group.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1926.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1927.dat' design_dataset.dat && echo 'merge.groups( design=design_dataset.dat ,count=group.dat ,fasta=fasta.dat ,method=median )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:59:20.306073", "params": {"dbkey": "\"hg17\"", "label": "null", "design": "{\"source\": \"hist\", \"design_dataset\": {\"values\": [{\"src\": \"hda\", \"id\": 1927}]}, \"__current_case__\": 0}", "groups": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"median\"", "otu": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "27759", "id": "966d85c09a3ba224", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_merge_groups.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"design\|groupings_1\|groups": "pasture", "otu": {"src": "hda", "id": "f4fa0c7fbb0e3e2c"}, "design\|groupings_1\|name": "dalek", "design\|source": "build", "design\|groupings_0\|name": "tardis", "design\|groupings_0\|groups": "forest"}, "job": {"inputs": {"otu": {"src": "hda", "id": "f4fa0c7fbb0e3e2c", "uuid": "bf95dd8a-844f-44de-948f-c2a3f12be527"}}, "update_time": "2018-02-08T17:59:43.854854", "tool_id": "mothur_merge_groups", "outputs": {"merged_shared": {"src": "hda", "id": "531aa3b82ca54fa4", "uuid": "ae812da7-ca13-425d-b496-10763dd23c3c"}, "logfile": {"src": "hda", "id": "d6bfe7e8caebca0c", "uuid": "797514f7-25de-4561-876c-0419c3f03080"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > merge.groups(design=generated_design.dat,shared=otu.dat,method=sum)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.merge.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1930.dat' otu.dat && ln -s 'None' group.dat && ln -s 'None' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/job_working_directory/000/515/tmpqonpbe' generated_design.dat && echo 'merge.groups( design=generated_design.dat ,shared=otu.dat ,method=sum )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:59:40.668151", "params": {"group": "null", "dbkey": "\"hg17\"", "label": "null", "design": "{\"source\": \"build\", \"__current_case__\": 1, \"groupings\": [{\"__index__\": 0, \"name\": \"tardis\", \"groups\": \"forest\"}, {\"__index__\": 1, \"name\": \"dalek\", \"groups\": \"pasture\"}]}", "groups": "null", "fasta": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"sum\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "27855", "id": "499ab5633737b2d3", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_merge_groups.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"input": [{"src": "hda", "id": "ebca6ff66bc47ca1"}, {"src": "hda", "id": "a3e90b92a8eb33dd"}]}, "job": {"inputs": {"input2": {"src": "hda", "id": "a3e90b92a8eb33dd", "uuid": "3a88c872-f075-41ba-88e3-1918baa76798"}, "input": {"src": "hda", "id": "ebca6ff66bc47ca1", "uuid": "8adc62cb-4747-49d1-b76a-2d67dab4f20b"}, "input1": {"src": "hda", "id": "ebca6ff66bc47ca1", "uuid": "8adc62cb-4747-49d1-b76a-2d67dab4f20b"}}, "update_time": "2018-02-08T18:00:05.520447", "tool_id": "mothur_merge_sfffiles", "outputs": {"output": {"src": "hda", "id": "2c072c8536d83576", "uuid": "954a0bc5-6d95-4df0-a108-937947278295"}, "logfile": {"src": "hda", "id": "cfb1f8928a5313e1", "uuid": "ab073c04-3281-4dbe-9c2e-4e9f798c9477"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > merge.sfffiles(sff=input0.dat-input1.dat,output=/tmp/saskia/tmpKSDp0p/f \riles/001/dataset_1936.dat)\n\nMerging info from input0.dat ...\n10\nIt took 0 secs to merge 10.\n\nMerging info from input1.dat ...\n10\nIt took 0 secs to merge 10.\n\nOutput File Names: \n/tmp/saskia/tmpKSDp0p/files/001/dataset_1936.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1933.dat' input0.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1934.dat' input1.dat && echo 'merge.sfffiles( sff=input0.dat-input1.dat-, output=/tmp/saskia/tmpKSDp0p/files/001/dataset_1936.dat )' \| sed 's/ //g' \| sed 's/-,/,/g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:00:02.377604", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "27963", "id": "93ee5b88b9257311", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_merge_sfffiles.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input": [{"src": "hda", "id": "b0e21127fa89f6b7"}, {"src": "hda", "id": "d5b0791da63d7742"}]}, "job": {"inputs": {"input2": {"src": "hda", "id": "d5b0791da63d7742", "uuid": "d24e9354-aa59-4ca3-9534-d33059c79a3a"}, "input": {"src": "hda", "id": "b0e21127fa89f6b7", "uuid": "45c7f81e-3ec8-42db-a7cf-7843326d2ef2"}, "input1": {"src": "hda", "id": "b0e21127fa89f6b7", "uuid": "45c7f81e-3ec8-42db-a7cf-7843326d2ef2"}}, "update_time": "2018-02-08T18:00:27.242056", "tool_id": "mothur_merge_taxsummary", "outputs": {"output": {"src": "hda", "id": "0a1e7528e524af83", "uuid": "d4525a7a-178e-49f0-b2b7-832a173efeeb"}, "logfile": {"src": "hda", "id": "d8247bdcb1ad4f59", "uuid": "01051fd2-1cdf-4514-9f3f-a46f8633c19b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > merge.taxsummary(input=input0.dat-input1.dat,output=/tmp/saskia/tmpKSDp \r0p/files/001/dataset_1940.dat)\n\nOutput File Names: \n/tmp/saskia/tmpKSDp0p/files/001/dataset_1940.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1937.dat' input0.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1938.dat' input1.dat && echo 'merge.taxsummary( input=input0.dat-input1.dat-, output=/tmp/saskia/tmpKSDp0p/files/001/dataset_1940.dat )' \| sed 's/ //g' \| sed 's/-,/,/g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:00:24.083311", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28083", "id": "17228a24cf52bb1d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_merge_taxsummary.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"design": {"src": "hda", "id": "ccfc4e50dfc4db8c"}, "otu": {"src": "hda", "id": "5c8c831e231041b4"}}, "job": {"inputs": {"design": {"src": "hda", "id": "ccfc4e50dfc4db8c", "uuid": "0856f7dd-c311-4b6a-b610-c3e61e131c2d"}, "otu": {"src": "hda", "id": "5c8c831e231041b4", "uuid": "98c0269c-613d-4f6b-945b-b03e15c2eef8"}}, "update_time": "2018-02-08T18:00:49.964815", "tool_id": "mothur_metastats", "outputs": {"__new_primary_file_unique.tardis_dalek\|0.25.tardis_dalek__": {"src": "hda", "id": "23edcc4e5b71eb61", "uuid": "e254a57d-6b92-485b-94b2-696a0f583f48"}, "__new_primary_file_unique.tardis_dalek\|0.10.tardis_dalek__": {"src": "hda", "id": "6488c2c82f28f195", "uuid": "9d4229d8-efcf-49eb-8a99-7db53404486c"}, "__new_primary_file_unique.tardis_dalek\|unique.tardis_dalek__": {"src": "hda", "id": "d5d307ba80698737", "uuid": "323b9c27-cfd3-4404-b148-460f4ae42f08"}, "__new_primary_file_unique.tardis_dalek\|0.14.tardis_dalek__": {"src": "hda", "id": "0dd59bf0ff2d1808", "uuid": "dfe825b4-560d-46a6-a3fe-0ac86cc953f2"}, "__new_primary_file_unique.tardis_dalek\|0.08.tardis_dalek__": {"src": "hda", "id": "8a43e709b6288a8e", "uuid": "7a35cb2e-6457-415a-b628-7c6428c66950"}, "__new_primary_file_unique.tardis_dalek\|0.16.tardis_dalek__": {"src": "hda", "id": "e6e401f2a6b47613", "uuid": "e1a05933-bbad-4222-8b53-7677210586ab"}, "__new_primary_file_unique.tardis_dalek\|0.17.tardis_dalek__": {"src": "hda", "id": "b1038f71a0d34df9", "uuid": "8e37a662-e02b-4176-a95b-fabfbd1b54c0"}, "__new_primary_file_unique.tardis_dalek\|0.05.tardis_dalek__": {"src": "hda", "id": "89a6b602b1c79537", "uuid": "25ef581d-b984-4e1a-86e3-92a5c09ff2ea"}, "__new_primary_file_unique.tardis_dalek\|0.13.tardis_dalek__": {"src": "hda", "id": "be88353ca733c0a1", "uuid": "f887bb42-5613-4c7f-b8ce-1a7e359f4d86"}, "__new_primary_file_unique.tardis_dalek\|0.15.tardis_dalek__": {"src": "hda", "id": "6aa2efcb07ffa2aa", "uuid": "1c0e7350-e2a9-409a-9d75-f567ad255b0c"}, "__new_primary_file_unique.tardis_dalek\|0.11.tardis_dalek__": {"src": "hda", "id": "b033e717893f975b", "uuid": "4af371eb-6d68-4208-b8a7-963d774c3d81"}, "__new_primary_file_unique.tardis_dalek\|0.12.tardis_dalek__": {"src": "hda", "id": "c81b3d5aeaa214d9", "uuid": "0db9589f-a364-4371-8181-877bd52bdaca"}, "__new_primary_file_unique.tardis_dalek\|0.32.tardis_dalek__": {"src": "hda", "id": "f438c8126c9bf9b0", "uuid": "1d1e9de4-e49b-4959-9b7b-cbd46afa9329"}, "__new_primary_file_unique.tardis_dalek\|0.29.tardis_dalek__": {"src": "hda", "id": "f44604ff22d877c1", "uuid": "1899c047-5d53-4daa-86dd-d17c5916e643"}, "__new_primary_file_unique.tardis_dalek\|0.07.tardis_dalek__": {"src": "hda", "id": "128c838a8d0d8ae0", "uuid": "97c67190-a01f-41cf-bedc-4dd3961ff510"}, "__new_primary_file_unique.tardis_dalek\|0.04.tardis_dalek__": {"src": "hda", "id": "f3e6c274e0f9a8e4", "uuid": "2dc69c47-4aae-4a5e-ab1e-30b1373dc644"}, "__new_primary_file_unique.tardis_dalek\|0.36.tardis_dalek__": {"src": "hda", "id": "03e89c7d01c2bc89", "uuid": "6b97a604-d0a5-448d-a089-ab2b10bc01a8"}, "__new_primary_file_unique.tardis_dalek\|0.06.tardis_dalek__": {"src": "hda", "id": "976e02c1336449e2", "uuid": "04f6416e-10fa-42d7-af71-fd9beb5985fb"}, "__new_primary_file_unique.tardis_dalek\|0.03.tardis_dalek__": {"src": "hda", "id": "26c4db6085811fea", "uuid": "4929f085-b59f-4194-bc17-1383398f70b3"}, "__new_primary_file_unique.tardis_dalek\|0.09.tardis_dalek__": {"src": "hda", "id": "4981d0805809f979", "uuid": "8a11f0ad-8c4c-4d12-97e4-6bd9d22581c1"}, "__new_primary_file_unique.tardis_dalek\|0.18.tardis_dalek__": {"src": "hda", "id": "81eed33b79c62dd6", "uuid": "fe2f8394-859e-4a4b-9ebe-4372133e3df7"}, "__new_primary_file_unique.tardis_dalek\|0.01.tardis_dalek__": {"src": "hda", "id": "c17cb498f643f865", "uuid": "bbfb19a1-2947-41ab-b79d-db72dad84646"}, "__new_primary_file_unique.tardis_dalek\|0.19.tardis_dalek__": {"src": "hda", "id": "e0803aa76a0a1bc2", "uuid": "afdb1fec-9dde-461d-ad0e-6a5ae28017fa"}, "__new_primary_file_unique.tardis_dalek\|0.23.tardis_dalek__": {"src": "hda", "id": "5a2b531ed34953ef", "uuid": "cf779b61-a8ea-4883-87f5-c91c3e292dd9"}, "__new_primary_file_unique.tardis_dalek\|0.55.tardis_dalek__": {"src": "hda", "id": "d275e0f086e8ba53", "uuid": "f5572494-b2a1-467c-a450-59d5ddee16c6"}, "__new_primary_file_unique.tardis_dalek\|0.41.tardis_dalek__": {"src": "hda", "id": "a30e41ecd967d7a3", "uuid": "210829b9-80c0-465c-a757-f398c22b056a"}, "__new_primary_file_unique.tardis_dalek\|0.38.tardis_dalek__": {"src": "hda", "id": "a93799b0b587d22c", "uuid": "a233d11b-6442-4375-ac8e-0fd1a4352846"}, "__new_primary_file_unique.tardis_dalek\|0.22.tardis_dalek__": {"src": "hda", "id": "3eb471ae316d5ad9", "uuid": "f392ddea-025a-4c4d-8edf-a40147cb5a79"}, "__new_primary_file_unique.tardis_dalek\|0.26.tardis_dalek__": {"src": "hda", "id": "c37b0acee3e6ddf8", "uuid": "a8c15b1f-1e11-4233-9f2f-4b151ac8cce6"}, "__new_primary_file_unique.tardis_dalek\|0.33.tardis_dalek__": {"src": "hda", "id": "97255621df457a9d", "uuid": "9c76e42d-2704-4ca7-bc5e-941fc0640f2c"}, "__new_primary_file_unique.tardis_dalek\|0.20.tardis_dalek__": {"src": "hda", "id": "f8c8bf4b82d11e77", "uuid": "4c8e26a6-19dd-44d6-812c-99d1043ee603"}, "__new_primary_file_unique.tardis_dalek\|0.24.tardis_dalek__": {"src": "hda", "id": "19a2bc99dc38847c", "uuid": "1a182621-41c5-45e6-84b5-3c37158ba384"}, "__new_primary_file_unique.tardis_dalek\|0.27.tardis_dalek__": {"src": "hda", "id": "7cddf8abc6fb76de", "uuid": "29a51c5e-589a-41e9-b6d3-cf95d9255dfc"}, "__new_primary_file_unique.tardis_dalek\|0.21.tardis_dalek__": {"src": "hda", "id": "0bb6efe930f641f6", "uuid": "86a71f87-c4d6-493e-b5a1-09e26728f8a9"}, "logfile": {"src": "hda", "id": "21321643249e498c", "uuid": "b00f8c3e-8a53-4d25-b87d-906fd2778752"}, "__new_primary_file_unique.tardis_dalek\|0.45.tardis_dalek__": {"src": "hda", "id": "8ecc395ead7daa5b", "uuid": "52cf9561-ba5e-4430-ba24-776b1fd17c80"}, "__new_primary_file_unique.tardis_dalek\|0.02.tardis_dalek__": {"src": "hda", "id": "fe80aaa5fa3c02fc", "uuid": "60280cc1-03f0-4df8-9587-8cd48eeb6f91"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > metastats(shared=otu.dat,design=design.dat,iters=1000,threshold=0.05,pr \rocessors=1)\n\nUsing 1 processors.\nunique\nComparing tardis and dalek...\n\n\n\n0.01\nComparing tardis and dalek...\n\n\n\n0.02\nComparing tardis and dalek...\n\n\n\n0.03\nComparing tardis and dalek...\n\n\n\n0.04\nComparing tardis and dalek...\n\n\n\n0.05\nComparing tardis and dalek...\n\n\n\n0.06\nComparing tardis and dalek...\n\n\n\n0.07\nComparing tardis and dalek...\n\n\n\n0.08\nComparing tardis and dalek...\n\n\n\n0.09\nComparing tardis and dalek...\n\n\n\n0.10\nComparing tardis and dalek...\n\n\n\n0.11\nComparing tardis and dalek...\n\n\n\n0.12\nComparing tardis and dalek...\n\n\n\n0.13\nComparing tardis and dalek...\n\n\n\n0.14\nComparing tardis and dalek...\n\n\n\n0.15\nComparing tardis and dalek...\n\n\n\n0.16\nComparing tardis and dalek...\n\n\n\n0.17\nComparing tardis and dalek...\n\n\n\n0.18\nComparing tardis and dalek...\n\n\n\n0.19\nComparing tardis and dalek...\n\n\n\n0.20\nComparing tardis and dalek...\n\n\n\n0.21\nComparing tardis and dalek...\n\n\n\n0.22\nComparing tardis and dalek...\n\n\n\n0.23\nComparing tardis and dalek...\n\n\n\n0.24\nComparing tardis and dalek...\n\n\n\n0.25\nComparing tardis and dalek...\n\n\n\n0.26\nComparing tardis and dalek...\n\n\n\n0.27\nComparing tardis and dalek...\n\n\n\n0.29\nComparing tardis and dalek...\n\n\n\n0.32\nComparing tardis and dalek...\n\n\n\n0.33\nComparing tardis and dalek...\n\n\n\n0.36\nComparing tardis and dalek...\n\n\n\n0.38\nComparing tardis and dalek...\n\n\n\n0.41\nComparing tardis and dalek...\n\n\n\n0.45\nComparing tardis and dalek...\n\n\n\n0.55\nComparing tardis and dalek...\n\n\n\n\nOutput File Names: \notu.unique.tardis_dalek.metastats\notu.0.01.tardis_dalek.metastats\notu.0.02.tardis_dalek.metastats\notu.0.03.tardis_dalek.metastats\notu.0.04.tardis_dalek.metastats\notu.0.05.tardis_dalek.metastats\notu.0.06.tardis_dalek.metastats\notu.0.07.tardis_dalek.metastats\notu.0.08.tardis_dalek.metastats\notu.0.09.tardis_dalek.metastats\notu.0.10.tardis_dalek.metastats\notu.0.11.tardis_dalek.metastats\notu.0.12.tardis_dalek.metastats\notu.0.13.tardis_dalek.metastats\notu.0.14.tardis_dalek.metastats\notu.0.15.tardis_dalek.metastats\notu.0.16.tardis_dalek.metastats\notu.0.17.tardis_dalek.metastats\notu.0.18.tardis_dalek.metastats\notu.0.19.tardis_dalek.metastats\notu.0.20.tardis_dalek.metastats\notu.0.21.tardis_dalek.metastats\notu.0.22.tardis_dalek.metastats\notu.0.23.tardis_dalek.metastats\notu.0.24.tardis_dalek.metastats\notu.0.25.tardis_dalek.metastats\notu.0.26.tardis_dalek.metastats\notu.0.27.tardis_dalek.metastats\notu.0.29.tardis_dalek.metastats\notu.0.32.tardis_dalek.metastats\notu.0.33.tardis_dalek.metastats\notu.0.36.tardis_dalek.metastats\notu.0.38.tardis_dalek.metastats\notu.0.41.tardis_dalek.metastats\notu.0.45.tardis_dalek.metastats\notu.0.55.tardis_dalek.metastats\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1941.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1942.dat' design.dat && echo 'metastats( shared=otu.dat, design=design.dat, iters=1000, threshold=0.05, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:00:44.770100", "params": {"iters": "\"1000\"", "dbkey": "\"hg17\"", "label": "null", "groups": "null", "sets": "null", "threshold": "\"0.05\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28202", "id": "9c170123467f3230", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_metastats.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"iters": "42", "label": ["0.03", "0.05", "0.23"], "design": {"src": "hda", "id": "f5f83a2c2e2df452"}, "groups": ["forest", "pasture"], "sets": ["tardis", "dalek"], "threshold": "0.1", "otu": {"src": "hda", "id": "16015188b50ec89d"}}, "job": {"inputs": {"design": {"src": "hda", "id": "f5f83a2c2e2df452", "uuid": "b2bfb765-b8ed-45fb-8868-718771a6b982"}, "otu": {"src": "hda", "id": "16015188b50ec89d", "uuid": "ee5a9e25-e463-4fe6-94ca-fec5c0b46ae0"}}, "update_time": "2018-02-08T18:01:12.674158", "tool_id": "mothur_metastats", "outputs": {"__new_primary_file_0.23.tardis_dalek\|0.03.tardis_dalek__": {"src": "hda", "id": "d300bc462cc13705", "uuid": "f876c2bb-7428-4ce4-81b8-3088bff3409f"}, "logfile": {"src": "hda", "id": "1f58a7ab4f77b22a", "uuid": "8984636b-b45c-4592-a0ee-afce3170e0c5"}, "__new_primary_file_0.23.tardis_dalek\|0.23.tardis_dalek__": {"src": "hda", "id": "e03f21306103e4ea", "uuid": "f048a2fc-77e9-41ce-99bb-40045453e1e2"}, "__new_primary_file_0.23.tardis_dalek\|0.05.tardis_dalek__": {"src": "hda", "id": "262c1246e01f8d26", "uuid": "47ee5a3d-772d-401e-b3e3-de1424399d36"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > metastats(shared=otu.dat,design=design.dat,label=0.03-0.05-0.23,groups= \rforest-pasture,sets=tardis-dalek,iters=42,threshold=0.1,processors=1)\n\nUsing 1 processors.\n0.03\nComparing tardis and dalek...\n\n\n\n0.05\nComparing tardis and dalek...\n\n\n\n0.23\nComparing tardis and dalek...\n\n\n\n\nOutput File Names: \notu.0.03.tardis_dalek.metastats\notu.0.05.tardis_dalek.metastats\notu.0.23.tardis_dalek.metastats\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1980.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1981.dat' design.dat && echo 'metastats( shared=otu.dat, design=design.dat, label=0.03-0.05-0.23, groups=forest-pasture, sets=tardis-dalek, iters=42, threshold=0.1, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:01:09.437646", "params": {"iters": "\"42\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\", \"0.23\"]", "groups": "[\"forest\", \"pasture\"]", "sets": "[\"tardis\", \"dalek\"]", "threshold": "\"0.1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28310", "id": "c9376b9862484ed4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_metastats.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"biosample_in": {"src": "hda", "id": "783b5c0953b1d59f"}}, "job": {"inputs": {"biosample_in": {"src": "hda", "id": "783b5c0953b1d59f", "uuid": "f04d010f-490e-47d7-9c58-638de0a0f112"}}, "update_time": "2018-02-08T18:01:30.104939", "tool_id": "mothur_mimarks_attributes", "outputs": {"logfile": {"src": "hda", "id": "7fc2bbf196a6c236", "uuid": "380bef89-2a78-4c3e-874a-739dcb8e6b44"}, "source_out": {"src": "hda", "id": "484bc14fb0641f5d", "uuid": "5f2c33dd-8ec2-49ef-8273-f4070a612f4b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > mimarks.attributes(xml=biosample_in.dat)\n\nOutput File Names: \nbiosample_in.source\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1986.dat' biosample_in.dat && echo 'mimarks.attributes( xml=biosample_in.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:01:27.084739", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28401", "id": "a15361ef356dda4c", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_mimarks_attributes.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"maxiters": "500", "dist": {"src": "hda", "id": "b5c63bdc9af8cbfc"}, "iters": "10", "epsilon": "1e-12", "axes": {"src": "hda", "id": "79c845a60c77ee0a"}, "mindim": "1", "maxdim": "2"}, "job": {"inputs": {"axes": {"src": "hda", "id": "79c845a60c77ee0a", "uuid": "daa0cf22-d069-4512-92c4-00ccec312827"}, "dist": {"src": "hda", "id": "b5c63bdc9af8cbfc", "uuid": "a5bd2d21-a2d7-4102-877c-fd2380c0f335"}}, "update_time": "2018-02-08T18:01:52.474808", "tool_id": "mothur_nmds", "outputs": {"nmds_axes": {"src": "hda", "id": "fb839e143095d9fa", "uuid": "081a3528-a9b7-4eaa-a884-7ff38c3a8191"}, "logfile": {"src": "hda", "id": "69390d7537a983f9", "uuid": "154d81fb-90af-4c69-82af-c808c507e7ae"}, "nmds_stress": {"src": "hda", "id": "ad8f0faec2def4cc", "uuid": "2323c312-fef4-440b-957e-a17723a6996e"}, "nmds_iters": {"src": "hda", "id": "d227a40fd9141984", "uuid": "2f3b4e0e-a3ce-41e0-8619-22f3456e16bf"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > nmds(phylip=dist.dat,axes=axes.dat,mindim=1,maxdim=2,iters=10,maxiters= \r500,epsilon=0.000000000001)\nProcessing Dimension: 1\n1\n2\n3\n4\n5\n6\n7\n8\n9\n10\nProcessing Dimension: 2\n1\n2\n3\n4\n5\n6\n7\n8\n9\n10\n\nNumber of dimensions:\t2\nLowest stress :\t0.291989\nR-squared for configuration:\t0.672714\n\nOutput File Names: \ndist.nmds.iters\ndist.nmds.stress\ndist.nmds.axes\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1989.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1990.dat' axes.dat && echo 'nmds( phylip=dist.dat ,axes=axes.dat ,mindim=1 ,maxdim=2 ,iters=10 ,maxiters=500 ,epsilon=0.000000000001 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:01:48.716400", "params": {"iters": "\"10\"", "epsilon": "\"1e-12\"", "maxiters": "\"500\"", "dbkey": "\"hg17\"", "mindim": "\"1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "maxdim": "\"2\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28517", "id": "9cb939e9f07d29cd", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_nmds.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "48c25e118b57ff38"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "48c25e118b57ff38", "uuid": "8a3f167d-d835-41c1-a038-18adbb58214e"}}, "update_time": "2018-02-08T18:02:08.863250", "tool_id": "mothur_normalize_shared", "outputs": {"__new_primary_file_unique.norm\|0.07.norm__": {"src": "hda", "id": "7759c88734df315e", "uuid": "a75f4462-3a2f-4cc2-b859-9a340492b5a7"}, "__new_primary_file_unique.norm\|0.19.norm__": {"src": "hda", "id": "e15558a60db6ce87", "uuid": "05f65c04-ef5e-4021-b38c-b24d1edabb41"}, "__new_primary_file_unique.norm\|0.21.norm__": {"src": "hda", "id": "49f819ba53a576ae", "uuid": "287b454e-235d-448d-beb9-72c57e385e9f"}, "__new_primary_file_unique.norm\|0.27.norm__": {"src": "hda", "id": "272369349a8921ab", "uuid": "c50e231d-00fb-4c12-aacd-2c55c6aed2b1"}, "__new_primary_file_unique.norm\|0.02.norm__": {"src": "hda", "id": "c2d6d1dec01a4ef9", "uuid": "d5787ed8-9289-4c0d-8654-4559c8b67bd4"}, "__new_primary_file_unique.norm\|0.10.norm__": {"src": "hda", "id": "90fe3cef3e1f3d0a", "uuid": "0dce828e-85e6-4778-9f4d-a737f5bf061d"}, "__new_primary_file_unique.norm\|0.15.norm__": {"src": "hda", "id": "cfc3a68225d7a57a", "uuid": "fe6355f9-4e84-4c08-941d-f686872e9fa9"}, "__new_primary_file_unique.norm\|0.32.norm__": {"src": "hda", "id": "3a39b817c56902e0", "uuid": "c50f8300-a0e6-4171-a176-b7b7eded04cc"}, "__new_primary_file_unique.norm\|0.17.norm__": {"src": "hda", "id": "2f054c8ffebf41aa", "uuid": "5accca94-4b16-42d9-9947-ef9a7e2ffb6e"}, "__new_primary_file_unique.norm\|0.16.norm__": {"src": "hda", "id": "46333212c23a3768", "uuid": "b5d1bda0-7373-413b-acbf-eeb5146961e2"}, "__new_primary_file_unique.norm\|0.36.norm__": {"src": "hda", "id": "75cd1d05bb846784", "uuid": "77ba217e-f20f-474f-94f3-5f21264485f4"}, "__new_primary_file_unique.norm\|0.18.norm__": {"src": "hda", "id": "b87b913e52a5d5c9", "uuid": "74191fb6-286c-44ee-a8f1-2ed5bdbdf1e9"}, "__new_primary_file_unique.norm\|0.09.norm__": {"src": "hda", "id": "27e1efdc333ce8f0", "uuid": "8d783925-c7e6-447e-8cc7-6d3b3bfb94ec"}, "__new_primary_file_unique.norm\|0.13.norm__": {"src": "hda", "id": "2d594f1751c3f1ca", "uuid": "9ba75684-ca69-4ab3-ac4a-e03abe56de6d"}, "__new_primary_file_unique.norm\|0.04.norm__": {"src": "hda", "id": "1e9ece54ea08d532", "uuid": "3647f93e-adbb-46b8-be78-b4dd866a3c1a"}, "__new_primary_file_unique.norm\|0.25.norm__": {"src": "hda", "id": "2c56b3e8d1933dff", "uuid": "bd5cb805-5151-4fa8-b6ad-04cd367774ec"}, "__new_primary_file_unique.norm\|0.08.norm__": {"src": "hda", "id": "d1c342b47833ac58", "uuid": "01a00306-6ea4-4f89-af13-fecec911d3d0"}, "__new_primary_file_unique.norm\|0.14.norm__": {"src": "hda", "id": "3c42490c0523ccef", "uuid": "77eda36d-e783-4d80-98b1-a478e6b72e29"}, "__new_primary_file_unique.norm\|0.01.norm__": {"src": "hda", "id": "c824299315999632", "uuid": "fd126526-1c4c-40a5-aa68-bd3ab81d043d"}, "__new_primary_file_unique.norm\|0.12.norm__": {"src": "hda", "id": "a47b8bff4e8d501d", "uuid": "3043e307-5930-4373-a1cf-d0b4f8652103"}, "__new_primary_file_unique.norm\|0.20.norm__": {"src": "hda", "id": "73da0ed5a2fb6fff", "uuid": "a68dd3f4-94f3-4214-b2aa-885b42bad8e3"}, "__new_primary_file_unique.norm\|0.11.norm__": {"src": "hda", "id": "40b29ef9311f652c", "uuid": "5a54bdc9-f200-46fd-bcda-65cc9a198ddb"}, "__new_primary_file_unique.norm\|0.24.norm__": {"src": "hda", "id": "b54047d5cce3c175", "uuid": "046417cb-59f0-49bb-b84e-217d6f9fc6df"}, "__new_primary_file_unique.norm\|0.33.norm__": {"src": "hda", "id": "36c9940fe6749118", "uuid": "facb3a3c-29f8-4b19-91eb-7f9d9cebb1eb"}, "__new_primary_file_unique.norm\|0.06.norm__": {"src": "hda", "id": "81ad05cab5ca23e3", "uuid": "52ee6aff-4754-400d-871e-b63c5a579dac"}, "logfile": {"src": "hda", "id": "f6fa49db00a5d176", "uuid": "49c3d551-24d6-4177-aa4d-f30a2ed85679"}, "__new_primary_file_unique.norm\|0.22.norm__": {"src": "hda", "id": "3d07c4b2ea0d3aa3", "uuid": "fd2adbbe-a2a9-46ed-b5e3-d851f5d8c826"}, "__new_primary_file_unique.norm\|0.23.norm__": {"src": "hda", "id": "8d52c605ebf1b6c9", "uuid": "0c921b87-30c0-49c6-8055-863f572a2d44"}, "__new_primary_file_unique.norm\|unique.norm__": {"src": "hda", "id": "60c77f9904c7dacb", "uuid": "4f1c6b3b-c49e-4cde-9bcf-bc3b9b24bf92"}, "__new_primary_file_unique.norm\|0.55.norm__": {"src": "hda", "id": "ecbc034f3494529a", "uuid": "f5274456-1f23-4cb1-8d2a-8a283213cd9a"}, "__new_primary_file_unique.norm\|0.29.norm__": {"src": "hda", "id": "977623ec5ac25552", "uuid": "49ca3d12-5f9b-43d5-99d2-bc253f076536"}, "__new_primary_file_unique.norm\|0.05.norm__": {"src": "hda", "id": "43b804562da00ba8", "uuid": "6ef2e7b3-cbad-4fa8-b8ac-ef215b7a04ba"}, "__new_primary_file_unique.norm\|0.41.norm__": {"src": "hda", "id": "eeea002e11b8cacd", "uuid": "b683fd5c-efcc-49d6-8bd8-005ee6c05de2"}, "__new_primary_file_unique.norm\|0.45.norm__": {"src": "hda", "id": "eceb0fa9b153422c", "uuid": "82f45968-c33c-4374-a80e-58acd43b3a5f"}, "__new_primary_file_unique.norm\|0.26.norm__": {"src": "hda", "id": "a9b1685bdd21a57d", "uuid": "e8ec4d17-2204-45d2-901b-7763a9eb00c6"}, "__new_primary_file_unique.norm\|0.38.norm__": {"src": "hda", "id": "85d4d338e8b329c0", "uuid": "2be1bc01-fadd-4ae6-ae51-fc2fa9b83bb6"}, "__new_primary_file_unique.norm\|0.03.norm__": {"src": "hda", "id": "ae1816dcf1be843e", "uuid": "5d23b3c7-215f-4720-ac0c-8fce664b4c0d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > normalize.shared(shared=otu.dat,makerelabund=false,method=totalgroup)\nNormalizing to 49.\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.unique.norm.shared\notu.0.01.norm.shared\notu.0.02.norm.shared\notu.0.03.norm.shared\notu.0.04.norm.shared\notu.0.05.norm.shared\notu.0.06.norm.shared\notu.0.07.norm.shared\notu.0.08.norm.shared\notu.0.09.norm.shared\notu.0.10.norm.shared\notu.0.11.norm.shared\notu.0.12.norm.shared\notu.0.13.norm.shared\notu.0.14.norm.shared\notu.0.15.norm.shared\notu.0.16.norm.shared\notu.0.17.norm.shared\notu.0.18.norm.shared\notu.0.19.norm.shared\notu.0.20.norm.shared\notu.0.21.norm.shared\notu.0.22.norm.shared\notu.0.23.norm.shared\notu.0.24.norm.shared\notu.0.25.norm.shared\notu.0.26.norm.shared\notu.0.27.norm.shared\notu.0.29.norm.shared\notu.0.32.norm.shared\notu.0.33.norm.shared\notu.0.36.norm.shared\notu.0.38.norm.shared\notu.0.41.norm.shared\notu.0.45.norm.shared\notu.0.55.norm.shared\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1995.dat' otu.dat && echo 'normalize.shared( shared=otu.dat, makerelabund=false ,method=totalgroup )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:02:04.195701", "params": {"makerelabund": "\"false\"", "dbkey": "\"hg17\"", "label": "null", "groups": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"totalgroup\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28605", "id": "9c51eb665ea2103a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_normalize_shared.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "9ba5a8797c4d0c42"}, "method": "zscore", "groups": ["forest", "pasture"], "label": ["0.03", "0.05", "0.22", "0.26"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "9ba5a8797c4d0c42", "uuid": "a4a49ce3-1b9f-49ae-aa48-ea0fc8e7daa7"}}, "update_time": "2018-02-08T18:02:27.725869", "tool_id": "mothur_normalize_shared", "outputs": {"__new_primary_file_0.26.norm\|0.22.norm__": {"src": "hda", "id": "657c12bf3606453d", "uuid": "29a1882d-2c27-4382-8da0-48f9a2b9d275"}, "__new_primary_file_0.26.norm\|0.03.norm__": {"src": "hda", "id": "0cced470bd87c555", "uuid": "6c7a4cab-4a52-4632-a961-fd87ee7abfe5"}, "logfile": {"src": "hda", "id": "d13e42b04e9821cb", "uuid": "7b373694-be5e-4685-a6a5-a70069e6c927"}, "__new_primary_file_0.26.norm\|0.05.norm__": {"src": "hda", "id": "e58fc15b0924c233", "uuid": "3afbd0b9-3417-4574-a7c2-f5d92de0c7c2"}, "__new_primary_file_0.26.norm\|0.26.norm__": {"src": "hda", "id": "4b63a0979ffefabe", "uuid": "084e8dac-f27e-40d4-a25a-2f528d29542f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > normalize.shared(relabund=otu.dat,label=0.03-0.05-0.22-0.26,groups=fore \rst-pasture,method=zscore)\n0.03\n0.05\n0.22\n0.26\n\nOutput File Names: \notu.0.03.norm.shared\notu.0.05.norm.shared\notu.0.22.norm.shared\notu.0.26.norm.shared\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2033.dat' otu.dat && echo 'normalize.shared( relabund=otu.dat ,label=0.03-0.05-0.22-0.26 ,groups=forest-pasture ,method=zscore )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:02:24.473973", "params": {"makerelabund": "\"false\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\", \"0.22\", \"0.26\"]", "groups": "[\"forest\", \"pasture\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"zscore\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28697", "id": "3511dc9f211ca562", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_normalize_shared.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "87078348debd31f2"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "87078348debd31f2", "uuid": "9ff0bf1b-34a4-4486-a449-18e55d1e5577"}}, "update_time": "2018-02-08T18:02:47.222922", "tool_id": "mothur_otu_association", "outputs": {"__new_primary_file_unique.pearson\|0.21.pearson__": {"src": "hda", "id": "c1f9b7f85ff447a6", "uuid": "a1aac0c9-3045-45c0-836d-1493ca8e591e"}, "__new_primary_file_unique.pearson\|0.09.pearson__": {"src": "hda", "id": "7d1fdfaaecdf4192", "uuid": "190d3ceb-dbac-42b7-86f2-431ef542ade1"}, "__new_primary_file_unique.pearson\|0.14.pearson__": {"src": "hda", "id": "15af681009ecbcd4", "uuid": "829a2d25-1d1f-4bd1-a94f-728b71ed4a8b"}, "__new_primary_file_unique.pearson\|0.17.pearson__": {"src": "hda", "id": "114f907721fad498", "uuid": "b8e86fe8-b44b-43dd-832c-ccf1c29b1b49"}, "__new_primary_file_unique.pearson\|0.32.pearson__": {"src": "hda", "id": "5c5398d0729f4c9a", "uuid": "f52b9ec3-a517-4374-8f13-d04f44eb252d"}, "__new_primary_file_unique.pearson\|0.02.pearson__": {"src": "hda", "id": "c236b8a59d75a9c2", "uuid": "27ad07c8-efeb-4c4b-9c95-a68738ffb41e"}, "__new_primary_file_unique.pearson\|0.12.pearson__": {"src": "hda", "id": "2c136d847c62c788", "uuid": "412122c9-714d-4070-8454-555b9ef659e1"}, "__new_primary_file_unique.pearson\|0.25.pearson__": {"src": "hda", "id": "d771d09f3a90c00d", "uuid": "4a14d774-50c2-4eba-80e0-922cc5f421da"}, "__new_primary_file_unique.pearson\|0.08.pearson__": {"src": "hda", "id": "72e972e8ff63ac2f", "uuid": "dabda07b-48d8-4e6f-875d-563a245f844d"}, "__new_primary_file_unique.pearson\|0.38.pearson__": {"src": "hda", "id": "e3439702cb80e218", "uuid": "9612f8ee-101d-41d9-b93b-661a0e535b7a"}, "__new_primary_file_unique.pearson\|unique.pearson__": {"src": "hda", "id": "aace3805315e657d", "uuid": "dc3a07bf-337a-4ec1-919a-f66776445489"}, "__new_primary_file_unique.pearson\|0.01.pearson__": {"src": "hda", "id": "16d9810a1d73b5f1", "uuid": "597d9503-922e-40af-a9c1-984353ba0c8e"}, "__new_primary_file_unique.pearson\|0.20.pearson__": {"src": "hda", "id": "c2043a758b5f655f", "uuid": "2a04f889-eb09-432c-9a25-3b114d0c5a41"}, "__new_primary_file_unique.pearson\|0.41.pearson__": {"src": "hda", "id": "1fee3aaaf06b954f", "uuid": "cc55fe95-9ef5-4624-9387-90d471c056f0"}, "__new_primary_file_unique.pearson\|0.04.pearson__": {"src": "hda", "id": "404e8272e390459f", "uuid": "d8f51365-827d-4a9a-ab9b-e2c8571868d0"}, "__new_primary_file_unique.pearson\|0.45.pearson__": {"src": "hda", "id": "86b4eaf5162d2e94", "uuid": "966213a6-ce22-4c59-b398-d62b43dab95b"}, "__new_primary_file_unique.pearson\|0.10.pearson__": {"src": "hda", "id": "018540e5bb755e48", "uuid": "7a545f3e-65a3-41a6-a5a8-11f2e53b34f3"}, "__new_primary_file_unique.pearson\|0.11.pearson__": {"src": "hda", "id": "567e98a779203439", "uuid": "8ecdc785-ec0b-4254-9a79-2a7cc0cf79ac"}, "__new_primary_file_unique.pearson\|0.18.pearson__": {"src": "hda", "id": "64554a81865d2173", "uuid": "c0bbdbf2-ee93-4e47-8d98-9909d31ab095"}, "__new_primary_file_unique.pearson\|0.03.pearson__": {"src": "hda", "id": "54d5b172655ab5cf", "uuid": "4194c71d-db60-4f42-a995-90167d782a67"}, "__new_primary_file_unique.pearson\|0.15.pearson__": {"src": "hda", "id": "7fcc2597b7ad9954", "uuid": "c6309615-8880-49ce-b9f5-a386be8bc8b7"}, "__new_primary_file_unique.pearson\|0.36.pearson__": {"src": "hda", "id": "b60f79d04dee2eec", "uuid": "9ca41100-7ad9-45e8-a03a-64df3b213dbf"}, "__new_primary_file_unique.pearson\|0.24.pearson__": {"src": "hda", "id": "94b253c013da9d07", "uuid": "03736b3b-ccba-4d40-a0de-b6d3d1709a5d"}, "__new_primary_file_unique.pearson\|0.05.pearson__": {"src": "hda", "id": "cfcb788085ab492e", "uuid": "18fc98fb-2238-46e4-91cf-9a318eb3207a"}, "__new_primary_file_unique.pearson\|0.33.pearson__": {"src": "hda", "id": "6e262c2ae2545ffb", "uuid": "06429343-666a-449b-bc23-94c807213edf"}, "logfile": {"src": "hda", "id": "73ed1fba7da78f4b", "uuid": "b005fd48-2d12-4e18-8471-b6a413a03e5e"}, "__new_primary_file_unique.pearson\|0.19.pearson__": {"src": "hda", "id": "bc441ceb5a3223e1", "uuid": "7d6a6527-1daa-4624-b0fb-de3377b58c4c"}, "__new_primary_file_unique.pearson\|0.16.pearson__": {"src": "hda", "id": "aa452a61ad24963a", "uuid": "1393e52e-a590-4174-9947-e9794deb3a10"}, "__new_primary_file_unique.pearson\|0.55.pearson__": {"src": "hda", "id": "872f8bbac826a355", "uuid": "62d76d7a-216e-471b-9bc0-7db49cc077a4"}, "__new_primary_file_unique.pearson\|0.13.pearson__": {"src": "hda", "id": "9c4915c8de2f90d1", "uuid": "4509cd1a-0c95-422e-84f4-e9c9a57fb559"}, "__new_primary_file_unique.pearson\|0.27.pearson__": {"src": "hda", "id": "632437ce271bb8aa", "uuid": "8aa8d928-c084-41ec-83e4-c597839d9da7"}, "__new_primary_file_unique.pearson\|0.26.pearson__": {"src": "hda", "id": "a842af6d14177fe6", "uuid": "1fa98059-5386-4b6f-9794-9cff5e7c3e67"}, "__new_primary_file_unique.pearson\|0.22.pearson__": {"src": "hda", "id": "01ae29ee518639b6", "uuid": "5a789cc3-468b-4649-a3f5-7428b8f80c58"}, "__new_primary_file_unique.pearson\|0.07.pearson__": {"src": "hda", "id": "3ac2939147b22342", "uuid": "0676e856-b147-48a4-9137-565323c071b6"}, "__new_primary_file_unique.pearson\|0.29.pearson__": {"src": "hda", "id": "56dae71a8dfd28e4", "uuid": "4972bf5f-dc51-4616-8368-13e49a8b2efe"}, "__new_primary_file_unique.pearson\|0.06.pearson__": {"src": "hda", "id": "13d8dea9ad27b203", "uuid": "0bb6d052-9c47-4c2d-9ff6-253d68a9705a"}, "__new_primary_file_unique.pearson\|0.23.pearson__": {"src": "hda", "id": "652cc733e38b3fd8", "uuid": "a9988dbd-1aa0-400a-b0e7-cdd1473ae7b7"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > otu.association(shared=otu.dat,method=pearson)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.unique.pearson.otu.corr\notu.0.01.pearson.otu.corr\notu.0.02.pearson.otu.corr\notu.0.03.pearson.otu.corr\notu.0.04.pearson.otu.corr\notu.0.05.pearson.otu.corr\notu.0.06.pearson.otu.corr\notu.0.07.pearson.otu.corr\notu.0.08.pearson.otu.corr\notu.0.09.pearson.otu.corr\notu.0.10.pearson.otu.corr\notu.0.11.pearson.otu.corr\notu.0.12.pearson.otu.corr\notu.0.13.pearson.otu.corr\notu.0.14.pearson.otu.corr\notu.0.15.pearson.otu.corr\notu.0.16.pearson.otu.corr\notu.0.17.pearson.otu.corr\notu.0.18.pearson.otu.corr\notu.0.19.pearson.otu.corr\notu.0.20.pearson.otu.corr\notu.0.21.pearson.otu.corr\notu.0.22.pearson.otu.corr\notu.0.23.pearson.otu.corr\notu.0.24.pearson.otu.corr\notu.0.25.pearson.otu.corr\notu.0.26.pearson.otu.corr\notu.0.27.pearson.otu.corr\notu.0.29.pearson.otu.corr\notu.0.32.pearson.otu.corr\notu.0.33.pearson.otu.corr\notu.0.36.pearson.otu.corr\notu.0.38.pearson.otu.corr\notu.0.41.pearson.otu.corr\notu.0.45.pearson.otu.corr\notu.0.55.pearson.otu.corr\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2039.dat' otu.dat && ln -s 'None' metadata.dat && echo 'otu.association( shared=otu.dat ,method=pearson )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:02:41.990561", "params": {"cutoff": "\"\"", "dbkey": "\"hg17\"", "label": "null", "groups": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"pearson\"", "metadata": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28785", "id": "c068ba61abe27ec2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_otu_association.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "a97c4449eeee3c89"}, "method": "kendall", "groups": ["forest", "pasture"], "label": ["0.03", "0.05", "0.36", "0.41", "0.55"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "a97c4449eeee3c89", "uuid": "2cc5e442-b3e7-4d4d-a33e-e8686510537f"}}, "update_time": "2018-02-08T18:03:05.842709", "tool_id": "mothur_otu_association", "outputs": {"__new_primary_file_0.55.kendall\|0.05.kendall__": {"src": "hda", "id": "4f7f3fb5673240e3", "uuid": "75bfd5a1-ecd4-40d3-86d3-f46714fb2c06"}, "__new_primary_file_0.55.kendall\|0.36.kendall__": {"src": "hda", "id": "b3f5ff2369d9d249", "uuid": "9750ce01-eeb2-49e6-bc87-8c742b5f7aca"}, "__new_primary_file_0.55.kendall\|0.55.kendall__": {"src": "hda", "id": "9a70aaebc3d20bdd", "uuid": "96a76da6-1781-4a91-a55d-932954e630a4"}, "__new_primary_file_0.55.kendall\|0.41.kendall__": {"src": "hda", "id": "d821d43764c03acb", "uuid": "5afaa011-1328-4ec7-9993-beebf0e70c38"}, "logfile": {"src": "hda", "id": "f7caa003b2842495", "uuid": "1d334062-244f-40a8-9707-99ea5d501792"}, "__new_primary_file_0.55.kendall\|0.03.kendall__": {"src": "hda", "id": "664177380bb275d4", "uuid": "d146fe80-0495-49b1-8eb0-74d10be9c287"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > otu.association(relabund=otu.dat,label=0.03-0.05-0.36-0.41-0.55,groups= \rforest-pasture,method=kendall)\n0.03\n0.05\n0.36\n0.41\n0.55\n\nOutput File Names: \notu.0.03.kendall.otu.corr\notu.0.05.kendall.otu.corr\notu.0.36.kendall.otu.corr\notu.0.41.kendall.otu.corr\notu.0.55.kendall.otu.corr\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2077.dat' otu.dat && ln -s 'None' metadata.dat && echo 'otu.association( relabund=otu.dat ,label=0.03-0.05-0.36-0.41-0.55 ,groups=forest-pasture ,method=kendall )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:03:02.491040", "params": {"cutoff": "\"\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\", \"0.36\", \"0.41\", \"0.55\"]", "groups": "[\"forest\", \"pasture\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"kendall\"", "metadata": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28873", "id": "aa43a28a12fcf867", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_otu_association.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"label1": "0.05", "label2": "0.03", "otu": {"src": "hda", "id": "8b1e72fab2ca9b47"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "8b1e72fab2ca9b47", "uuid": "ae2d5b50-ae44-4ed1-b9bf-1406cf8f52a4"}}, "update_time": "2018-02-08T18:03:26.014987", "tool_id": "mothur_otu_hierarchy", "outputs": {"hierarchy": {"src": "hda", "id": "143cb76ef3d4aedc", "uuid": "c008d314-8736-4660-bacf-06cd5e994100"}, "logfile": {"src": "hda", "id": "e4517ef02489f4b1", "uuid": "e4848545-6f0c-4a9f-b6b9-540bfef39a71"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > otu.hierarchy(list=otu.dat,label=0.05-0.03,output=name)\n\nOutput File Names: \notu.0.03._.0.05.otu.hierarchy\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2084.dat' otu.dat && echo 'otu.hierarchy( list=otu.dat, label=0.05-0.03, output=name )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:03:22.868182", "params": {"label1": "\"0.05\"", "label2": "\"0.03\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "output": "\"name\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28961", "id": "bb9931d062678360", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_otu_hierarchy.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"cutoff": "0.0", "countends": true, "align": "needleman", "scoring\|setby": "default", "output": "", "fasta": {"src": "hda", "id": "68cdc65b079e45ae"}, "calc": ""}, "job": {"inputs": {"fasta": {"src": "hda", "id": "68cdc65b079e45ae", "uuid": "a7869ff0-be51-454d-b445-4196d2c581e8"}}, "update_time": "2018-02-08T18:03:58.606414", "tool_id": "mothur_pairwise_seqs", "outputs": {"logfile": {"src": "hda", "id": "af3d6ad9d44f4b02", "uuid": "c4bc8b57-1e3c-4ef7-8950-19ac34479089"}, "out_dist": {"src": "hda", "id": "ff2fd427cb51c4ed", "uuid": "06c4d160-9614-45c9-a917-495ada390c3d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pairwise.seqs(fasta=fasta.dat,align=needleman,processors=1)\n\nUsing 1 processors.\nProcessing sequences from fasta.dat ...\n0\t0\n95\t15\nIt took 15 to calculate the distances for 96 sequences.\n\nOutput File Names: \nfasta.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2087.dat' fasta.dat && echo 'pairwise.seqs( fasta=fasta.dat, align=needleman, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:03:40.313049", "params": {"scoring": "{\"setby\": \"default\", \"__current_case__\": 0}", "cutoff": "\"0.0\"", "countends": "\"true\"", "align": "\"needleman\"", "dbkey": "\"hg17\"", "output": "\"\"", "calc": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29057", "id": "76880adb125efe03", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pairwise_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"cutoff": "0.01", "countends": false, "align": "gotoh", "scoring\|gapopen": "-2", "scoring\|mismatch": "-1", "scoring\|match": "2", "output": "lt", "fasta": {"src": "hda", "id": "5b02825370c62dc1"}, "calc": "onegap", "scoring\|gapextend": "-1", "scoring\|setby": "user"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "5b02825370c62dc1", "uuid": "88a82267-fcb7-4a89-99f7-e5a2f4d6d863"}}, "update_time": "2018-02-08T18:04:36.354756", "tool_id": "mothur_pairwise_seqs", "outputs": {"logfile": {"src": "hda", "id": "fccad1b547140dd3", "uuid": "9d3772a7-d94e-4aa0-9c2c-ce4092e51ef0"}, "out_dist": {"src": "hda", "id": "41944e51b7eea955", "uuid": "1cdb9228-8450-4900-a3e2-f1f9e88e38a9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pairwise.seqs(fasta=fasta.dat,align=gotoh,calc=onegap,countends=false,c \rutoff=0.01,match=2,mismatch=-1,gapopen=-2,gapextend=-1,output=lt,processors=1)\n\nUsing 1 processors.\nProcessing sequences from fasta.dat ...\n0\t0\n95\t18\nIt took 18 to calculate the distances for 96 sequences.\n\nOutput File Names: \nfasta.phylip.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2090.dat' fasta.dat && echo 'pairwise.seqs( fasta=fasta.dat, align=gotoh, calc=onegap, countends=false, cutoff=0.01, match=2, mismatch=-1, gapopen=-2, gapextend=-1, output=lt, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:04:14.828791", "params": {"scoring": "{\"gapopen\": \"-2\", \"mismatch\": \"-1\", \"__current_case__\": 1, \"setby\": \"user\", \"gapextend\": \"-1\", \"match\": \"2\"}", "cutoff": "\"0.01\"", "countends": "\"false\"", "align": "\"gotoh\"", "dbkey": "\"hg17\"", "output": "\"lt\"", "calc": "\"onegap\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29149", "id": "d36e0ad5b4ecc523", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pairwise_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"group": {"src": "hda", "id": "8afc4a870dadbd7d"}, "otu": {"src": "hda", "id": "31dbd8c6e9452ac3"}}, "job": {"inputs": {"group": {"src": "hda", "id": "8afc4a870dadbd7d", "uuid": "25515fae-47a6-4415-b726-2fca639df012"}, "otu": {"src": "hda", "id": "31dbd8c6e9452ac3", "uuid": "8f530433-634c-450d-a355-5baccd582764"}}, "update_time": "2018-02-08T18:05:00.623647", "tool_id": "mothur_parse_list", "outputs": {"__new_primary_file_pasture.unique\|forest.0.13__": {"src": "hda", "id": "a85c51ad73ace21c", "uuid": "6a23b166-7009-4719-b04c-ffa7759be524"}, "__new_primary_file_pasture.unique\|pasture.0.12__": {"src": "hda", "id": "3c9aa8dc96dd4037", "uuid": "cf71aa9d-2a2b-4b2c-aec0-2db9f47dc1b5"}, "__new_primary_file_pasture.unique\|forest.0.06__": {"src": "hda", "id": "7407f06b1e052c43", "uuid": "47a0ec11-c781-4b0c-bbf4-2bb9f195e479"}, "__new_primary_file_pasture.unique\|pasture.0.03__": {"src": "hda", "id": "afb54b8f1c8a1903", "uuid": "56eb91fa-64a2-486b-b9e9-f5a08781d96f"}, "__new_primary_file_pasture.unique\|pasture.0.15__": {"src": "hda", "id": "a8ff40a3a195a77b", "uuid": "2a43e9cb-4686-4340-bce7-fecf5fc11fcc"}, "__new_primary_file_pasture.unique\|forest.0.12__": {"src": "hda", "id": "57e39bb156480887", "uuid": "118bfa82-db72-4d78-98db-3b4ab0317f5f"}, "__new_primary_file_pasture.unique\|forest.0.19__": {"src": "hda", "id": "3a89aaf65b4da934", "uuid": "38235792-7034-4faf-95a0-d62535622980"}, "__new_primary_file_pasture.unique\|pasture.0.41__": {"src": "hda", "id": "686eaf07510a6daf", "uuid": "cc0ac23e-6c7a-4939-950f-8b014748f64c"}, "__new_primary_file_pasture.unique\|forest.0.15__": {"src": "hda", "id": "03658f5433e82a2e", "uuid": "550438fa-1846-4449-9298-e05def3a211d"}, "__new_primary_file_pasture.unique\|pasture.0.08__": {"src": "hda", "id": "bf4177214178aaac", "uuid": "6530c0a2-e3aa-4d5e-9e00-94a7eb76eebf"}, "__new_primary_file_pasture.unique\|pasture.0.27__": {"src": "hda", "id": "ec73fd31f7fdd7ff", "uuid": "df4c822c-04d1-4daf-83d3-631aa695b6bf"}, "__new_primary_file_pasture.unique\|forest.0.20__": {"src": "hda", "id": "947633482a2c76a9", "uuid": "645bfcc6-1f94-4944-a8e5-348033e8c9a5"}, "__new_primary_file_pasture.unique\|forest.0.14__": {"src": "hda", "id": "387443286670d506", "uuid": "cc1c344e-c0e2-4b5d-8e9c-499b01b40486"}, "__new_primary_file_pasture.unique\|forest.0.32__": {"src": "hda", "id": "ac851b4ae8518708", "uuid": "166ce5e6-b08d-40cb-88bf-038d4f768d59"}, "__new_primary_file_pasture.unique\|pasture.0.13__": {"src": "hda", "id": "ca88bfbe9bd4fae9", "uuid": "6550f023-a974-4444-814c-5c14fbfd6dc3"}, "__new_primary_file_pasture.unique\|pasture.0.09__": {"src": "hda", "id": "201c302e615535c1", "uuid": "0d637c85-d3ac-4c65-92fb-19b9d456ec3d"}, "__new_primary_file_pasture.unique\|pasture.0.26__": {"src": "hda", "id": "7cec0fee27e98af5", "uuid": "7814f8bd-1d47-4b38-9e7d-4fb2433a3ad2"}, 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"stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > parse.list(list=otu.dat,group=group.dat)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.forest.unique.list\notu.pasture.unique.list\notu.forest.0.01.list\notu.pasture.0.01.list\notu.forest.0.02.list\notu.pasture.0.02.list\notu.forest.0.03.list\notu.pasture.0.03.list\notu.forest.0.04.list\notu.pasture.0.04.list\notu.forest.0.05.list\notu.pasture.0.05.list\notu.forest.0.06.list\notu.pasture.0.06.list\notu.forest.0.07.list\notu.pasture.0.07.list\notu.forest.0.08.list\notu.pasture.0.08.list\notu.forest.0.09.list\notu.pasture.0.09.list\notu.forest.0.10.list\notu.pasture.0.10.list\notu.forest.0.11.list\notu.pasture.0.11.list\notu.forest.0.12.list\notu.pasture.0.12.list\notu.forest.0.13.list\notu.pasture.0.13.list\notu.forest.0.14.list\notu.pasture.0.14.list\notu.forest.0.15.list\notu.pasture.0.15.list\notu.forest.0.16.list\notu.pasture.0.16.list\notu.forest.0.17.list\notu.pasture.0.17.list\notu.forest.0.18.list\notu.pasture.0.18.list\notu.forest.0.19.list\notu.pasture.0.19.list\notu.forest.0.20.list\notu.pasture.0.20.list\notu.forest.0.21.list\notu.pasture.0.21.list\notu.forest.0.22.list\notu.pasture.0.22.list\notu.forest.0.23.list\notu.pasture.0.23.list\notu.forest.0.24.list\notu.pasture.0.24.list\notu.forest.0.25.list\notu.pasture.0.25.list\notu.forest.0.26.list\notu.pasture.0.26.list\notu.forest.0.27.list\notu.pasture.0.27.list\notu.forest.0.29.list\notu.pasture.0.29.list\notu.forest.0.32.list\notu.pasture.0.32.list\notu.forest.0.33.list\notu.pasture.0.33.list\notu.forest.0.36.list\notu.pasture.0.36.list\notu.forest.0.38.list\notu.pasture.0.38.list\notu.forest.0.41.list\notu.pasture.0.41.list\notu.forest.0.45.list\notu.pasture.0.45.list\notu.forest.0.55.list\notu.pasture.0.55.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2093.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2094.dat' group.dat && ln -s 'None' count.dat && echo 'parse.list( list=otu.dat, group=group.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:04:52.955670", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29272", "id": "d1010cb72bf991e5", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_parse_list.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"group": {"src": "hda", "id": "e26b78b0e6def9bf"}, "otu": {"src": "hda", "id": "c7007f9410f08c64"}, "label": ["0.03", "0.05"]}, "job": {"inputs": {"group": {"src": "hda", "id": "e26b78b0e6def9bf", "uuid": "353c7160-a417-41fe-9d37-24159b022544"}, "otu": {"src": "hda", "id": "c7007f9410f08c64", "uuid": "0232831f-981d-49df-a50a-dabcf1d42762"}}, "update_time": "2018-02-08T18:05:28.674033", "tool_id": "mothur_parse_list", "outputs": {"__new_primary_file_pasture.0.05\|pasture.0.03__": {"src": "hda", "id": "a3a2a175eac37c19", "uuid": "8bf3d63a-41e5-4a62-94d6-9d03c0ce81da"}, "__new_primary_file_pasture.0.05\|forest.0.05__": {"src": "hda", "id": "9d88bce42e8c40da", "uuid": "ac2a67fa-77a2-4541-b7f7-bcb08303b8db"}, "logfile": {"src": "hda", "id": "3253f225acee3abb", "uuid": "ab23c433-574e-4176-8076-26879bc1ec86"}, "__new_primary_file_pasture.0.05\|forest.0.03__": {"src": "hda", "id": "41d22b61843cac3f", "uuid": "0ecb66d9-a4c4-49fd-aaaf-0acca12e6040"}, "__new_primary_file_pasture.0.05\|pasture.0.05__": {"src": "hda", "id": "defef927024814c1", "uuid": "5264fd79-68a4-43fa-8ef4-a5b5173ca3ea"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > parse.list(list=otu.dat,label=0.03-0.05,group=group.dat)\n0.03\n0.05\n\nOutput File Names: \notu.forest.0.03.list\notu.pasture.0.03.list\notu.forest.0.05.list\notu.pasture.0.05.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2168.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2169.dat' group.dat && ln -s 'None' count.dat && echo 'parse.list( list=otu.dat, label=0.03-0.05, group=group.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:05:25.394023", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29383", "id": "731d7fc7f6176125", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_parse_list.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"iters": "1000", "group": {"src": "hda", "id": "8ad407aea9325e76"}, "tree": {"src": "hda", "id": "44f326e1f448e78e"}, "name": {"src": "hda", "id": "97c6d122e81a6846"}, "groups": ["green", "orange"]}, "job": {"inputs": {"group": {"src": "hda", "id": "8ad407aea9325e76", "uuid": "9afc0a9e-9933-453c-9ab5-2fe30abaa2a5"}, "tree": {"src": "hda", "id": "44f326e1f448e78e", "uuid": "cf76b161-6124-4cb0-9ca4-e8882434ae2f"}, "name": {"src": "hda", "id": "97c6d122e81a6846", "uuid": "fad7abb3-74cd-46a0-9322-375ac06a7c01"}}, "update_time": "2018-02-08T18:05:47.450319", "tool_id": "mothur_parsimony", "outputs": {"psummary": {"src": "hda", "id": "483b2e2bc94213c3", "uuid": "9d5ba257-ce53-4043-aa08-6f39cdf6e5c8"}, "logfile": {"src": "hda", "id": "9d39ac49f9104593", "uuid": "b181eea4-4af0-4ef3-a44d-4e7b460501ca"}, "parsimony": {"src": "hda", "id": "4af28ef0562c6c37", "uuid": "7812f1e8-93bf-4e9f-992b-ef1acae68b9d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > parsimony(tree=tree.dat,iters=1000,group=group.dat,name=name.dat,proces \rsors=1)\n\nUsing 1 processors.\n****************###########\nComparing to random:\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n********************************************************************\nTree#\tGroups\tParsScore\tParsSig\n1\tgreen-orange\t1\t1\n\n\nOutput File Names: \ntree.dat.parsimony\ntree.dat.psummary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2175.dat' tree.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2176.dat' group.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2177.dat' name.dat && echo 'parsimony( tree=tree.dat, iters=1000, group=group.dat, name=name.dat, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:05:44.236142", "params": {"count": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groups": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29525", "id": "2768baa09f52abc1", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_parsimony.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "1dcb63b7594c0a53"}, "groups": ["forest", "pasture"], "label": ["0.22", "0.55"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "1dcb63b7594c0a53", "uuid": "a2a67477-8ad3-4223-ae96-7001aeb2c40c"}}, "update_time": "2018-02-08T18:06:09.968465", "tool_id": "mothur_pca", "outputs": {"logfile": {"src": "hda", "id": "56e06f89792449a5", "uuid": "5af0509a-8a5f-476a-813e-b59c99931dcc"}, "__new_primary_file_0.55\|0.22__": {"src": "hda", "id": "29057053eabeecf0", "uuid": "a6491f79-3680-4a2d-b5d6-2f64c3ee6145"}, "__new_primary_file_0.55\|0.55__": {"src": "hda", "id": "009d092a3f629c9d", "uuid": "6e201424-5c1f-460f-943f-1ae330180131"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pca(shared=otu.dat,label=0.22-0.55,groups=forest-pasture,metric=true)\n\nProcessing 0.22\nRsq 1 axis: 0\nRsq 2 axis: 0\nRsq 3 axis: 0\n\nProcessing 0.55\nRsq 1 axis: 0\nRsq 2 axis: 0\nRsq 3 axis: 0\n\nOutput File Names: \notu.0.22.pca.axes\notu.0.22.pca.loadings\notu.0.55.pca.axes\notu.0.55.pca.loadings\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2181.dat' otu.dat && echo 'pca( shared=otu.dat, label=0.22-0.55, groups=forest-pasture, metric=true )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:06:06.690813", "params": {"metric": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groups": "[\"forest\", \"pasture\"]", "label": "[\"0.22\", \"0.55\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29614", "id": "f4b2790380ce04e0", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pca.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"phylip": {"src": "hda", "id": "3b036687d3b15bc3"}}, "job": {"inputs": {"phylip": {"src": "hda", "id": "3b036687d3b15bc3", "uuid": "66da62a2-02ab-4a91-be6c-7c70de565a19"}}, "update_time": "2018-02-08T18:06:32.566231", "tool_id": "mothur_pcoa", "outputs": {"loadings": {"src": "hda", "id": "98b8d8437f7c5552", "uuid": "d5956ef8-bd0d-4945-b284-133ec75977e2"}, "logfile": {"src": "hda", "id": "8648246ff30fc2ff", "uuid": "ed6046d3-743c-47a4-beaa-bf7e553cd006"}, "pcoa": {"src": "hda", "id": "07469086593c8cef", "uuid": "5b7c51a9-9f60-474b-9a97-ad62f9075f8b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pcoa(phylip=phylip.dat,metric=true)\n\nProcessing...\nRsq 1 axis: 0.200353\nRsq 2 axis: 0.413022\nRsq 3 axis: 0.430959\n\nOutput File Names: \nphylip.pcoa.axes\nphylip.pcoa.loadings\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2187.dat' phylip.dat && echo 'pcoa( phylip=phylip.dat, metric=true )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:06:29.476405", "params": {"metric": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29703", "id": "1e4cd37e942f1647", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pcoa.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"trim\|method": "position", "keepdots": true, "trim\|start": "0", "pdiffs": "0", "fasta": {"src": "hda", "id": "ff8a6faa7e9cbc52"}, "trim\|end": "0"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "ff8a6faa7e9cbc52", "uuid": "a94786f1-845b-43c2-9fa4-8e6317262ac5"}}, "update_time": "2018-02-08T18:06:45.075942", "tool_id": "mothur_pcr_seqs", "outputs": {"pcr_fasta": {"src": "hda", "id": "1d3a87989430d70d", "uuid": "28ee543c-eda1-4753-ab66-6276df887cd4"}, "logfile": {"src": "hda", "id": "ca4fcaac5d3c0250", "uuid": "2f22eeaf-a736-430c-b68e-749a87271586"}, "scrap_fasta": {"src": "hda", "id": "69896066c3f7be04", "uuid": "c91b7e23-f408-4f74-962c-60bbc1f4759e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pcr.seqs(fasta=fasta.dat,start=0,pdiffs=0,rdiffs=0,processors=1)\n\nUsing 1 processors.\nProcessing sequence: 3\n\nOutput File Names: \nfasta.pcr.dat\n\n\nIt took 0 secs to screen 3 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2191.dat' fasta.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' taxonomy_in.dat && echo 'pcr.seqs( fasta=fasta.dat, start=0, pdiffs=0, rdiffs=0, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:06:41.597226", "params": {"trim": "{\"start\": \"0\", \"end\": \"0\", \"method\": \"position\", \"__current_case__\": 2}", "keepdots": "\"true\"", "pdiffs": "\"0\"", "dbkey": "\"hg17\"", "rdiffs": "\"0\"", "group_in": "null", "taxonomy_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29791", "id": "9a68e8442a2ae0ec", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pcr_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"trim\|method": "reference", "keepdots": false, "pdiffs": "2", "trim\|ecoli": {"src": "hda", "id": "296c8570502f7d16"}, "fasta": {"src": "hda", "id": "296c8570502f7d16"}, "name_in": {"src": "hda", "id": "540d8ccadbb41cf8"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "296c8570502f7d16", "uuid": "9362aefb-8832-4e03-acd5-680564bde786"}, "ecoli": {"src": "hda", "id": "296c8570502f7d16", "uuid": "9362aefb-8832-4e03-acd5-680564bde786"}, "name_in": {"src": "hda", "id": "540d8ccadbb41cf8", "uuid": "e965dcc8-4320-413e-a48d-622e06334dae"}}, "update_time": "2018-02-08T18:07:16.938130", "tool_id": "mothur_pcr_seqs", "outputs": {"name_out": {"src": "hda", "id": "4e45b45a46840de7", "uuid": "ae7a5725-f8c7-4614-b22a-9b40d80745fc"}, "pcr_fasta": {"src": "hda", "id": "9b9da51b3cf3788c", "uuid": "5051221e-11db-45e7-b92a-9fe5b093f5e9"}, "logfile": {"src": "hda", "id": "b595ca7d5e4a4806", "uuid": "92c2c87b-8df3-4ce4-a91e-1ee540f139ba"}, "scrap_fasta": {"src": "hda", "id": "6566db4438049123", "uuid": "59a0a26d-b5b0-4a68-986d-821d65b390af"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pcr.seqs(fasta=fasta.dat,name=name_in.dat,ecoli=trim.ecoli.dat,pdiffs=2 \r,rdiffs=0,keepdots=false,processors=1)\n\nUsing 1 processors.\nProcessing sequence: 3\nRemoved 0 sequences from your name file.\n\nOutput File Names: \nfasta.pcr.dat\nname_in.pcr.dat\n\n\nIt took 0 secs to screen 3 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2196.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2197.dat' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' taxonomy_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2196.dat' trim.ecoli.dat && echo 'pcr.seqs( fasta=fasta.dat, name=name_in.dat, ecoli=trim.ecoli.dat, pdiffs=2, rdiffs=0, keepdots=false, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:07:13.398222", "params": {"trim": "{\"ecoli\": {\"values\": [{\"src\": \"hda\", \"id\": 2196}]}, \"method\": \"reference\", \"__current_case__\": 1}", "keepdots": "\"false\"", "pdiffs": "\"2\"", "dbkey": "\"hg17\"", "rdiffs": "\"0\"", "group_in": "null", "taxonomy_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29923", "id": "7e283a4b4d60f5b4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pcr_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"trim\|method": "oligos", "trim\|oligos": {"src": "hda", "id": "a5b878b864addf4f"}, "group_in": {"src": "hda", "id": "a8982932cfaa9c91"}, "taxonomy_in": {"src": "hda", "id": "9c06f06735014421"}, "fasta": {"src": "hda", "id": "82820d47475784db"}, "name_in": {"src": "hda", "id": "9d35880b3bb3f3cb"}}, "job": {"inputs": {"group_in": {"src": "hda", "id": "a8982932cfaa9c91", "uuid": "66e3ae35-39b3-423e-b941-33461b54a7ad"}, "fasta": {"src": "hda", "id": "82820d47475784db", "uuid": "ceb90772-927b-440c-8052-73805f4ccb50"}, "taxonomy_in": {"src": "hda", "id": "9c06f06735014421", "uuid": "f15d0b71-c377-4c34-8371-bc21d18145a8"}, "name_in": {"src": "hda", "id": "9d35880b3bb3f3cb", "uuid": "564d66d5-2513-4e32-a3ba-dd22ef1f8415"}, "oligos": {"src": "hda", "id": "a5b878b864addf4f", "uuid": "0f5c7aab-d848-4e2a-992d-8983af54dd90"}}, "update_time": "2018-02-08T18:08:02.125280", "tool_id": "mothur_pcr_seqs", "outputs": {"accnos_out": {"src": "hda", "id": "c125545fbb84cf3f", "uuid": "afc10ef8-549d-46d6-9d0c-c126de31a2c5"}, "name_out": {"src": "hda", "id": "464ab120d73bbfdd", "uuid": "698fcaa6-b392-42c7-8fdf-381e07307454"}, "group_out": {"src": "hda", "id": "f8ee9f073d3c51fa", "uuid": "09c46081-7102-442e-8599-95f7369596f4"}, "taxonomy_out": {"src": "hda", "id": "d4da91f5a7beed4d", "uuid": "83fa36a7-fcb7-446d-8775-7224901b3c40"}, "scrap_fasta": {"src": "hda", "id": "daf83ea457bd17e1", "uuid": "209a1adf-26ab-4ca2-be19-af5749eb1cb9"}, "pcr_fasta": {"src": "hda", "id": "a103d4e65eccf231", "uuid": "75fffd97-8e82-4d4a-ae7f-f6e8e184586c"}, "logfile": {"src": "hda", "id": "5480ea63371d722e", "uuid": "62241193-8520-4216-9a1e-8f9969fa2327"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pcr.seqs(fasta=fasta.dat,name=name_in.dat,group=group_in.dat,taxonomy=t \raxonomy_in.dat,oligos=trim.oligos.dat,nomatch=reject,pdiffs=0,rdiffs=0,processor \rs=1)\n\nUsing 1 processors.\nProcessing sequence: 3\nRemoved 3 sequences from your name file.\nRemoved 3 sequences from your group file.\nRemoved 3 sequences from your taxonomy file.\n\nOutput File Names: \nfasta.pcr.dat\nfasta.bad.accnos\nfasta.scrap.pcr.dat\nname_in.pcr.dat\ngroup_in.pcr.dat\ntaxonomy_in.pcr.dat\n\n\nIt took 0 secs to screen 3 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2202.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2205.dat' name_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2206.dat' group_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2204.dat' taxonomy_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2203.dat' trim.oligos.dat && echo 'pcr.seqs( fasta=fasta.dat, name=name_in.dat, group=group_in.dat, taxonomy=taxonomy_in.dat, oligos=trim.oligos.dat, nomatch=reject, pdiffs=0, rdiffs=0, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:07:57.811767", "params": {"trim": "{\"oligos\": {\"values\": [{\"src\": \"hda\", \"id\": 2203}]}, \"keepprimer\": \"false\", \"method\": \"oligos\", \"__current_case__\": 0, \"nomatch\": \"reject\"}", "keepdots": "\"true\"", "dbkey": "\"hg17\"", "rdiffs": "\"0\"", "pdiffs": "\"0\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "30108", "id": "b82be0a67dfc3ead", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pcr_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"grouping\|use": "no", "tree": {"src": "hda", "id": "7b73c9ba1609e7c1"}}, "job": {"inputs": {"tree": {"src": "hda", "id": "7b73c9ba1609e7c1", "uuid": "6d09350d-19d7-4732-add6-9545698ec688"}}, "update_time": "2018-02-08T18:08:47.617108", "tool_id": "mothur_phylo_diversity", "outputs": {"logfile": {"src": "hda", "id": "a957edb6cc1a8c18", "uuid": "de495382-5ca6-4e53-836d-f49489766a65"}, "summary_out": {"src": "hda", "id": "19b2c8d8c6d10b1a", "uuid": "55aaf68f-798e-4b74-9e5b-1bc9f46456b4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > phylo.diversity(tree=tree.dat,iters=1000,freq=100.0,scale=false,collect \r=false,rarefy=false,summary=true,processors=1)\n\nUsing 1 processors.\nIt took 0 secs to run phylo.diversity.\n\nOutput File Names: \ntree.1.phylodiv.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2214.dat' tree.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && echo 'phylo.diversity( tree=tree.dat, iters=1000, freq=100.0, scale=false, collect=false, rarefy=false, summary=true, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:08:44.453569", "params": {"count": "null", "scale": "\"false\"", "name": "null", "iters": "\"1000\"", "rarefy": "\"false\"", "dbkey": "\"hg17\"", "summary": "\"true\"", "collect": "\"false\"", "freq": "\"100.0\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "grouping": "{\"use\": \"no\", \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "30220", "id": "c097cce02f6efe06", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_phylo_diversity.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"grouping\|group": {"src": "hda", "id": "a37203f14505a5c8"}, "tree": {"src": "hda", "id": "687d98d0d3ddbb66"}, "rarefy": true, "grouping\|groups": ["orange", "green"], "collect": true, "grouping\|use": "yes"}, "job": {"inputs": {"group": {"src": "hda", "id": "a37203f14505a5c8", "uuid": "2870715f-70ac-4788-a64c-0dfba78c0ed2"}, "tree": {"src": "hda", "id": "687d98d0d3ddbb66", "uuid": "13a48277-9c45-4c94-a7be-9689972e7ada"}}, "update_time": "2018-02-08T18:09:08.852562", "tool_id": "mothur_phylo_diversity", "outputs": {"rarefaction_out": {"src": "hda", "id": "d57c2a3df64722d8", "uuid": "b82bc970-f0bd-4e15-9227-204614fbc92f"}, "logfile": {"src": "hda", "id": "010d9b650278df16", "uuid": "dc09882d-c97c-4773-9ff0-78bd2e02bcde"}, "summary_out": {"src": "hda", "id": "7c14b8cbe6ecfd6a", "uuid": "0a80c49c-3f99-4742-addd-efafe3433cc5"}, "collectors_out": {"src": "hda", "id": "8609b632c86cf056", "uuid": "8019ed27-81e8-4730-bdf3-ef44cc51c37f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > phylo.diversity(tree=tree.dat,group=grouping.group.dat,iters=1000,freq= \r100.0,scale=false,collect=true,rarefy=true,summary=true,processors=1)\n\nUsing 1 processors.\nIt took 0 secs to run phylo.diversity.\n\nOutput File Names: \ntree.1.phylodiv.summary\ntree.1.phylodiv.rarefaction\ntree.1.phylodiv\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2217.dat' tree.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2218.dat' grouping.group.dat && echo 'phylo.diversity( tree=tree.dat, group=grouping.group.dat, iters=1000, freq=100.0, scale=false, collect=true, rarefy=true, summary=true, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:09:05.222478", "params": {"count": "null", "scale": "\"false\"", "name": "null", "iters": "\"1000\"", "rarefy": "\"true\"", "dbkey": "\"hg17\"", "summary": "\"true\"", "collect": "\"true\"", "freq": "\"100.0\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "grouping": "{\"use\": \"yes\", \"group\": {\"values\": [{\"src\": \"hda\", \"id\": 2218}]}, \"groups\": null, \"__current_case__\": 0}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "30335", "id": "dad37bad3e582a03", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_phylo_diversity.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"taxonomy": {"src": "hda", "id": "d277a827d7315f6a"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "d277a827d7315f6a", "uuid": "64965276-ce26-4135-afc9-702956d01e25"}}, "update_time": "2018-02-08T18:09:39.122665", "tool_id": "mothur_phylotype", "outputs": {"rabund": {"src": "hda", "id": "ae543f1a0583f8de", "uuid": "80a208ce-97f3-4e0f-8213-f2234b6e2b58"}, "logfile": {"src": "hda", "id": "982a3dd88517c4ae", "uuid": "0f6b7512-e7e5-4631-af21-5ca5ab0fa359"}, "otulist": {"src": "hda", "id": "905d0f9f657a61a3", "uuid": "b6e5a5dd-bd2e-4caf-a2e9-58dad1375c99"}, "sabund": {"src": "hda", "id": "a05060b14eba45e1", "uuid": "1ab81d82-d202-475e-bee9-ba9efb8b4683"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > phylotype(taxonomy=taxonomy.dat)\n1\n2\n3\n4\n5\n6\n\nOutput File Names: \ntaxonomy.tx.sabund\ntaxonomy.tx.rabund\ntaxonomy.tx.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2223.dat' taxonomy.dat && ln -s 'None' name.dat && echo 'phylotype( taxonomy=taxonomy.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:09:35.816289", "params": {"cutoff": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name": "null", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "30429", "id": "66041b9fc316678f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_phylotype.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"taxonomy": {"src": "hda", "id": "9b8e3eac2c41c663"}, "cutoff": "5", "label": ["1", "4", "5"]}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "9b8e3eac2c41c663", "uuid": "e85d537c-b3b3-41ee-892f-a5c4380c1157"}}, "update_time": "2018-02-08T18:10:06.761247", "tool_id": "mothur_phylotype", "outputs": {"rabund": {"src": "hda", "id": "9633d2046ccd09af", "uuid": "87a5b313-4033-449a-823e-760b4c678d47"}, "logfile": {"src": "hda", "id": "eea2aea36ad87984", "uuid": "b1729cf2-133b-4726-9a90-dec25423d7af"}, "otulist": {"src": "hda", "id": "d32d60f54a1f25d7", "uuid": "0ad1d6ff-cbf5-4aa5-bb8f-0ef07d6f4155"}, "sabund": {"src": "hda", "id": "da701c510c7a233c", "uuid": "5b1e28a8-09d8-4043-80cc-d7188e013864"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > phylotype(taxonomy=taxonomy.dat,cutoff=5,label=1-4-5)\n1\n4\n5\n\nOutput File Names: \ntaxonomy.tx.sabund\ntaxonomy.tx.rabund\ntaxonomy.tx.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2228.dat' taxonomy.dat && ln -s 'None' name.dat && echo 'phylotype( taxonomy=taxonomy.dat ,cutoff=5 ,label=1-4-5 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:10:03.466586", "params": {"cutoff": "\"5\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name": "null", "dbkey": "\"hg17\"", "label": "[\"1\", \"4\", \"5\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "30522", "id": "f39983d675d72056", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_phylotype.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "12970ab350c1c4c1"}, "name": {"src": "hda", "id": "9954064f1597ebe8"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "12970ab350c1c4c1", "uuid": "eeea6a4b-d253-4b79-b884-25c80efe11d2"}, "name": {"src": "hda", "id": "9954064f1597ebe8", "uuid": "aa55e0a2-e8ce-422e-91ea-9bef6ab0bff7"}}, "update_time": "2018-02-08T18:10:38.444598", "tool_id": "mothur_pre_cluster", "outputs": {"__new_primary_file_fasta\|fasta__": {"src": "hda", "id": "64228473c8483b3a", "uuid": "9e959b52-5138-4af8-aa5f-ce6b5c6fe494"}, "logfile": {"src": "hda", "id": "3eccd2a5f82af3af", "uuid": "820915eb-6709-42dc-a244-e086ff84c973"}, "names_out": {"src": "hda", "id": "dd319f1126fd20f4", "uuid": "336785bd-3ca5-4a7e-9f23-35ac0956eab3"}, "fasta_out": {"src": "hda", "id": "9d62bd31039db014", "uuid": "82dd042c-1999-40cf-86e6-d0e0e1d319a6"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pre.cluster(fasta=fasta.dat,name=name.dat,diffs=1,match=1,mismatch=-1,g \rapopen=-2,gapextend=-1,topdown=true,processors=1)\n\nUsing 1 processors.\n0\t5\t0\n5\t5\t0\nTotal number of sequences before precluster was 5.\npre.cluster removed 0 sequences.\n\nIt took 0 secs to cluster 5 sequences.\n\nOutput File Names: \nfasta.precluster.dat\nfasta.precluster.names\nfasta.precluster.map\n\n\nmothur > quit\n>U68589\nTAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG\n>U68590\nTAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC\n>U68591\nCGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT\n>U68592\nTAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT\n>U68593\nTAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG\n>U68589\nTAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG\n>U68590\nTAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC\n>U68591\nCGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT\n>U68592\nTAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT\n>U68593\nTAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG\nideal_seq_1\t1\nU68589\t1\t0\tTAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG\n\nideal_seq_2\t1\nU68590\t1\t0\tTAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC\n\nideal_seq_3\t1\nU68591\t1\t0\tCGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT\n\nideal_seq_4\t1\nU68592\t1\t0\tTAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT\n\nideal_seq_5\t1\nU68593\t1\t0\tTAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG\n\nU68589\tU68589\nU68590\tU68590\nU68591\tU68591\nU68592\tU68592\nU68593\tU68593\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2233.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2234.dat' name.dat && ln -s 'None' group.dat && echo 'pre.cluster( fasta=fasta.dat, name=name.dat, diffs=1, match=1, mismatch=-1, gapopen=-2, gapextend=-1, topdown=true, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && cat fasta && if [ -f fasta.precluster.map ]; then mv fasta.precluster.map fasta.precluster.fasta.map; fi", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:10:34.343955", "params": {"diffs": "\"1\"", "group": "null", "topdown": "\"true\"", "gapopen": "\"-2\"", "mismatch": "\"-1\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "gapextend": "\"-1\"", "match": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "30644", "id": "acb17c34a39829bc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pre_cluster.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "50a92933398c2e4e"}, "name": {"src": "hda", "id": "4e38a27672f3cb4b"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "50a92933398c2e4e", "uuid": "883de2f2-5301-413e-a278-8d845b20062d"}, "name": {"src": "hda", "id": "4e38a27672f3cb4b", "uuid": "e07df41b-7fa8-46f1-a60e-ce78d88c9225"}}, "update_time": "2018-02-08T18:11:11.834281", "tool_id": "mothur_pre_cluster", "outputs": {"__new_primary_file_fasta\|fasta__": {"src": "hda", "id": "a0dcd297bbc9a51b", "uuid": "482c1fa4-2755-4dab-8e1c-af59d8ea02c1"}, "logfile": {"src": "hda", "id": "3fffea1ce04dc068", "uuid": "b41f03ac-b8c9-49a3-90fc-541837d2c668"}, "count_out": {"src": "hda", "id": "ef0fbc54739e8d83", "uuid": "736eccac-1a6d-4663-8f24-6ec335df2110"}, "fasta_out": {"src": "hda", "id": "99645864eaeb63bc", "uuid": "574e34be-d03e-4896-99a9-10bb098d47c8"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pre.cluster(fasta=fasta.dat,count=name.dat,diffs=1,match=1,mismatch=-1, \rgapopen=-2,gapextend=-1,topdown=true,processors=1)\n\nUsing 1 processors.\n0\t5\t0\n5\t5\t0\nTotal number of sequences before precluster was 5.\npre.cluster removed 0 sequences.\n\nIt took 0 secs to cluster 5 sequences.\n\nOutput File Names: \nfasta.precluster.dat\nfasta.precluster.count_table\nfasta.precluster.map\n\n\nmothur > quit\n>U68589\nTAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG\n>U68590\nTAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC\n>U68591\nCGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT\n>U68592\nTAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT\n>U68593\nTAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG\nRepresentative_Sequence\ttotal\nU68589\t1\nU68590\t1\nU68591\t1\nU68592\t1\nU68593\t1\n>U68589\nTAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG\n>U68590\nTAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC\n>U68591\nCGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT\n>U68592\nTAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT\n>U68593\nTAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG\nideal_seq_1\t1\nU68589\t1\t0\tTAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG\n\nideal_seq_2\t1\nU68590\t1\t0\tTAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC\n\nideal_seq_3\t1\nU68591\t1\t0\tCGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT\n\nideal_seq_4\t1\nU68592\t1\t0\tTAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT\n\nideal_seq_5\t1\nU68593\t1\t0\tTAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG\n\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2239.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2240.dat' name.dat && ln -s 'None' group.dat && echo 'pre.cluster( fasta=fasta.dat, count=name.dat, diffs=1, match=1, mismatch=-1, gapopen=-2, gapextend=-1, topdown=true, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && cat fasta* && if [ -f fasta.precluster.map ]; then mv fasta.precluster.map fasta.precluster.fasta.map; fi", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:11:08.174971", "params": {"diffs": "\"1\"", "group": "null", "topdown": "\"true\"", "gapopen": "\"-2\"", "mismatch": "\"-1\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "gapextend": "\"-1\"", "match": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "30761", "id": "bd5643b7bad6c5ee", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pre_cluster.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otulabel": "Otu1", "fasta": {"src": "hda", "id": "f5f5b5fcc20d3bfb"}, "otu": {"src": "hda", "id": "605677fb26a1d5d5"}, "label": "0.30"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "f5f5b5fcc20d3bfb", "uuid": "0249750c-f281-46b5-843e-160d09ed0d5a"}, "otu": {"src": "hda", "id": "605677fb26a1d5d5", "uuid": "be246a42-2fea-4653-b9cf-d3fb15ca4900"}}, "update_time": "2018-02-08T18:11:45.843827", "tool_id": "mothur_primer_design", "outputs": {"logfile": {"src": "hda", "id": "7e1d0ae02135b35e", "uuid": "838f32be-609c-44d2-afae-f925ffd59147"}, "list_out": {"src": "hda", "id": "01b4d9af49cf5af2", "uuid": "74f50cd4-de52-4c80-bbab-12493bb9139f"}, "summary_out": {"src": "hda", "id": "61fd885aefd5193f", "uuid": "55010ccf-de2c-407a-b483-f17be1f1b8ef"}, "fasta_out": {"src": "hda", "id": "6df628d23dd00405", "uuid": "89ece71b-206a-48ac-81aa-55dfbf5e2f31"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > primer.design(fasta=fasta.dat,list=otu.dat,label=0.30,otulabel=Otu1,pdi \rffs=0,length=18,processors=1)\n\nUsing 1 processors.\n\nFinding consensus sequences for each otu...Done.\n\nIt took 1 secs to process 2 OTUs.\n\nOutput File Names: \notu.0.30.otu.cons.fasta\notu.0.30.primer.summary\notu.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2245.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2246.dat' otu.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && echo 'primer.design( fasta=fasta.dat, list=otu.dat, label=0.30, otulabel=Otu1, pdiffs=0, length=18, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:11:42.160085", "params": {"count": "null", "cutoff": "\"\"", "name": "null", "otulabel": "\"Otu1\"", "mintm": "\"\"", "length": "\"18\"", "dbkey": "\"hg17\"", "label": "\"0.30\"", "pdiffs": "\"0\"", "maxtm": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "30895", "id": "2e05a675c8e4effa", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_primer_design.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "970eee70888a4aa6"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "970eee70888a4aa6", "uuid": "ae7991ee-0c1b-4f75-b3d9-b55a0be692f8"}}, "update_time": "2018-02-08T18:12:16.539106", "tool_id": "mothur_rarefaction_shared", "outputs": {"logfile": {"src": "hda", "id": "49a829891848cb74", "uuid": "9c41a416-c997-4435-806e-17a51309f45e"}, "rarefaction": {"src": "hda", "id": "b5c3e3c24268afba", "uuid": "8d1c764c-846a-4fab-90c5-2e031d0581f9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > rarefaction.shared(shared=otu.dat,calc=sharedobserved,iters=1000)\nunique\t\n0.01\t\n0.02\t\n0.03\t\n0.04\t\n0.05\t\n0.06\t\n0.07\t\n0.08\t\n0.09\t\n0.10\t\n0.11\t\n0.12\t\n0.13\t\n0.14\t\n0.15\t\n0.16\t\n0.17\t\n0.18\t\n0.19\t\n0.20\t\n0.21\t\n0.22\t\n0.23\t\n0.24\t\n0.25\t\n0.26\t\n0.27\t\n0.29\t\n0.32\t\n0.33\t\n0.36\t\n0.38\t\n0.41\t\n0.45\t\n0.55\t\n\nOutput File Names: \notu.shared.rarefaction\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2251.dat' otu.dat && echo 'rarefaction.shared( shared=otu.dat, calc=sharedobserved, iters=1000 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:12:13.076005", "params": {"iters": "\"1000\"", "dbkey": "\"hg17\"", "label": "null", "subsample": "{\"__current_case__\": 1, \"usess\": \"no\"}", "designc": "{\"usedesign\": \"no\", \"__current_case__\": 1}", "groups": "null", "jumble": "\"false\"", "calc": "\"sharedobserved\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31000", "id": "89c39e6bc9d1ed43", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_rarefaction_shared.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"calc": ["sharedobserved", "sharednseqs"], "otu": {"src": "hda", "id": "3895de01123aa786"}, "groups": ["forest", "pasture"], "label": ["0.22", "0.55"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "3895de01123aa786", "uuid": "88a38bca-3103-4bda-81ea-699d70bd90d0"}}, "update_time": "2018-02-08T18:12:32.107121", "tool_id": "mothur_rarefaction_shared", "outputs": {"logfile": {"src": "hda", "id": "8261f0fefe52b3d8", "uuid": "5354b0af-28d8-460c-9093-62d09996e000"}, "rarefaction": {"src": "hda", "id": "2778f88774dcfec9", "uuid": "410e0a28-c294-4bdd-b96c-b61a50529113"}, "rarefaction2": {"src": "hda", "id": "1eaf0a2d8c29e47a", "uuid": "de7d8886-eeff-4af4-a8ed-5b282a2a569e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > rarefaction.shared(shared=otu.dat,label=0.22-0.55,groups=forest-pasture \r,calc=sharedobserved-sharednseqs,iters=1000)\n0.22\t\n0.55\t\n\nOutput File Names: \notu.shared.rarefaction\notu.shared.r_nseqs\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2254.dat' otu.dat && echo 'rarefaction.shared( shared=otu.dat, label=0.22-0.55, groups=forest-pasture, calc=sharedobserved-sharednseqs, iters=1000 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:12:28.634254", "params": {"iters": "\"1000\"", "dbkey": "\"hg17\"", "label": "[\"0.22\", \"0.55\"]", "subsample": "{\"__current_case__\": 1, \"usess\": \"no\"}", "designc": "{\"usedesign\": \"no\", \"__current_case__\": 1}", "groups": "[\"forest\", \"pasture\"]", "jumble": "\"false\"", "calc": "[\"sharedobserved\", \"sharednseqs\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31087", "id": "5f0fd33b40be7b90", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_rarefaction_shared.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"designc\|sets": ["tardis", "dalek"], "designc\|usedesign": "yes", "otu": {"src": "hda", "id": "8d08869cf0678e94"}, "designc\|design": {"src": "hda", "id": "8e702b0abbcab5be"}}, "job": {"inputs": {"design": {"src": "hda", "id": "8e702b0abbcab5be", "uuid": "9cc7a81b-4869-448e-9751-e599dff8e2ac"}, "otu": {"src": "hda", "id": "8d08869cf0678e94", "uuid": "4254f44a-9b85-4acd-9b43-834923a84ca8"}}, "update_time": "2018-02-08T18:12:48.699173", "tool_id": "mothur_rarefaction_shared", "outputs": {"logfile": {"src": "hda", "id": "c2f3aa02e3d98e9a", "uuid": "4484d484-ce5c-4a20-a616-fb7694fbf3ae"}, "group_rarefaction": {"src": "hda", "id": "3c471526d7d3b609", "uuid": "df5365f0-a83d-4c34-898c-86bd2237bfd7"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > rarefaction.shared(shared=otu.dat,design=designc.design.dat,sets=tardis \r-dalek,calc=sharedobserved,iters=1000)\nunique\tdalek\n0.01\tdalek\n0.02\tdalek\n0.03\tdalek\n0.04\tdalek\n0.05\tdalek\n0.06\tdalek\n0.07\tdalek\n0.08\tdalek\n0.09\tdalek\n0.10\tdalek\n0.11\tdalek\n0.12\tdalek\n0.13\tdalek\n0.14\tdalek\n0.15\tdalek\n0.16\tdalek\n0.17\tdalek\n0.18\tdalek\n0.19\tdalek\n0.20\tdalek\n0.21\tdalek\n0.22\tdalek\n0.23\tdalek\n0.24\tdalek\n0.25\tdalek\n0.26\tdalek\n0.27\tdalek\n0.29\tdalek\n0.32\tdalek\n0.33\tdalek\n0.36\tdalek\n0.38\tdalek\n0.41\tdalek\n0.45\tdalek\n0.55\tdalek\nunique\ttardis\n0.01\ttardis\n0.02\ttardis\n0.03\ttardis\n0.04\ttardis\n0.05\ttardis\n0.06\ttardis\n0.07\ttardis\n0.08\ttardis\n0.09\ttardis\n0.10\ttardis\n0.11\ttardis\n0.12\ttardis\n0.13\ttardis\n0.14\ttardis\n0.15\ttardis\n0.16\ttardis\n0.17\ttardis\n0.18\ttardis\n0.19\ttardis\n0.20\ttardis\n0.21\ttardis\n0.22\ttardis\n0.23\ttardis\n0.24\ttardis\n0.25\ttardis\n0.26\ttardis\n0.27\ttardis\n0.29\ttardis\n0.32\ttardis\n0.33\ttardis\n0.36\ttardis\n0.38\ttardis\n0.41\ttardis\n0.45\ttardis\n0.55\ttardis\n\nOutput File Names: \notu.groups.rarefaction\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2258.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2259.dat' designc.design.dat && echo 'rarefaction.shared( shared=otu.dat, design=designc.design.dat, sets=tardis-dalek, calc=sharedobserved, iters=1000 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:12:45.102451", "params": {"iters": "\"1000\"", "dbkey": "\"hg17\"", "label": "null", "subsample": "{\"__current_case__\": 1, \"usess\": \"no\"}", "designc": "{\"usedesign\": \"yes\", \"design\": {\"values\": [{\"src\": \"hda\", \"id\": 2259}]}, \"__current_case__\": 0, \"sets\": [\"tardis\", \"dalek\"]}", "groups": "null", "jumble": "\"false\"", "calc": "\"sharedobserved\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31201", "id": "8cf2c4d96fac8f30", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_rarefaction_shared.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "8a6106ba2478bdbd"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "8a6106ba2478bdbd", "uuid": "0f90ab92-22ce-4056-8a79-dcd71b3eeb92"}}, "update_time": "2018-02-08T18:13:04.886441", "tool_id": "mothur_rarefaction_single", "outputs": {"logfile": {"src": "hda", "id": "b15916a29e3c3d1e", "uuid": "52b8eb55-fb32-4e5d-8207-a3baa4c9d25e"}, "__new_primary_file_sobs\|sobs__": {"src": "hda", "id": "5d9e2e480e0229ed", "uuid": "fd7ca367-f723-483b-a814-f0c35e2270b3"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > rarefaction.single(shared=otu.dat,calc=sobs,abund=10,iters=1000,freq=10 \r0.0,processors=1)\n\nUsing 1 processors.\n\nProcessing group forest\n\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nProcessing group pasture\n\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.groups.rarefaction\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2262.dat' otu.dat && echo 'rarefaction.single( shared=otu.dat, calc=sobs, abund=10, iters=1000, freq=100.0, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv otu\\.rarefaction otu.r_sobs", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:13:00.863804", "params": {"abund": "\"10\"", "iters": "\"1000\"", "dbkey": "\"hg17\"", "label": "null", "freq": "\"100.0\"", "calc": "\"sobs\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31288", "id": "aaec100bcea4a774", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_rarefaction_single.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"calc": ["ace", "bootstrap", "chao", "jack", "sobs", "simpsoneven", "shannoneven", "heip", "smithwilson", "coverage", "simpson", "invsimpson", "shannon", "npshannon", "nseqs"], "otu": {"src": "hda", "id": "d8c76c99cfcf0ce5"}, "label": ["0.03", "0.05", "0.36", "0.55"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "d8c76c99cfcf0ce5", "uuid": "f8adb6cf-945c-4639-90f4-153241a99cb3"}}, "update_time": "2018-02-08T18:13:25.506137", "tool_id": "mothur_rarefaction_single", "outputs": {"__new_primary_file_sobs\|coverage__": {"src": "hda", "id": "3b7ff9e5c7d690b4", "uuid": "8a034c17-5081-444f-9a9e-174ebd07999d"}, "__new_primary_file_sobs\|shannon__": {"src": "hda", "id": "e3b08db904631c4c", "uuid": "6f3a3840-7c8b-49ae-a8dc-b24a34691cdb"}, "__new_primary_file_sobs\|ace__": {"src": "hda", "id": "f45423591c0f7733", "uuid": "85350342-20d0-4e47-94ce-561b936f8e75"}, "__new_primary_file_sobs\|nseqs__": {"src": "hda", "id": "bc738157a4fad361", "uuid": "2c68d624-9dba-4141-8051-641f9405fb5a"}, "__new_primary_file_sobs\|invsimpson__": {"src": "hda", "id": "b0defc02722ab4d6", "uuid": "b39df22c-4d22-4ecc-a4d4-fea145725628"}, "__new_primary_file_sobs\|bootstrap__": {"src": "hda", "id": "8b044c65de596171", "uuid": "f5a42c19-8c80-4ebf-8bc3-a5e7a778393d"}, "__new_primary_file_sobs\|smithwilson__": {"src": "hda", "id": "cbfc85f745f39a3e", "uuid": "33ce0af3-307b-4fa7-8df6-75627e428aa1"}, "__new_primary_file_sobs\|heip__": {"src": "hda", "id": "16ff13d461ecce2e", "uuid": "2732840c-8e2c-4b39-8acb-20145fb3a2a1"}, "__new_primary_file_sobs\|sobs__": {"src": "hda", "id": "901603caef1d8ee8", "uuid": "28bfa969-271e-43ed-b4f9-ec078107ea7d"}, "__new_primary_file_sobs\|shannoneven__": {"src": "hda", "id": "c556bb1d585cd085", "uuid": "bcdf20c5-5987-4889-b27c-d9edd5204e1a"}, "__new_primary_file_sobs\|simpsoneven__": {"src": "hda", "id": "0de71dd17c089dd9", "uuid": "5d8b588c-00e4-4d82-a6fb-83eb5cd9d27b"}, "__new_primary_file_sobs\|chao__": {"src": "hda", "id": "d4a5fd64bf471cbc", "uuid": "bfb3c23f-8324-40a5-8fcc-c6f06ca92700"}, "__new_primary_file_sobs\|jack__": {"src": "hda", "id": "adb88159fa7b3775", "uuid": "cc7c2da1-c45e-4fc5-91ea-9c66cbe6b06e"}, "__new_primary_file_sobs\|npshannon__": {"src": "hda", "id": "47f7483d27dc8522", "uuid": "101cf724-e313-4e6c-bd51-b830e86b8dde"}, "logfile": {"src": "hda", "id": "70d430aeade00c09", "uuid": "cae16ed2-c51a-4ba7-a8b7-822fd4f265c1"}, "__new_primary_file_sobs\|simpson__": {"src": "hda", "id": "2091b9e5d015e899", "uuid": "ff84dee4-e777-4d24-a760-e151adf22e3d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > rarefaction.single(shared=otu.dat,label=0.03-0.05-0.36-0.55,calc=ace-bo \rotstrap-chao-jack-sobs-simpsoneven-shannoneven-heip-smithwilson-coverage-simpson \r-invsimpson-shannon-npshannon-nseqs,abund=10,iters=1000,freq=100.0,processors=1) \r\u001b[A\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[K)\n\nUsing 1 processors.\n\nProcessing group forest\n\n0.03\n0.05\n0.36\n0.55\n\nProcessing group pasture\n\n0.03\n0.05\n0.36\n0.55\n\nOutput File Names: \notu.groups.r_ace\notu.groups.r_bootstrap\notu.groups.r_chao\notu.groups.r_coverage\notu.groups.r_heip\notu.groups.r_invsimpson\notu.groups.r_jack\notu.groups.r_npshannon\notu.groups.r_nseqs\notu.groups.r_shannon\notu.groups.r_shannoneven\notu.groups.r_simpson\notu.groups.r_simpsoneven\notu.groups.r_smithwilson\notu.groups.rarefaction\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2265.dat' otu.dat && echo 'rarefaction.single( shared=otu.dat, label=0.03-0.05-0.36-0.55, calc=ace-bootstrap-chao-jack-sobs-simpsoneven-shannoneven-heip-smithwilson-coverage-simpson-invsimpson-shannon-npshannon-nseqs, abund=10, iters=1000, freq=100.0, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv otu\\.rarefaction otu.r_sobs", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:13:21.254753", "params": {"abund": "\"10\"", "iters": "\"1000\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\", \"0.36\", \"0.55\"]", "freq": "\"100.0\"", "calc": "[\"ace\", \"bootstrap\", \"chao\", \"jack\", \"sobs\", \"simpsoneven\", \"shannoneven\", \"heip\", \"smithwilson\", \"coverage\", \"simpson\", \"invsimpson\", \"shannon\", \"npshannon\", \"nseqs\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31377", "id": "ed97b3e2ab207f95", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_rarefaction_single.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|dist": {"src": "hda", "id": "9377ba4c4b447a14"}, "input\|source": "phylip", "accnos": {"src": "hda", "id": "9963fdf634013460"}}, "job": {"inputs": {"accnos": {"src": "hda", "id": "9963fdf634013460", "uuid": "b928989e-2b62-415c-bff5-74f13a5d7c34"}, "dist": {"src": "hda", "id": "9377ba4c4b447a14", "uuid": "6ecd1791-70d0-43da-8f83-310f7c259672"}}, "update_time": "2018-02-08T18:13:48.134708", "tool_id": "mothur_remove_dists", "outputs": {"logfile": {"src": "hda", "id": "0e8331efcfcf7646", "uuid": "ef7d16e8-1735-4873-871a-3b2fe6866839"}, "pick_dist": {"src": "hda", "id": "8221ac349ab6487f", "uuid": "102ef663-b92e-438f-a2ee-b654258fb954"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.dists(accnos=accnos.dat,phylip=input_dist.dat)\nRemoved 8 groups or sequences from your phylip file.\n\nOutput File names: \ninput_dist.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2283.dat' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2282.dat' input_dist.dat && echo 'remove.dists( accnos=accnos.dat, phylip=input_dist.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:13:45.005251", "params": {"input": "{\"source\": \"phylip\", \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 2282}]}, \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31491", "id": "9fbd2c401152ab55", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_dists.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"groupnames\|groups": "pasture", "groupnames\|shared_in": {"src": "hda", "id": "7cd2d53bde5c0add"}, "groupnames\|source": "shared"}, "job": {"inputs": {"shared_in": {"src": "hda", "id": "7cd2d53bde5c0add", "uuid": "9fc9bf7a-54c3-46a7-98c1-6c34d55e6493"}}, "update_time": "2018-02-08T18:14:07.678472", "tool_id": "mothur_remove_groups", "outputs": {"__new_primary_file_unique\|0.10__": {"src": "hda", "id": "6b7768dc0d7faad7", "uuid": "52eaf5c0-1c63-4c6c-810a-cb578e07f35c"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "f0a5105eaf2bfd75", "uuid": "6326cda0-94d7-4c15-9dfd-4564c1d99e95"}, "__new_primary_file_unique\|0.17__": {"src": "hda", "id": "9189bcfe7a4f9acb", "uuid": "850ecac9-5693-424b-b406-cc0f7ec2dbd1"}, "__new_primary_file_unique\|0.02__": {"src": "hda", "id": "95a9440ff1992c74", "uuid": "c6690a15-1f6d-4594-9281-42266a8f206b"}, "__new_primary_file_unique\|0.21__": {"src": "hda", "id": "bc85128d647d7567", "uuid": "290c9a03-ddb4-436d-b2b5-007a67af45da"}, "__new_primary_file_unique\|0.16__": {"src": "hda", "id": "945066983ff522f4", "uuid": "d13a6213-50bb-4fb7-a41e-1adfe97db47f"}, "__new_primary_file_unique\|0.45__": {"src": "hda", "id": "76b454b70e887011", "uuid": "04ea0f09-ff28-48db-80d1-c2ecbe35cd9d"}, "__new_primary_file_unique\|0.03__": {"src": "hda", "id": "1eb9c4a1b6283f8b", "uuid": "7a142fbc-2114-4cb3-8d6b-8b1662076b6f"}, "__new_primary_file_unique\|0.15__": {"src": "hda", "id": "119e335ad3ed5286", "uuid": "9d58df98-0918-427b-a6ed-16ff74b4c563"}, "__new_primary_file_unique\|0.08__": {"src": "hda", "id": "098d7fe116d7a465", "uuid": "c6aea6dc-234c-4eb4-b5a5-00d80e49e5ea"}, "__new_primary_file_unique\|0.14__": {"src": "hda", "id": "9dc99095cef129ee", "uuid": "4a584369-937c-4a50-bac2-715c486f0cbd"}, "__new_primary_file_unique\|0.13__": {"src": "hda", "id": "222b3bca2d12ce45", "uuid": "e1d76e2c-74b5-46fa-b24d-8ce47e3fed27"}, "__new_primary_file_unique\|0.09__": {"src": "hda", "id": "f35d48acb5b4927b", "uuid": "b459fadf-aec6-426d-9592-e6469bdac959"}, "__new_primary_file_unique\|0.12__": {"src": "hda", "id": "4db0932fb7553ad2", "uuid": "508d6ab7-f650-4b40-865b-7f944c0d7708"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "ad125357e7c3e87b", "uuid": "ce80010f-02b5-4a66-b4c3-5d503159c131"}, "__new_primary_file_unique\|0.11__": {"src": "hda", "id": "cb25081baf7393e6", "uuid": "1b5c8138-1926-4860-a8dc-3faf16fc08c9"}, "__new_primary_file_unique\|0.41__": {"src": "hda", "id": "6f03d3200088c6d4", "uuid": "688d58fe-be06-4732-a939-5c6383d2ff38"}, "__new_primary_file_unique\|0.06__": {"src": "hda", "id": "50d24fe68016bea8", "uuid": "1b876dae-ba70-4e10-99f2-cb0bd6bda909"}, "__new_primary_file_unique\|0.25__": {"src": "hda", "id": "17e5da6fef26fa49", "uuid": "fb0545f6-73e3-4eaa-8f8f-eac7226ac969"}, "__new_primary_file_unique\|0.22__": {"src": "hda", "id": "7e316548162b36ff", "uuid": "8c561f2b-f96b-44cd-81c4-2e5ba77246ff"}, "__new_primary_file_unique\|0.36__": {"src": "hda", "id": "6a9f3b4b5ee84850", "uuid": "9f5a2c4c-b778-474a-b1aa-3a8f5c82de76"}, "__new_primary_file_unique\|0.04__": {"src": "hda", "id": "da24b85de09d096b", "uuid": "13bf9e55-cb11-49e9-8bef-b0ac93f6a05e"}, "__new_primary_file_unique\|0.23__": {"src": "hda", "id": "592e977e25982094", "uuid": "95e8440a-a46e-4c30-b120-6dddf2132d0a"}, "__new_primary_file_unique\|0.33__": {"src": "hda", "id": "c3a2d976a363681a", "uuid": "c1037b1f-37f6-4cd7-853f-495eecdfbfca"}, "logfile": {"src": "hda", "id": "f484cc634deaf2d7", "uuid": "af4651b4-a073-4a02-a828-c9e80e42f9c4"}, "__new_primary_file_unique\|0.20__": {"src": "hda", "id": "fae2800d127612ca", "uuid": "4e3bf2cb-1e57-4555-8a88-a70f3d3fff6c"}, "__new_primary_file_unique\|0.29__": {"src": "hda", "id": "f216775375f843a9", "uuid": "303ab49e-cd2e-4a82-8f79-380437279aed"}, "__new_primary_file_unique\|0.38__": {"src": "hda", "id": "809583a7f7d24a94", "uuid": "d500d714-fbe9-4eb4-8530-d30a30c828e2"}, "__new_primary_file_unique\|0.55__": {"src": "hda", "id": "953bda5fbdb92d27", "uuid": "cc738eb5-12eb-4492-bda6-95eae883806e"}, "__new_primary_file_unique\|0.07__": {"src": "hda", "id": "52627054db660e78", "uuid": "72f56beb-88be-42ae-a8aa-a637feee5026"}, "__new_primary_file_unique\|0.26__": {"src": "hda", "id": "e25f46671ff63694", "uuid": "6338dc42-8971-412c-8476-0a4e1319c4cb"}, "__new_primary_file_unique\|0.32__": {"src": "hda", "id": "d92cab7da43877a2", "uuid": "e5d9fc6a-5d11-471d-99cf-8526c01ae1b0"}, "__new_primary_file_unique\|0.27__": {"src": "hda", "id": "a8c47f290140529a", "uuid": "31b6efd0-20f9-4205-9da4-896acd31f0a3"}, "__new_primary_file_unique\|0.19__": {"src": "hda", "id": "12ab43a2c559fd70", "uuid": "2429c020-1da4-4394-984a-1e7fc01753ab"}, "__new_primary_file_unique\|0.01__": {"src": "hda", "id": "cc13e7b5b3a20008", "uuid": "f0e71ae2-2903-4585-a382-41a731ff0ed7"}, "__new_primary_file_unique\|0.24__": {"src": "hda", "id": "39ce81f662090b83", "uuid": "00450dbd-ee23-4fc9-b219-2e25eebb3ea9"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "64ce508563105809", "uuid": "ad7ab1f7-8c29-4ff8-bd3c-d4943f4549e4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.groups(shared=groupnames_shared_in.dat,groups=pasture)\nRemoved groups: pasture from your shared file.\n\nOutput File names: \ngroupnames_shared_in.unique.pick.dat\ngroupnames_shared_in.0.01.pick.dat\ngroupnames_shared_in.0.02.pick.dat\ngroupnames_shared_in.0.03.pick.dat\ngroupnames_shared_in.0.04.pick.dat\ngroupnames_shared_in.0.05.pick.dat\ngroupnames_shared_in.0.06.pick.dat\ngroupnames_shared_in.0.07.pick.dat\ngroupnames_shared_in.0.08.pick.dat\ngroupnames_shared_in.0.09.pick.dat\ngroupnames_shared_in.0.10.pick.dat\ngroupnames_shared_in.0.11.pick.dat\ngroupnames_shared_in.0.12.pick.dat\ngroupnames_shared_in.0.13.pick.dat\ngroupnames_shared_in.0.14.pick.dat\ngroupnames_shared_in.0.15.pick.dat\ngroupnames_shared_in.0.16.pick.dat\ngroupnames_shared_in.0.17.pick.dat\ngroupnames_shared_in.0.18.pick.dat\ngroupnames_shared_in.0.19.pick.dat\ngroupnames_shared_in.0.20.pick.dat\ngroupnames_shared_in.0.21.pick.dat\ngroupnames_shared_in.0.22.pick.dat\ngroupnames_shared_in.0.23.pick.dat\ngroupnames_shared_in.0.24.pick.dat\ngroupnames_shared_in.0.25.pick.dat\ngroupnames_shared_in.0.26.pick.dat\ngroupnames_shared_in.0.27.pick.dat\ngroupnames_shared_in.0.29.pick.dat\ngroupnames_shared_in.0.32.pick.dat\ngroupnames_shared_in.0.33.pick.dat\ngroupnames_shared_in.0.36.pick.dat\ngroupnames_shared_in.0.38.pick.dat\ngroupnames_shared_in.0.41.pick.dat\ngroupnames_shared_in.0.45.pick.dat\ngroupnames_shared_in.0.55.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2286.dat' groupnames_shared_in.dat && echo 'remove.groups( shared=groupnames_shared_in.dat ,groups=pasture )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:14:02.554551", "params": {"groupnames": "{\"source\": \"shared\", \"shared_in\": {\"values\": [{\"src\": \"hda\", \"id\": 2286}]}, \"groups\": \"pasture\", \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31584", "id": "11f90d7d2e7018d3", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_groups.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"groupnames\|fasta_in": {"src": "hda", "id": "834c7bc81907531a"}, "groupnames\|group_in": {"src": "hda", "id": "1ae0e921e8a5c2cf"}, "groupnames\|list_in": {"src": "hda", "id": "2dddc34ce42fd89f"}, "groupnames\|name_in": {"src": "hda", "id": "511d67f899681d88"}, "groupnames\|source": "other", "groupnames\|taxonomy_in": {"src": "hda", "id": "a0efceb0cae627df"}, "groupnames\|groups": "pasture"}, "job": {"inputs": {"group_in": {"src": "hda", "id": "1ae0e921e8a5c2cf", "uuid": "5f2e2590-4c79-43f0-af0d-25436dd84f90"}, "taxonomy_in": {"src": "hda", "id": "a0efceb0cae627df", "uuid": "f179b10b-16a7-477b-9295-fedc1fc19a3f"}, "fasta_in": {"src": "hda", "id": "834c7bc81907531a", "uuid": "f554b893-67c6-4207-93ab-bf2fac70ed15"}, "list_in": {"src": "hda", "id": "2dddc34ce42fd89f", "uuid": "4f3dd394-cf1f-438a-b333-4d7e02f5ba59"}, "name_in": {"src": "hda", "id": "511d67f899681d88", "uuid": "3b977018-74eb-4b17-aa0e-3b8200e38105"}}, "update_time": "2018-02-08T18:14:44.254800", "tool_id": "mothur_remove_groups", "outputs": {"__new_primary_file_unique\|0.10__": {"src": "hda", "id": "538d841fdb1747d9", "uuid": "7f614d2c-59f1-4934-951a-e7b3ac38e607"}, "fasta_out": {"src": "hda", "id": "379ef8aadc41efc2", "uuid": "bc8b8938-fbd1-45c2-8106-20e561e90f55"}, "__new_primary_file_unique\|0.17__": {"src": "hda", "id": "fd811d57601c2a53", "uuid": "94cc848c-3ced-47cd-b630-9d388be1b6d3"}, "name_out": {"src": "hda", "id": "a57ffcdbbf6f1e3c", "uuid": "751e63d8-425f-457a-96c7-8d7e2cc79bea"}, "__new_primary_file_unique\|0.02__": {"src": "hda", "id": "7b968d941cfc816e", "uuid": "abaccccb-c543-4076-bbb1-4d9b11dad510"}, "__new_primary_file_unique\|0.21__": {"src": "hda", "id": "a279471fedaa0571", "uuid": "5f667714-7be9-49db-bc3c-ab67b2d8f34b"}, "__new_primary_file_unique\|0.16__": {"src": "hda", "id": "6f48ba503e841429", "uuid": "a1199478-3710-4fca-a69d-8bb672b49a3c"}, "__new_primary_file_unique\|0.45__": {"src": "hda", "id": "017619ce8af22a72", "uuid": "d2f879bd-0e5f-411c-9b15-e053903ef6ba"}, "__new_primary_file_unique\|0.25__": {"src": "hda", "id": "82ef8e67e7fbf772", "uuid": "e5bd2cfe-e419-4a76-9d98-e6d2dec5ceeb"}, "__new_primary_file_unique\|0.15__": {"src": "hda", "id": "b07a8d87cf378c5c", "uuid": "3b3f28f8-7b16-4752-ab56-5fb231bc75bc"}, "__new_primary_file_unique\|0.08__": {"src": "hda", "id": "ed7a9161dcea674f", "uuid": "04e9cb1e-1d2e-4e4e-99b1-f33d69abb52c"}, "__new_primary_file_unique\|0.14__": {"src": "hda", "id": "77dc19e4d38b61eb", "uuid": "d32b36ea-3488-4378-86ca-903a97d8c342"}, "__new_primary_file_unique\|0.13__": {"src": "hda", "id": "329c49f5b129c529", "uuid": "18877da9-fb37-4d29-8327-783e65d4d3de"}, "__new_primary_file_unique\|0.09__": {"src": "hda", "id": "e152883985a9587a", "uuid": "ca435832-ec37-45bb-b334-12c1a60e9d56"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "d953aaed8dbb68b6", "uuid": "4b9236a6-d383-46ff-93d2-a13205f630c6"}, "__new_primary_file_unique\|0.12__": {"src": "hda", "id": "2901353778bc9bab", "uuid": "1929f6b3-459f-4ff3-aeba-09eac2503eb0"}, "__new_primary_file_unique\|0.19__": {"src": "hda", "id": "c2b20c6dcfa71d17", "uuid": "da641b6f-a6a5-4b4a-9df9-efe6bd1eeb43"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "22914d39b2b730a1", "uuid": "70abbaed-7677-4355-9afa-233bc72baff7"}, "__new_primary_file_unique\|0.11__": {"src": "hda", "id": "fe166579c3479639", "uuid": "73748fc9-5352-4ec9-8bce-2a4e9cbf49d7"}, "__new_primary_file_unique\|0.41__": {"src": "hda", "id": "919fc57758c35349", "uuid": "524cfd5b-5f80-44d2-8be5-5a1b2c1880db"}, "__new_primary_file_unique\|0.06__": {"src": "hda", "id": "47d62a7ea7c59a47", "uuid": "7929d82e-e335-4c1a-8f1c-bdc0a0a23663"}, "__new_primary_file_unique\|0.03__": {"src": "hda", "id": "d17e43f40c7b280e", "uuid": "f39b4998-1885-4a4c-afb2-ad9298c89c28"}, "__new_primary_file_unique\|0.04__": {"src": "hda", "id": "5ab0e040a82c9257", "uuid": "27a0e294-4ef3-45fe-addd-d866f364c10a"}, "__new_primary_file_unique\|0.36__": {"src": "hda", "id": "e7a119cd3c5740ed", "uuid": "886c83f7-6f69-4f10-bbce-8fa934177fb4"}, "__new_primary_file_unique\|0.22__": {"src": "hda", "id": "587a4a63fe83b80d", "uuid": "aec15976-5eec-40b3-b4fd-e8edb832801c"}, "__new_primary_file_unique\|0.23__": {"src": "hda", "id": "9e190863641df143", "uuid": "e7d3492c-0143-46ae-a44b-7c0e49ab3524"}, "__new_primary_file_unique\|0.33__": {"src": "hda", "id": "ff3f7fa6cf2588ee", "uuid": "b5f79860-46c3-4b66-a3cf-6e6c8398339f"}, "logfile": {"src": "hda", "id": "295945eae8ee0845", "uuid": "2e1d3528-177d-4161-940d-bbf57f0ffc3c"}, "__new_primary_file_unique\|0.20__": {"src": "hda", "id": "91547bc6b52d15e0", "uuid": "81da8bf2-74a2-4d6f-92d5-5bb64e320e9e"}, "__new_primary_file_unique\|0.29__": {"src": "hda", "id": "2b2e28ff432ff04c", "uuid": "53bea491-e5a0-4808-895f-74df32c455f1"}, "__new_primary_file_unique\|0.38__": {"src": "hda", "id": "2783f52461a8e0f8", "uuid": "4f01b970-6761-478c-8f83-76482de991d0"}, "__new_primary_file_unique\|0.55__": {"src": "hda", "id": "25a6596e48ff11f8", "uuid": "9ca8c213-cedc-4d59-91a9-e8135c64adad"}, "group_out": {"src": "hda", "id": "44f8738bed3b883e", "uuid": "f7ebf868-97b1-475a-a1f7-14cc02aa2f0b"}, "__new_primary_file_unique\|0.07__": {"src": "hda", "id": "c2205b1bae1af899", "uuid": "4292a3b8-6edc-47b6-92d9-97eb03bd0c44"}, "__new_primary_file_unique\|0.26__": {"src": "hda", "id": "704100c2f064b409", "uuid": "1df841f9-0466-435b-96b0-9e7122a8c05f"}, "__new_primary_file_unique\|0.32__": {"src": "hda", "id": "052e581adee82db7", "uuid": "e6f5cd12-1eb1-44fb-b452-76fe29d57671"}, "__new_primary_file_unique\|0.27__": {"src": "hda", "id": "be2f9646583e3df7", "uuid": "e4692991-1e4f-4595-a46e-14c689b6ff47"}, "taxonomy_out": {"src": "hda", "id": "9baff05b3688be9e", "uuid": "ecc211a5-1969-4669-a4d2-6534670051c1"}, "__new_primary_file_unique\|0.01__": {"src": "hda", "id": "890f24b7838786dd", "uuid": "c84f631a-8807-474b-8723-5609c8d5b552"}, "__new_primary_file_unique\|0.24__": {"src": "hda", "id": "decd1f544b8f4602", "uuid": "6d116afa-e9ac-48f9-9835-4ee3691cf677"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "99bfead4bdf5ed3d", "uuid": "a00cdfde-cec4-45b5-9e69-c9ee754ff2a5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.groups(group=groupnames_group_in.dat,fasta=groupnames_fasta_in.d \rat,name=groupnames_name_in.dat,list=groupnames_list_in.dat,taxonomy=groupnames_t \raxonomy_in.dat,groups=pasture)\nRemoved 49 sequences from your name file.\nRemoved 49 sequences from your fasta file.\nRemoved 49 sequences from your group file.\nRemoved 49 sequences from your list file.\nRemoved 49 sequences from your taxonomy file.\n\nOutput File names: \ngroupnames_name_in.pick.dat\ngroupnames_fasta_in.pick.dat\ngroupnames_group_in.pick.dat\ngroupnames_list_in.unique.pick.dat\ngroupnames_list_in.0.01.pick.dat\ngroupnames_list_in.0.02.pick.dat\ngroupnames_list_in.0.03.pick.dat\ngroupnames_list_in.0.04.pick.dat\ngroupnames_list_in.0.05.pick.dat\ngroupnames_list_in.0.06.pick.dat\ngroupnames_list_in.0.07.pick.dat\ngroupnames_list_in.0.08.pick.dat\ngroupnames_list_in.0.09.pick.dat\ngroupnames_list_in.0.10.pick.dat\ngroupnames_list_in.0.11.pick.dat\ngroupnames_list_in.0.12.pick.dat\ngroupnames_list_in.0.13.pick.dat\ngroupnames_list_in.0.14.pick.dat\ngroupnames_list_in.0.15.pick.dat\ngroupnames_list_in.0.16.pick.dat\ngroupnames_list_in.0.17.pick.dat\ngroupnames_list_in.0.18.pick.dat\ngroupnames_list_in.0.19.pick.dat\ngroupnames_list_in.0.20.pick.dat\ngroupnames_list_in.0.21.pick.dat\ngroupnames_list_in.0.22.pick.dat\ngroupnames_list_in.0.23.pick.dat\ngroupnames_list_in.0.24.pick.dat\ngroupnames_list_in.0.25.pick.dat\ngroupnames_list_in.0.26.pick.dat\ngroupnames_list_in.0.27.pick.dat\ngroupnames_list_in.0.29.pick.dat\ngroupnames_list_in.0.32.pick.dat\ngroupnames_list_in.0.33.pick.dat\ngroupnames_list_in.0.36.pick.dat\ngroupnames_list_in.0.38.pick.dat\ngroupnames_list_in.0.41.pick.dat\ngroupnames_list_in.0.45.pick.dat\ngroupnames_list_in.0.55.pick.dat\ngroupnames_taxonomy_in.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2324.dat' groupnames_group_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2325.dat' groupnames_fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2326.dat' groupnames_name_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2327.dat' groupnames_list_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2328.dat' groupnames_taxonomy_in.dat && echo 'remove.groups( group=groupnames_group_in.dat ,fasta=groupnames_fasta_in.dat ,name=groupnames_name_in.dat ,list=groupnames_list_in.dat ,taxonomy=groupnames_taxonomy_in.dat ,groups=pasture )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:14:37.618375", "params": {"groupnames": "{\"__current_case__\": 0, \"group_in\": {\"values\": [{\"src\": \"hda\", \"id\": 2324}]}, \"fasta_in\": {\"values\": [{\"src\": \"hda\", \"id\": 2325}]}, \"source\": \"other\", \"taxonomy_in\": {\"values\": [{\"src\": \"hda\", \"id\": 2328}]}, \"groups\": \"pasture\", \"list_in\": {\"values\": [{\"src\": \"hda\", \"id\": 2327}]}, \"name_in\": {\"values\": [{\"src\": \"hda\", \"id\": 2326}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31756", "id": "6dd0e474af427e2d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_groups.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"count": {"src": "hda", "id": "b4b60426d425f16d"}, "file\|taxonomy": {"src": "hda", "id": "37986503f50eefa5"}, "file\|filetype": "usetaxonomy", "taxon": "Bacteria;Firmicutes;"}, "job": {"inputs": {"count": {"src": "hda", "id": "b4b60426d425f16d", "uuid": "d3102d63-f063-4f49-9358-a9204932afa5"}, "taxonomy": {"src": "hda", "id": "37986503f50eefa5", "uuid": "d3943489-f9bc-4e8f-b7fa-47058d56089a"}}, "update_time": "2018-02-08T18:15:26.271587", "tool_id": "mothur_remove_lineage", "outputs": {"logfile": {"src": "hda", "id": "f1a6b922e4c3946b", "uuid": "614bb54e-30c0-4890-aec7-0081dbee7bdf"}, "taxonomy_out": {"src": "hda", "id": "4b38cb8245b4e765", "uuid": "a9ddb677-1dab-4ebf-9e68-e8ea6af15451"}, "count_out": {"src": "hda", "id": "0160af6439ac70dc", "uuid": "14df1388-869a-42d5-a461-262f0dca79ac"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.lineage(taxonomy=file.taxonomy.dat,taxon='Bacteria;Firmicutes;', \rcount=count.dat)\n\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n\nOutput File Names: \nfile.taxonomy.pick.dat\ncount.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2370.dat' file.taxonomy.dat && ln -s 'None' fasta_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' name_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2371.dat' count.dat && echo 'remove.lineage( taxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Firmicutes;'\"' ,count=count.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:15:23.028671", "params": {"dups": "\"true\"", "fasta_in": "null", "taxon": "\"Bacteria;Firmicutes;\"", "dbkey": "\"hg17\"", "group_in": "null", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 2370}]}, \"filetype\": \"usetaxonomy\", \"taxons\": null, \"__current_case__\": 0}", "alignreport_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31874", "id": "0988466323c56cdf", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_lineage.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta_in": {"src": "hda", "id": "94ffe1907bbe589a"}, "taxon": "Bacteria;Firmicutes;,Bacteria;Actinobacteria;", "list_in": {"src": "hda", "id": "a9cef69b5a19731f"}, "group_in": {"src": "hda", "id": "ca154bf63cdc8557"}, "file\|taxonomy": {"src": "hda", "id": "7b13643ca1c390d8"}, "alignreport_in": {"src": "hda", "id": "e3e164d6ab182280"}, "file\|filetype": "usetaxonomy", "name_in": {"src": "hda", "id": "4cc77546f573b2d0"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "7b13643ca1c390d8", "uuid": "a450e3b8-6804-43fe-823a-9cb57a712356"}, "fasta_in": {"src": "hda", "id": "94ffe1907bbe589a", "uuid": "fe69accc-1298-42f3-bfe2-28a855239d6f"}, "group_in": {"src": "hda", "id": "ca154bf63cdc8557", "uuid": "dbc42af8-2faa-4e02-bb57-5a7217ecb809"}, "alignreport_in": {"src": "hda", "id": "e3e164d6ab182280", "uuid": "d78e1f6e-58b5-425c-9670-14708fcb21e3"}, "list_in": {"src": "hda", "id": "a9cef69b5a19731f", "uuid": "92e9416c-6784-438f-b095-94328935f7ea"}, "name_in": {"src": "hda", "id": "4cc77546f573b2d0", "uuid": "96af4f9b-9c52-4b47-a5e3-3cde1fbb8fd7"}}, "update_time": "2018-02-08T18:15:53.229707", "tool_id": "mothur_remove_lineage", "outputs": {"__new_primary_file_unique\|0.10__": {"src": "hda", "id": "35df3e45f29e684d", "uuid": "b57fd9af-0c5a-49d5-81a2-d949025c7d33"}, "fasta_out": {"src": "hda", "id": "154b33b739461382", "uuid": "f99759ef-0ea0-4bc2-b49b-6b3d962f7ad7"}, "__new_primary_file_unique\|0.17__": {"src": "hda", "id": "39ac9d7d68a18ba7", "uuid": "060bf7ce-0b28-42c1-9f72-d46a07a677a3"}, "name_out": {"src": "hda", "id": "966910197fb6271c", "uuid": "3a77e387-fe91-4e61-a86b-067989473500"}, "__new_primary_file_unique\|0.02__": {"src": "hda", "id": "1fe329e39785826e", "uuid": "34ed1f23-984d-4ebe-b793-8ff8f4b4078b"}, "__new_primary_file_unique\|0.21__": {"src": "hda", "id": "7ba9e4d18c68940c", "uuid": "dfb2a6e1-e8a9-40b2-b831-1de06f934a1a"}, "__new_primary_file_unique\|0.16__": {"src": "hda", "id": "7b6cf8e7ca9d489b", "uuid": "aeb38b27-2272-4bd6-bc16-88f8b16e8a70"}, "__new_primary_file_unique\|0.45__": {"src": "hda", "id": "ebb161f2aaac9134", "uuid": "e38efc93-7800-498b-b7e3-daff6a00ad43"}, "__new_primary_file_unique\|0.25__": {"src": "hda", "id": "892ed2ca0d452bf1", "uuid": "76067942-5b7d-4cdf-b3f3-cc476a170d56"}, "__new_primary_file_unique\|0.15__": {"src": "hda", "id": "32d3c44266e502db", "uuid": "1d7490a3-4f7c-425c-b1dc-598b22db89d0"}, "__new_primary_file_unique\|0.08__": {"src": "hda", "id": "e7f38b62472c64c3", "uuid": "4e8c6090-0995-43f9-abe3-5533dd48c1c6"}, "__new_primary_file_unique\|0.14__": {"src": "hda", "id": "54362bd1402420de", "uuid": "18d2356b-d07a-4cae-ba0d-4a99c5999d54"}, "__new_primary_file_unique\|0.13__": {"src": "hda", "id": "dd9637d99eee3c9a", "uuid": "bf35fdfc-f9c8-4abe-b5d1-a5404ba227cc"}, "__new_primary_file_unique\|0.09__": {"src": "hda", "id": "2b2a8e7a960a22fa", "uuid": "381b3d66-aad2-4fe1-aba6-848f29164cbd"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "9a4998a57b4c0d76", "uuid": "83125373-a266-410f-9eb1-aed2d893afcc"}, "__new_primary_file_unique\|0.12__": {"src": "hda", "id": "805aa78c406b7f16", "uuid": "63e6ba39-b3bb-42d5-a22c-7441eae9c452"}, "alignreport_out": {"src": "hda", "id": "8b80c2f064b944ad", "uuid": "f543a295-d0c4-4100-8a54-5167862c3d7f"}, "__new_primary_file_unique\|0.19__": {"src": "hda", "id": "681ee48f048bfa32", "uuid": "64896760-acab-4742-ae43-ae02551402b0"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "5f7b03e27cadea29", "uuid": "9cc904d5-e08c-42d4-81bd-af5283278209"}, "__new_primary_file_unique\|0.11__": {"src": "hda", "id": "67254bb77b4cd837", "uuid": "47a70053-ca58-4d60-a0d1-7ce682cb2e03"}, "__new_primary_file_unique\|0.41__": {"src": "hda", "id": "c00f338d3be3421b", "uuid": "62c8c379-dcde-493c-bc3c-627e6469a663"}, "__new_primary_file_unique\|0.06__": {"src": "hda", "id": "4e2a688e84ed09ba", "uuid": "aa045ae7-fa22-4063-9da8-3e0b2b849fe8"}, "__new_primary_file_unique\|0.03__": {"src": "hda", "id": "e8e6125857b80021", "uuid": "4dc4da63-a755-4292-85bc-d9c7d538a032"}, "__new_primary_file_unique\|0.04__": {"src": "hda", "id": "edc838c8e1dee637", "uuid": "6d3bc26f-2de4-479d-b5db-5523f5ed1937"}, "__new_primary_file_unique\|0.36__": {"src": "hda", "id": "077990f262b60a5e", "uuid": "92ea14ba-6c77-4a9c-90d9-0cde541beeef"}, "__new_primary_file_unique\|0.22__": {"src": "hda", "id": "3151b1fe3738d9ad", "uuid": "e34e5a1a-5a77-48f2-9607-38ceaed666f3"}, "__new_primary_file_unique\|0.23__": {"src": "hda", "id": "cd0552060d28d57c", "uuid": "3cb838e3-dff0-44c6-842d-2859ecfb8326"}, "__new_primary_file_unique\|0.33__": {"src": "hda", "id": "9199779695f12b0d", "uuid": "bbd54f24-af02-462a-89a9-380299425388"}, "logfile": {"src": "hda", "id": "044d4dd6116ec211", "uuid": "ca36d78c-50a7-4745-b419-dac4ee3cb648"}, "__new_primary_file_unique\|0.20__": {"src": "hda", "id": "8a3d90f0472ffba1", "uuid": "90a0f0da-db5e-4d53-a9f0-5f1ee8b7111a"}, "__new_primary_file_unique\|0.29__": {"src": "hda", "id": "328d2c0dfb26d583", "uuid": "a16b25ca-5454-4a53-bfdd-12d4fe134a16"}, "__new_primary_file_unique\|0.38__": {"src": "hda", "id": "ea46dea1984f7f15", "uuid": "dd3b45ae-817f-4044-8d1d-aa76c21c24bd"}, "__new_primary_file_unique\|0.55__": {"src": "hda", "id": "85823b54d11c9421", "uuid": "832e1bc0-6570-4cde-a8ad-113d43ccccd1"}, "group_out": {"src": "hda", "id": "68a1cd10847ef2c7", "uuid": "dde1184e-4e0d-4082-879d-a1052559ad20"}, "__new_primary_file_unique\|0.07__": {"src": "hda", "id": "e2c9e714bcfe5f0a", "uuid": "4bd958da-db4b-4ada-9df6-819d8789a400"}, "__new_primary_file_unique\|0.26__": {"src": "hda", "id": "0f9e12470eed7630", "uuid": "13073578-c0ce-489f-9b51-d681adf6ebfb"}, "__new_primary_file_unique\|0.32__": {"src": "hda", "id": "3070aa5bf5842a22", "uuid": "7843242e-b223-419f-88a1-78a98232840e"}, "__new_primary_file_unique\|0.27__": {"src": "hda", "id": "1f2d20dc0bea074f", "uuid": "d330650b-bd3e-42d0-ab00-744aa59e3ea3"}, "taxonomy_out": {"src": "hda", "id": "f515de207b3cbff0", "uuid": "3ed1f17c-9b2e-466d-8d52-761b4c550138"}, "__new_primary_file_unique\|0.01__": {"src": "hda", "id": "77b0f6eda081c1d2", "uuid": "35f92abe-1f92-4ded-a945-494da0e27cab"}, "__new_primary_file_unique\|0.24__": {"src": "hda", "id": "ef503f389d24c62c", "uuid": "385b5438-9c5f-4d4e-bfb3-7c89bc0da895"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "4a0f32fd437d1f2f", "uuid": "597c450c-319f-4fb0-a221-f8bc15ed16b1"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.lineage(taxonomy=file.taxonomy.dat,taxon='Bacteria;Firmicutes;-B \racteria;Actinobacteria;',fasta=fasta_in.dat,group=group_in.dat,alignreport=align \rreport_in.dat,list=list_in.dat,name=name_in.dat,dups=true)\nYou did not provide a label, I will use the first label in your inputfile.\n\nOutput File Names: \nfile.taxonomy.pick.dat\nname_in.pick.dat\nfasta_in.pick.dat\ngroup_in.pick.dat\nalignreport_in.pick.align.report\nlist_in.unique.pick.dat\nlist_in.0.01.pick.dat\nlist_in.0.02.pick.dat\nlist_in.0.03.pick.dat\nlist_in.0.04.pick.dat\nlist_in.0.05.pick.dat\nlist_in.0.06.pick.dat\nlist_in.0.07.pick.dat\nlist_in.0.08.pick.dat\nlist_in.0.09.pick.dat\nlist_in.0.10.pick.dat\nlist_in.0.11.pick.dat\nlist_in.0.12.pick.dat\nlist_in.0.13.pick.dat\nlist_in.0.14.pick.dat\nlist_in.0.15.pick.dat\nlist_in.0.16.pick.dat\nlist_in.0.17.pick.dat\nlist_in.0.18.pick.dat\nlist_in.0.19.pick.dat\nlist_in.0.20.pick.dat\nlist_in.0.21.pick.dat\nlist_in.0.22.pick.dat\nlist_in.0.23.pick.dat\nlist_in.0.24.pick.dat\nlist_in.0.25.pick.dat\nlist_in.0.26.pick.dat\nlist_in.0.27.pick.dat\nlist_in.0.29.pick.dat\nlist_in.0.32.pick.dat\nlist_in.0.33.pick.dat\nlist_in.0.36.pick.dat\nlist_in.0.38.pick.dat\nlist_in.0.41.pick.dat\nlist_in.0.45.pick.dat\nlist_in.0.55.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2375.dat' file.taxonomy.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2376.dat' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2377.dat' group_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2378.dat' alignreport_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2379.dat' list_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2380.dat' name_in.dat && ln -s 'None' count.dat && echo 'remove.lineage( taxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Firmicutes;-Bacteria;Actinobacteria;'\"' ,fasta=fasta_in.dat ,group=group_in.dat ,alignreport=alignreport_in.dat ,list=list_in.dat ,name=name_in.dat ,dups=true )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:15:46.002408", "params": {"count": "null", "dups": "\"true\"", "taxon": "\"Bacteria;Firmicutes;,Bacteria;Actinobacteria;\"", "dbkey": "\"hg17\"", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 2375}]}, \"filetype\": \"usetaxonomy\", \"taxons\": null, \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "32079", "id": "028963dd9277afc4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_lineage.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"file\|taxonomy": {"src": "hda", "id": "ed2d3bd032d02491"}, "file\|taxons": ["Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Dorea(99);", "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(47);"], "file\|filetype": "usetaxonomy"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "ed2d3bd032d02491", "uuid": "d644aec4-7267-44fd-b5df-fb5e984e6a7b"}}, "update_time": "2018-02-08T18:16:32.338513", "tool_id": "mothur_remove_lineage", "outputs": {"logfile": {"src": "hda", "id": "9e8cf296dbef59b9", "uuid": "0de51807-6b53-4167-bffb-0e6be06a2fbe"}, "taxonomy_out": {"src": "hda", "id": "747c6fc35e775aa4", "uuid": "479efb57-7437-4758-995d-c2fce07b43e5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.lineage(taxonomy=file.taxonomy.dat,taxon='Bacteria;Firmicutes;Cl \rostridia;Clostridiales;Lachnospiraceae;Dorea;-Bacteria;Firmicutes;Clostridia;Clo \rstridiales;Lachnospiraceae;Roseburia;')\n\nOutput File Names: \nfile.taxonomy.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2423.dat' file.taxonomy.dat && ln -s 'None' fasta_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat && echo 'remove.lineage( taxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Dorea;-Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Roseburia;'\"' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:16:29.164896", "params": {"count": "null", "dups": "\"true\"", "fasta_in": "null", "taxon": "\"\"", "dbkey": "\"hg17\"", "group_in": "null", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 2423}]}, \"filetype\": \"usetaxonomy\", \"taxons\": [\"Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Dorea(99);\", \"Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(47);\"], \"__current_case__\": 0}", "alignreport_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "32183", "id": "f941dab79996470b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_lineage.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"file\|taxonomy": {"src": "hda", "id": "b1deaf4adb6e2b62"}, "file\|filetype": "useconstaxonomy", "taxon": "Bacteria;Bacteroidetes;"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "b1deaf4adb6e2b62", "uuid": "cad89d39-f18f-47c7-ae46-976e6995b23b"}}, "update_time": "2018-02-08T18:16:39.822280", "tool_id": "mothur_remove_lineage", "outputs": {"logfile": {"src": "hda", "id": "990b9da175c7f56f", "uuid": "13e9c57b-ff63-4da7-8cdb-a84d5c2374f1"}, "taxonomy_out": {"src": "hda", "id": "b879287775e7651a", "uuid": "510e5454-dc71-430a-a471-c8d98b2623ee"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.lineage(constaxonomy=file.taxonomy.dat,taxon='Bacteria;Bacteroid \retes;')\n\nOutput File Names: \nfile.taxonomy.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2426.dat' file.taxonomy.dat && ln -s 'None' file.shared.dat && ln -s 'None' file.list.dat && ln -s 'None' fasta_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat && echo 'remove.lineage( constaxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Bacteroidetes;'\"' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:16:36.478165", "params": {"count": "null", "dups": "\"true\"", "fasta_in": "null", "taxon": "\"Bacteria;Bacteroidetes;\"", "dbkey": "\"hg17\"", "group_in": "null", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 2426}]}, \"filetype\": \"useconstaxonomy\", \"list\": null, \"taxons\": null, \"__current_case__\": 1, \"shared\": null}", "alignreport_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "32280", "id": "3b489b444bd4d351", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_lineage.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"file\|taxonomy": {"src": "hda", "id": "f493e0cacca6ba40"}, "file\|taxons": ["Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;", "Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;"], "file\|filetype": "useconstaxonomy"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "f493e0cacca6ba40", "uuid": "0c8ec11a-5b60-494d-a66c-7e9e51c46569"}}, "update_time": "2018-02-08T18:16:46.831147", "tool_id": "mothur_remove_lineage", "outputs": {"logfile": {"src": "hda", "id": "6b6553db05727bc4", "uuid": "0cbf6caf-ee62-40c3-bc5c-89bb32db7ab4"}, "taxonomy_out": {"src": "hda", "id": "42de286dcd9bca3b", "uuid": "560bd4aa-7924-4454-acf6-5f4f0b173c55"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.lineage(constaxonomy=file.taxonomy.dat,taxon='Bacteria;Firmicute \rs;Clostridia;Clostridiales;Lachnospiraceae;unclassified;-Bacteria;Proteobacteria \r;Gammaproteobacteria;unclassified;unclassified;unclassified;')\n\nOutput File Names: \nfile.taxonomy.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2429.dat' file.taxonomy.dat && ln -s 'None' file.shared.dat && ln -s 'None' file.list.dat && ln -s 'None' fasta_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat && echo 'remove.lineage( constaxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;unclassified;-Bacteria;Proteobacteria;Gammaproteobacteria;unclassified;unclassified;unclassified;'\"' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:16:43.668260", "params": {"count": "null", "dups": "\"true\"", "fasta_in": "null", "taxon": "\"\"", "dbkey": "\"hg17\"", "group_in": "null", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 2429}]}, \"filetype\": \"useconstaxonomy\", \"list\": null, \"taxons\": [\"Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;\", \"Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;\"], \"__current_case__\": 1, \"shared\": null}", "alignreport_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "32375", "id": "ee234bf95ca1c311", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_lineage.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"infile\|label": "0.22", "accnos": {"src": "hda", "id": "ad5a23682f5a9de8"}, "infile\|otu": {"src": "hda", "id": "60c41917f147cedf"}, "infile\|intype": "in_shared"}, "job": {"inputs": {"accnos": {"src": "hda", "id": "ad5a23682f5a9de8", "uuid": "dfb149e3-265e-4981-a24f-f7c07789024f"}, "otu": {"src": "hda", "id": "60c41917f147cedf", "uuid": "246499f3-daf4-40f1-87b5-e811cadaafb8"}}, "update_time": "2018-02-08T18:16:58.146683", "tool_id": "mothur_remove_otulabels", "outputs": {"pick_out": {"src": "hda", "id": "e1054de073a99e69", "uuid": "b49a638e-3568-4829-9fd0-3ff32e10f5a9"}, "logfile": {"src": "hda", "id": "47efcc304726fc94", "uuid": "fd34616d-4328-4264-a888-df65224a1559"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.otulabels(list=infile.otu.dat,label=0.22,accnos=accnos.dat)\nRemoved 0 OTUs from your list file.\n\nOutput File Names: \ninfile.otu.0.22.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2433.dat' infile.otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2432.dat' accnos.dat && echo 'remove.otulabels( list=infile.otu.dat, label=0.22, accnos=accnos.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:16:54.307572", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_shared\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2433}]}, \"__current_case__\": 0, \"label\": \"0.22\"}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "32499", "id": "211650f16125cac7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_otulabels.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"infile\|intype": "in_other", "accnos": {"src": "hda", "id": "b96a437033ff865d"}, "infile\|otu": {"src": "hda", "id": "ad0fe0deb4088e0a"}}, "job": {"inputs": {"accnos": {"src": "hda", "id": "b96a437033ff865d", "uuid": "293f7fdd-29e5-4ec3-a842-6d2ac7e20f8a"}, "otu": {"src": "hda", "id": "ad0fe0deb4088e0a", "uuid": "e25e2bb1-a988-4495-aa5b-ae2109332f27"}}, "update_time": "2018-02-08T18:17:20.896014", "tool_id": "mothur_remove_otulabels", "outputs": {"pick_out": {"src": "hda", "id": "a18ae6974f6e6e5c", "uuid": "37fe3947-e0a5-4943-95f3-ced1916d0ef5"}, "logfile": {"src": "hda", "id": "dd40e5394130ccc4", "uuid": "3f7cb677-9d83-41cb-95fd-dd0ab28b6842"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.otulabels(corraxes=infile.otu.dat,accnos=accnos.dat)\nRemoved 3 lines from your corr.axes file.\n\nOutput File Names: \ninfile.otu.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2437.dat' infile.otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2436.dat' accnos.dat && echo 'remove.otulabels( corraxes=infile.otu.dat, accnos=accnos.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:17:17.819966", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_other\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2437}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "32611", "id": "a9fd5735f9e9e011", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_otulabels.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"infile\|label": "0.22", "accnos": {"src": "hda", "id": "dee9a2b956d615f3"}, "infile\|otu": {"src": "hda", "id": "95a921a378370eb3"}, "infile\|intype": "in_shared"}, "job": {"inputs": {"accnos": {"src": "hda", "id": "dee9a2b956d615f3", "uuid": "f312c82b-dd3e-4742-83b1-faa00ea52c47"}, "otu": {"src": "hda", "id": "95a921a378370eb3", "uuid": "d50ce77c-745b-4796-ad7c-97e06777ede2"}}, "update_time": "2018-02-08T18:17:42.585808", "tool_id": "mothur_remove_otus", "outputs": {"pick_out": {"src": "hda", "id": "a4a23a6f4654f48d", "uuid": "b69b56ee-6910-484f-8878-451c53a57842"}, "logfile": {"src": "hda", "id": "4dc446e75a5ecd3d", "uuid": "0b525a00-65a9-4875-8492-68c94c2daca8"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.otus(list=infile.otu.dat,label=0.22,accnos=accnos.dat)\nRemoved 0 OTUs from your list file.\n\nOutput File Names: \ninfile.otu.0.22.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2441.dat' infile.otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2440.dat' accnos.dat && echo 'remove.otus( list=infile.otu.dat, label=0.22, accnos=accnos.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:17:39.474122", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_shared\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2441}]}, \"__current_case__\": 0, \"label\": \"0.22\"}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "32731", "id": "e70b3a347edd9ca6", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_otus.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"infile\|intype": "in_other", "accnos": {"src": "hda", "id": "cbb415d7495a9afc"}, "infile\|otu": {"src": "hda", "id": "0f3352b51fa58ea1"}}, "job": {"inputs": {"accnos": {"src": "hda", "id": "cbb415d7495a9afc", "uuid": "22ef75e5-ca16-490c-86c4-86c8bdbced41"}, "otu": {"src": "hda", "id": "0f3352b51fa58ea1", "uuid": "5c49889c-5afb-4d18-92ef-1687076479eb"}}, "update_time": "2018-02-08T18:18:04.247034", "tool_id": "mothur_remove_otus", "outputs": {"pick_out": {"src": "hda", "id": "d3b44446654bd5f7", "uuid": "0e55b880-120c-401d-9d78-43466eef7469"}, "logfile": {"src": "hda", "id": "d02a20be41406d2e", "uuid": "92f22a11-d731-4b0c-8019-a7d9c3c48f30"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.otus(corraxes=infile.otu.dat,accnos=accnos.dat)\nRemoved 3 lines from your corr.axes file.\n\nOutput File Names: \ninfile.otu.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2445.dat' infile.otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2444.dat' accnos.dat && echo 'remove.otus( corraxes=infile.otu.dat, accnos=accnos.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:18:01.130590", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_other\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2445}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "388", "id": "8325c15a45021320", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_otus.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|source": "list", "input\|otu": {"src": "hda", "id": "34aad423ffafab1b"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "34aad423ffafab1b", "uuid": "a955bc96-7ca4-432c-8d66-f8e2731f1fa0"}}, "update_time": "2018-02-08T18:18:22.801087", "tool_id": "mothur_remove_rare", "outputs": {"logfile": {"src": "hda", "id": "ee9b6579bd835e40", "uuid": "a8cfb161-0cb1-4361-9c10-788601368a8b"}, "pick_otu": {"src": "hda", "id": "3308e08d6eccd8a7", "uuid": "ba89e863-a3c4-4703-ab0b-6618e9e81f78"}, "pick_group": {"src": "hda", "id": "a29b3ee6f6fed501", "uuid": "0b84979c-17af-4795-a581-e282687e4a64"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.rare(list=input_otu.dat,nseqs=1)\nFor the listfile you must select one label, using first label in your listfile.\n\nOutput File Names: \ninput_otu.unique.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2448.dat' input_otu.dat && ln -s 'None' input.group.dat && ln -s 'None' input.count.dat && echo 'remove.rare( list=input_otu.dat, nseqs=1 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:18:18.940186", "params": {"input": "{\"count\": null, \"group\": null, \"__current_case__\": 1, \"label\": null, \"source\": \"list\", \"groups\": null, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2448}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "nseqs": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "477", "id": "0679f69ae9556809", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_rare.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|group": {"src": "hda", "id": "c7eb5c5f4746140d"}, "input\|source": "list", "input\|groups": ["forest", "pasture"], "input\|otu": {"src": "hda", "id": "d7b7068fa7538c88"}}, "job": {"inputs": {"group": {"src": "hda", "id": "c7eb5c5f4746140d", "uuid": "7388ff4a-b437-4cfa-ae76-3ab6cd2a951e"}, "otu": {"src": "hda", "id": "d7b7068fa7538c88", "uuid": "8e56acb5-b99b-4966-b64b-674a19c8b445"}}, "update_time": "2018-02-08T18:18:45.594415", "tool_id": "mothur_remove_rare", "outputs": {"logfile": {"src": "hda", "id": "157ddde73282f3fb", "uuid": "bf5722f6-f5ef-414a-a842-1a8a893ecacd"}, "pick_otu": {"src": "hda", "id": "1b495114166d9bc3", "uuid": "d31b64a5-9178-4114-abd7-8c2681c0b2fb"}, "pick_group": {"src": "hda", "id": "97bd1ba524aaaf3a", "uuid": "844bd5b6-89bf-48aa-8a92-14e9032a1358"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.rare(list=input_otu.dat,group=input.group.dat,groups=forest-past \rure,nseqs=1)\nFor the listfile you must select one label, using first label in your listfile.\n\nOutput File Names: \ninput.group.pick.dat\ninput_otu.unique.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2452.dat' input_otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2453.dat' input.group.dat && ln -s 'None' input.count.dat && echo 'remove.rare( list=input_otu.dat, group=input.group.dat, groups=forest-pasture, nseqs=1 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:18:42.385738", "params": {"input": "{\"count\": null, \"group\": {\"values\": [{\"src\": \"hda\", \"id\": 2453}]}, \"__current_case__\": 1, \"label\": null, \"source\": \"list\", \"groups\": [\"forest\", \"pasture\"], \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2452}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "nseqs": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "599", "id": "2d4e92ce3c742824", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_rare.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|source": "shared", "input\|otu": {"src": "hda", "id": "3198a9da3f439604"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "3198a9da3f439604", "uuid": "9e9bb25b-8f5a-4777-a20a-e17460017e6f"}}, "update_time": "2018-02-08T18:19:10.034043", "tool_id": "mothur_remove_rare", "outputs": {"__new_primary_file_unique\|0.10__": {"src": "hda", "id": "610cd1f4e5b83a0c", "uuid": "6828233f-3774-4b20-8a93-6ab47ed28c1d"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "513d86575c74f7d0", "uuid": "f9b7f75c-4688-4b59-b99f-bf047b2ec04f"}, "__new_primary_file_unique\|0.17__": {"src": "hda", "id": "9baafa71c45079b3", "uuid": "bd5079b6-279a-4232-8469-33fafe2a5e66"}, "__new_primary_file_unique\|0.02__": {"src": "hda", "id": "e6f56cb50e173a01", "uuid": "f79063d9-0f95-450c-9704-955f89a2f8c5"}, "__new_primary_file_unique\|0.21__": {"src": "hda", "id": "700a0908817c405f", "uuid": "0f73604c-9a14-4e60-8896-aa61accb2fa7"}, "__new_primary_file_unique\|0.16__": {"src": "hda", "id": "322c8a381eeeb501", "uuid": "eff8980f-266e-4894-9e3c-648428eb6315"}, "__new_primary_file_unique\|0.45__": {"src": "hda", "id": "119999e59bd419d5", "uuid": "1cb26251-b37c-4d10-bc69-be079c4bf5df"}, "__new_primary_file_unique\|0.03__": {"src": "hda", "id": "e26c7b8f9677aad0", "uuid": "0cc9c609-507b-4f2b-ba4b-a831a6c92145"}, "__new_primary_file_unique\|0.15__": {"src": "hda", "id": "5d5adfb1fb49ce2c", "uuid": "cfbe6c7d-4028-48ba-b8c3-3ad5a5fc556f"}, "__new_primary_file_unique\|0.08__": {"src": "hda", "id": "ab8e8b2bc0c15acd", "uuid": "ba4ed452-675e-40bc-987e-caa800a389f4"}, "__new_primary_file_unique\|0.14__": {"src": "hda", "id": "8870c5f928bb333a", "uuid": "08d0a12a-e1ce-43be-9e09-6afd547c569e"}, "__new_primary_file_unique\|0.13__": {"src": "hda", "id": "d07a38806b24d453", "uuid": "aff7864c-9ab8-4d0e-bf7b-b8bd02af4b92"}, "__new_primary_file_unique\|0.09__": {"src": "hda", "id": "2297b690ab68e422", "uuid": "46827413-8dd3-43d1-a307-478eeb63c53e"}, "__new_primary_file_unique\|0.12__": {"src": "hda", "id": "31fece26dc8ce520", "uuid": "382f6308-a9b5-491b-98ee-3553f7ad604f"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "74e41b93abfa8004", "uuid": "68372d6c-15a2-43d8-9aa6-dae86d615854"}, "__new_primary_file_unique\|0.11__": {"src": "hda", "id": "10f3b133fbdfbf9f", "uuid": "4ef4f2fd-d729-4e2f-ba5e-d877b3f97900"}, "__new_primary_file_unique\|0.41__": {"src": "hda", "id": "636206ab34003c74", "uuid": "a450aefe-767d-44ee-b214-f8e1f6ffb340"}, "__new_primary_file_unique\|0.06__": {"src": "hda", "id": "0c81280a55e0de4e", "uuid": "2fefeb64-8dfb-4dab-940c-936c66ead31e"}, "__new_primary_file_unique\|0.25__": {"src": "hda", "id": "d0db099eee1d29bc", "uuid": "d59104f8-497e-46df-ab6f-c4e1b6008c2c"}, "__new_primary_file_unique\|0.22__": {"src": "hda", "id": "ab61d935d8b06603", "uuid": "93f026c8-2811-4d2c-90fd-39a3a90dd51a"}, "__new_primary_file_unique\|0.36__": {"src": "hda", "id": "e9fd1bfe3c966ddd", "uuid": "1b03c3da-4e99-4f22-8ac8-dc7c37d60392"}, "__new_primary_file_unique\|0.04__": {"src": "hda", "id": "9fe5ee644c2e6c63", "uuid": "60848a9f-fb38-47c8-ba99-62021b1b7e5f"}, "__new_primary_file_unique\|0.23__": {"src": "hda", "id": "c1bb74450083f46e", "uuid": "966d2046-3229-46cc-bc92-71626bf97c3d"}, "__new_primary_file_unique\|0.33__": {"src": "hda", "id": "fea0057dfc409953", "uuid": "759d9426-cbca-45b2-8ddb-43e8f7b013af"}, "logfile": {"src": "hda", "id": "4f898abf2bba8db9", "uuid": "b89ade31-ba94-42d9-b11d-31bbaecbeed0"}, "__new_primary_file_unique\|0.20__": {"src": "hda", "id": "f8361ca1fe7540ad", "uuid": "fdb8b86e-5762-4aad-8c1e-b538c0d9b67a"}, "__new_primary_file_unique\|0.29__": {"src": "hda", "id": "51c08c22772eba1c", "uuid": "a71e3585-6b7a-4088-83e3-5498dc932ea6"}, "__new_primary_file_unique\|0.38__": {"src": "hda", "id": "056c262b45795646", "uuid": "7a782f58-afde-4af4-b59b-ab246348e1d9"}, "__new_primary_file_unique\|0.55__": {"src": "hda", "id": "f0439ffc253b657d", "uuid": "0624d10f-a3c2-4a2e-ab25-66276206798e"}, "__new_primary_file_unique\|0.07__": {"src": "hda", "id": "98e41e589857cd09", "uuid": "ae4ba94b-efb1-468a-86c2-bc6728c6c22f"}, "__new_primary_file_unique\|0.26__": {"src": "hda", "id": "b96623e367bd8bc3", "uuid": "8ab8869f-0b1d-43de-872c-9bf4f3adaeb1"}, "__new_primary_file_unique\|0.32__": {"src": "hda", "id": "c6b3e47f9c11596c", "uuid": "f40112b7-48c5-4f23-9f21-63d8e091f6d0"}, "__new_primary_file_unique\|0.27__": {"src": "hda", "id": "7a0f2dde2b5d6619", "uuid": "2dba0c16-785b-4d60-b078-f08b165dbe1d"}, "__new_primary_file_unique\|0.19__": {"src": "hda", "id": "067ce3c7e559f632", "uuid": "19c6616d-8ef1-40b5-970c-d854e8fb9dbe"}, "__new_primary_file_unique\|0.01__": {"src": "hda", "id": "8363c828b832effc", "uuid": "7f70cb84-5b0e-48dc-aa87-e52282e370d6"}, "__new_primary_file_unique\|0.24__": {"src": "hda", "id": "23fa57f602461511", "uuid": "a20f6f57-2422-4dc6-a170-003a926b0a67"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "764ef33b86dc4158", "uuid": "e5f1280d-9dd8-48f4-bc74-cf5585849fc4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.rare(shared=input_otu.dat,bygroup=false,nseqs=1)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu.unique.pick.dat\ninput_otu.0.01.pick.dat\ninput_otu.0.02.pick.dat\ninput_otu.0.03.pick.dat\ninput_otu.0.04.pick.dat\ninput_otu.0.05.pick.dat\ninput_otu.0.06.pick.dat\ninput_otu.0.07.pick.dat\ninput_otu.0.08.pick.dat\ninput_otu.0.09.pick.dat\ninput_otu.0.10.pick.dat\ninput_otu.0.11.pick.dat\ninput_otu.0.12.pick.dat\ninput_otu.0.13.pick.dat\ninput_otu.0.14.pick.dat\ninput_otu.0.15.pick.dat\ninput_otu.0.16.pick.dat\ninput_otu.0.17.pick.dat\ninput_otu.0.18.pick.dat\ninput_otu.0.19.pick.dat\ninput_otu.0.20.pick.dat\ninput_otu.0.21.pick.dat\ninput_otu.0.22.pick.dat\ninput_otu.0.23.pick.dat\ninput_otu.0.24.pick.dat\ninput_otu.0.25.pick.dat\ninput_otu.0.26.pick.dat\ninput_otu.0.27.pick.dat\ninput_otu.0.29.pick.dat\ninput_otu.0.32.pick.dat\ninput_otu.0.33.pick.dat\ninput_otu.0.36.pick.dat\ninput_otu.0.38.pick.dat\ninput_otu.0.41.pick.dat\ninput_otu.0.45.pick.dat\ninput_otu.0.55.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2457.dat' input_otu.dat && echo 'remove.rare( shared=input_otu.dat, bygroup=false, nseqs=1 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:19:05.076315", "params": {"input": "{\"__current_case__\": 0, \"label\": null, \"source\": \"shared\", \"groups\": null, \"bygroup\": \"false\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2457}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "nseqs": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "705", "id": "ce49eab21f44c35b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_rare.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|bygroup": true, "input\|source": "shared", "input\|groups": ["forest", "pasture"], "input\|label": ["0.05", "0.22", "0.41"], "input\|otu": {"src": "hda", "id": "4eb6ee5cb7ab7d0b"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "4eb6ee5cb7ab7d0b", "uuid": "558df565-4a9f-4e34-b432-7fd50da71a74"}}, "update_time": "2018-02-08T18:19:29.011991", "tool_id": "mothur_remove_rare", "outputs": {"__new_primary_file_0.41\|0.05__": {"src": "hda", "id": "91b58ed15e4e89f3", "uuid": "7d23c7ed-f52c-43f9-a44e-5629055963a1"}, "logfile": {"src": "hda", "id": "7fb409cd94387402", "uuid": "63b2a24b-bc3a-4645-ac16-d548c4dc3540"}, "__new_primary_file_0.41\|0.22__": {"src": "hda", "id": "40de2667ff1e222c", "uuid": "e99fecc8-1e4a-4744-bf80-74d4b84e13db"}, "__new_primary_file_0.41\|0.41__": {"src": "hda", "id": "bed855b2598b1c7b", "uuid": "0876d651-f17d-43d0-8aa9-a02a1ea5f3af"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.rare(shared=input_otu.dat,bygroup=true,groups=forest-pasture,lab \rel=0.05-0.22-0.41,nseqs=1)\n0.05\n0.22\n0.41\n\nOutput File Names: \ninput_otu.0.05.pick.dat\ninput_otu.0.22.pick.dat\ninput_otu.0.41.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2495.dat' input_otu.dat && echo 'remove.rare( shared=input_otu.dat, bygroup=true, groups=forest-pasture, label=0.05-0.22-0.41, nseqs=1 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:19:25.682198", "params": {"input": "{\"__current_case__\": 0, \"label\": [\"0.05\", \"0.22\", \"0.41\"], \"source\": \"shared\", \"groups\": [\"forest\", \"pasture\"], \"bygroup\": \"true\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2495}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "nseqs": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "818", "id": "5e64ba0eb7841b04", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_rare.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|source": "default", "input\|otu": {"src": "hda", "id": "9a17ce6ea75b5c66"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "9a17ce6ea75b5c66", "uuid": "0bb489e2-6155-45bb-9c55-abcd6005d8f4"}}, "update_time": "2018-02-08T18:19:46.539468", "tool_id": "mothur_remove_rare", "outputs": {"logfile": {"src": "hda", "id": "e8e1ca0a2741d94b", "uuid": "1a71a491-0df2-4abb-8718-ae0417e59030"}, "pick_otu": {"src": "hda", "id": "773fd339f6505ca6", "uuid": "816dc85c-14d5-497e-8788-851d0d454a0d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.rare(sabund=input_otu.dat,nseqs=1)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2500.dat' input_otu.dat && echo 'remove.rare( sabund=input_otu.dat, nseqs=1 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:19:43.384733", "params": {"input": "{\"source\": \"default\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2500}]}, \"__current_case__\": 2, \"label\": null}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "nseqs": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "906", "id": "e561f0821a7a597e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_rare.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"accnos": {"src": "hda", "id": "071087e21ad6aa1c"}, "fasta_in": {"src": "hda", "id": "2543f1cad8cfe6a0"}, "dups": true}, "job": {"inputs": {"accnos": {"src": "hda", "id": "071087e21ad6aa1c", "uuid": "0a303147-c516-47a4-87d1-76275b3a1d87"}, "fasta_in": {"src": "hda", "id": "2543f1cad8cfe6a0", "uuid": "a84dc52b-f9a0-4db3-af0c-2a37f314d0a0"}}, "update_time": "2018-02-08T18:20:07.186595", "tool_id": "mothur_remove_seqs", "outputs": {"logfile": {"src": "hda", "id": "09b448289a70fe55", "uuid": "bd0555db-8faa-46df-9ed1-ffe62e57a2c6"}, "fasta_out": {"src": "hda", "id": "8534402e7f1fc070", "uuid": "d7e93696-6805-44b3-905f-0a4646138234"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.seqs(accnos=accnos.dat,fasta=fasta_in.dat)\nRemoved 3 sequences from your fasta file.\n\nOutput File Names: \nfasta_in.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2503.dat' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2504.dat' fasta_in.dat && ln -s 'None' fastq_in.dat && ln -s 'None' count_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' taxonomy_in.dat && echo 'remove.seqs( accnos=accnos.dat ,fasta=fasta_in.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:20:04.111975", "params": {"fastq_in": "null", "dups": "\"true\"", "count_in": "null", "dbkey": "\"hg17\"", "group_in": "null", "taxonomy_in": "null", "alignreport_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "1022", "id": "06788ac74a6156ce", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fastq_in": {"src": "hda", "id": "803a22dd93d75310"}, "accnos": {"src": "hda", "id": "7fcab135a6b69469"}}, "job": {"inputs": {"fastq_in": {"src": "hda", "id": "803a22dd93d75310", "uuid": "dbe6ac03-bfc0-4610-b76e-082ccfe2edb2"}, "accnos": {"src": "hda", "id": "7fcab135a6b69469", "uuid": "2666d05d-a61a-4485-a3ac-4fc14afbe333"}}, "update_time": "2018-02-08T18:20:22.881902", "tool_id": "mothur_remove_seqs", "outputs": {"logfile": {"src": "hda", "id": "9e8f20a034dacfe8", "uuid": "b7cb20a4-e2a9-43dd-b725-81d45c93b21d"}, "fastq_out": {"src": "hda", "id": "70e57fb8c96afc80", "uuid": "720c99b1-f772-434f-99fe-ac46d2f9c524"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.seqs(accnos=accnos.dat,fastq=fastq_in.dat)\nRemoved 3 sequences from your fastq file.\n\nOutput File Names: \nfastq_in.pick.dat\n\n[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2507.dat' accnos.dat && ln -s 'None' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2508.dat' fastq_in.dat && ln -s 'None' count_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' taxonomy_in.dat && echo 'remove.seqs( accnos=accnos.dat ,fastq=fastq_in.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:20:19.812919", "params": {"dups": "\"true\"", "fasta_in": "null", "count_in": "null", "dbkey": "\"hg17\"", "group_in": "null", "taxonomy_in": "null", "alignreport_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "1152", "id": "202ba766860ff920", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fastq_in": {"src": "hda", "id": "c6cb321db749c627"}, "accnos": {"src": "hda", "id": "414d94e35f77b812"}, "fasta_in": {"src": "hda", "id": "9277a644c0099152"}, "dups": true}, "job": {"inputs": {"fastq_in": {"src": "hda", "id": "c6cb321db749c627", "uuid": "b01b576b-5d5a-45c8-bd25-7f45aeca49ce"}, "fasta_in": {"src": "hda", "id": "9277a644c0099152", "uuid": "c7b740b4-e49b-4bfe-837e-bc7f23c821ce"}, "accnos": {"src": "hda", "id": "414d94e35f77b812", "uuid": "ab991a10-c2b0-4de4-95f7-85fc1c564ac2"}}, "update_time": "2018-02-08T18:20:42.483186", "tool_id": "mothur_remove_seqs", "outputs": {"fasta_out": {"src": "hda", "id": "c127cc24451df342", "uuid": "4ce1cdd4-5b9f-44fa-9c5e-4319b1e4447e"}, "logfile": {"src": "hda", "id": "0601f5ddca2878d9", "uuid": "ce56505f-8263-4a3d-91e5-59f0bfaf5823"}, "fastq_out": {"src": "hda", "id": "d14c18ee2831b4fc", "uuid": "40716292-1893-46d8-978c-cbb3c47f4138"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.seqs(accnos=accnos.dat,fasta=fasta_in.dat,fastq=fastq_in.dat)\nRemoved 3 sequences from your fasta file.\nRemoved 3 sequences from your fastq file.\n\nOutput File Names: \nfasta_in.pick.dat\nfastq_in.pick.dat\n\n[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2511.dat' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2512.dat' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2513.dat' fastq_in.dat && ln -s 'None' count_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' taxonomy_in.dat && echo 'remove.seqs( accnos=accnos.dat ,fasta=fasta_in.dat ,fastq=fastq_in.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:20:38.627569", "params": {"dups": "\"true\"", "count_in": "null", "dbkey": "\"hg17\"", "group_in": "null", "taxonomy_in": "null", "alignreport_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "1349", "id": "e9e479aeb9b0a25e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"accnos": {"src": "hda", "id": "99d15eac4014af78"}, "count_in": {"src": "hda", "id": "b52f2aa5944e8b7f"}}, "job": {"inputs": {"accnos": {"src": "hda", "id": "99d15eac4014af78", "uuid": "d794f030-ebfd-4785-a36d-69378c3012ba"}, "count_in": {"src": "hda", "id": "b52f2aa5944e8b7f", "uuid": "70c52661-c5f1-4ff3-a00d-c53810b2ea9e"}}, "update_time": "2018-02-08T18:21:01.217167", "tool_id": "mothur_remove_seqs", "outputs": {"logfile": {"src": "hda", "id": "8711290f7ce753d2", "uuid": "b9fe3c0f-3a24-483f-b49c-89942a95af63"}, "count_out": {"src": "hda", "id": "bd3c4aa291ca99da", "uuid": "c7d68414-b083-4bfb-944d-d3f34d581333"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.seqs(accnos=accnos.dat,count=count_in.dat)\nRemoved 8 sequences from your count file.\n\nOutput File Names: \ncount_in.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2517.dat' accnos.dat && ln -s 'None' fasta_in.dat && ln -s 'None' fastq_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2518.dat' count_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' taxonomy_in.dat && echo 'remove.seqs( accnos=accnos.dat ,count=count_in.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:20:58.127372", "params": {"fastq_in": "null", "dups": "\"true\"", "fasta_in": "null", "dbkey": "\"hg17\"", "group_in": "null", "taxonomy_in": "null", "alignreport_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "1467", "id": "3fcf4993e0bb2ff7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_seqs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "5eb53f4a9442659b"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "5eb53f4a9442659b", "uuid": "e3ddb07c-8bbc-41b4-93c4-ddff71162442"}}, "update_time": "2018-02-08T18:21:13.686851", "tool_id": "mothur_reverse_seqs", "outputs": {"logfile": {"src": "hda", "id": "65b29d046b1f849c", "uuid": "678bc632-03d6-4bfe-89b5-24cc0d8b74a6"}, "out_fasta": {"src": "hda", "id": "0b9cedc8ae8a94c2", "uuid": "56cac2ed-4bd3-4529-9b9f-ab9634842cf5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > reverse.seqs(fasta=fasta.dat)\n\nOutput File Names: \nfasta.rc.dat\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2521.dat' fasta.dat && echo 'reverse.seqs( fasta=fasta.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:21:10.537342", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "1561", "id": "be25131031e1ad95", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_reverse_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "32ef23706aa388fb"}, "maxambig": "0", "maxlength": "275"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "32ef23706aa388fb", "uuid": "67e84174-fade-41d6-9981-d71cd3961247"}}, "update_time": "2018-02-08T18:21:26.199184", "tool_id": "mothur_screen_seqs", "outputs": {"contigsreport_out": {"src": "hda", "id": "56599abe680f3751", "uuid": "60282443-d360-48bc-96f4-6027bb560515"}, "logfile": {"src": "hda", "id": "685f126dc635c97c", "uuid": "b6de5901-d7e0-47f8-a4af-fe9c8ec96549"}, "bad_accnos": {"src": "hda", "id": "66f064aa8763a5a7", "uuid": "65936755-bd92-4c42-ac7e-45bb284a00dd"}, "alignreport_out": {"src": "hda", "id": "c93f720e91f61f32", "uuid": "6c7dfd89-f8b2-4678-8433-59016e725bb0"}, "fasta_out": {"src": "hda", "id": "05a76bb0530e159c", "uuid": "508e7c6a-89d5-4e3a-955e-c8a4e7995ad2"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > screen.seqs(fasta=fasta.dat,minlength=10,maxlength=275,maxambig=0,proce \rssors=1)\n\nUsing 1 processors.\nProcessing sequence: 25\n\nOutput File Names: \nfasta.good.dat\nfasta.bad.accnos\n\n\nIt took 0 secs to screen 25 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2524.dat' fasta.dat && ln -s 'None' names.dat && ln -s 'None' groups.dat && ln -s 'None' qfile.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat && ln -s 'None' summary.dat && echo 'screen.seqs( fasta=fasta.dat ,minlength=10 ,maxlength=275 ,maxambig=0 ,processors='\"${GALAXY_SLOTS:-8}\"' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:21:22.835146", "params": {"count": "null", "criteria": "\"-1\"", "optimize": "null", "end": "\"-1\"", "taxonomy": "null", "contigsrep": "{\"__current_case__\": 1, \"usecontigs\": \"no\"}", "maxhomop": "\"-1\"", "dbkey": "\"hg17\"", "summary": "null", "alignrep": "{\"usealign\": \"no\", \"__current_case__\": 1}", "start": "\"-1\"", "maxambig": "\"0\"", "names": "null", "groups": "null", "minlength": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "qfile": "null", "maxlength": "\"275\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "1650", "id": "b07688f4168e93bf", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_screen_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"count": {"src": "hda", "id": "f0fe15730b8db9c4"}, "fasta": {"src": "hda", "id": "42af088b2abee145"}, "maxambig": "0", "maxlength": "500"}, "job": {"inputs": {"count": {"src": "hda", "id": "f0fe15730b8db9c4", "uuid": "7662f8fc-415b-4f23-9951-6eaea441232d"}, "fasta": {"src": "hda", "id": "42af088b2abee145", "uuid": "deb69949-3962-464d-b253-b02a76ae90b4"}}, "update_time": "2018-02-08T18:21:52.517139", "tool_id": "mothur_screen_seqs", "outputs": {"bad_accnos": {"src": "hda", "id": "37b038abf8b718f0", "uuid": "1127a6ef-c175-43ce-9605-0c783d3765d3"}, "count_out": {"src": "hda", "id": "00363558c5729a44", "uuid": "e46f23c4-7a89-4b61-8967-98adf21d4e77"}, "alignreport_out": {"src": "hda", "id": "4c2735cf7f715dcf", "uuid": "827bf85e-98b9-42a9-86bc-eccf04eb720f"}, "contigsreport_out": {"src": "hda", "id": "ba8cf376bccbc9b2", "uuid": "e128ed5f-7c04-41e8-bd39-cdcaf5965189"}, "fasta_out": {"src": "hda", "id": "c5b03287369c63ab", "uuid": "046994b4-43d1-4a23-9ecb-85c6db0420bb"}, "logfile": {"src": "hda", "id": "652751201af8821c", "uuid": "f869d649-38ad-4f61-a247-f3f3dcf2ba24"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > screen.seqs(fasta=fasta.dat,minlength=10,maxlength=500,maxambig=0,count \r=count.dat,processors=1)\n\nUsing 1 processors.\nProcessing sequence: 98\n\nOutput File Names: \nfasta.good.dat\nfasta.bad.accnos\ncount.good.dat\n\n\nIt took 0 secs to screen 98 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2530.dat' fasta.dat && ln -s 'None' names.dat && ln -s 'None' groups.dat && ln -s 'None' qfile.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2531.dat' count.dat && ln -s 'None' taxonomy.dat && ln -s 'None' summary.dat && echo 'screen.seqs( fasta=fasta.dat ,minlength=10 ,maxlength=500 ,maxambig=0 ,count=count.dat ,processors='\"${GALAXY_SLOTS:-8}\"' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:21:48.991211", "params": {"criteria": "\"-1\"", "optimize": "null", "end": "\"-1\"", "taxonomy": "null", "qfile": "null", "maxhomop": "\"-1\"", "dbkey": "\"hg17\"", "summary": "null", "alignrep": "{\"usealign\": \"no\", \"__current_case__\": 1}", "start": "\"-1\"", "maxambig": "\"0\"", "names": "null", "groups": "null", "minlength": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "contigsrep": "{\"__current_case__\": 1, \"usecontigs\": \"no\"}", "maxlength": "\"500\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "1773", "id": "978914f1b3729f41", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_screen_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"contigsrep\|mismatches": "18", "maxambig": "0", "contigsrep\|usecontigs": "yes", "maxlength": "275", "fasta": {"src": "hda", "id": "114c38d4ffc72675"}, "contigsrep\|contigsreport": {"src": "hda", "id": "b0a3d3266cc35e70"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "114c38d4ffc72675", "uuid": "997523f7-3cce-4812-b622-533a7a716ac1"}, "contigsreport": {"src": "hda", "id": "b0a3d3266cc35e70", "uuid": "e0c873e8-a140-432a-8092-89ac2f8e8028"}}, "update_time": "2018-02-08T18:22:24.263577", "tool_id": "mothur_screen_seqs", "outputs": {"contigsreport_out": {"src": "hda", "id": "5872d7bb294e738e", "uuid": "18b00001-2f90-4f54-9212-e728eb0e9a4b"}, "logfile": {"src": "hda", "id": "cf5adbe5b084422c", "uuid": "29bae6ca-b02b-41b8-bdc2-c0ecb10264d4"}, "bad_accnos": {"src": "hda", "id": "e561361d04e2dadf", "uuid": "3f576845-eeea-41aa-bc25-ab12359708e1"}, "alignreport_out": {"src": "hda", "id": "17a1b993567aec5b", "uuid": "5d18a664-e9d3-4ec3-9dc2-a332b94e914e"}, "fasta_out": {"src": "hda", "id": "e1b9ee8eba60a340", "uuid": "f416f012-b80d-4d91-a13d-2582f23c8991"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > screen.seqs(fasta=fasta.dat,minlength=10,maxlength=275,maxambig=0,conti \rgsreport=contigsreport.dat,minoverlap=-1,ostart=-1,oend=-1,mismatches=18,process \rors=1)\n\nUsing 1 processors.\nProcessing sequence: 25\n\nOutput File Names: \ncontigsreport.good.contigs.report\nfasta.good.dat\nfasta.bad.accnos\n\n\nIt took 0 secs to screen 25 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2538.dat' fasta.dat && ln -s 'None' names.dat && ln -s 'None' groups.dat && ln -s 'None' qfile.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat && ln -s 'None' summary.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2539.dat' contigsreport.dat && echo 'screen.seqs( fasta=fasta.dat ,minlength=10 ,maxlength=275 ,maxambig=0 ,contigsreport=contigsreport.dat ,minoverlap=-1 ,ostart=-1 ,oend=-1 ,mismatches=18 ,processors='\"${GALAXY_SLOTS:-8}\"' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:22:20.100609", "params": {"count": "null", "criteria": "\"-1\"", "optimize": "null", "end": "\"-1\"", "taxonomy": "null", "contigsrep": "{\"oend\": \"-1\", \"contigsreport\": {\"values\": [{\"src\": \"hda\", \"id\": 2539}]}, \"ostart\": \"-1\", \"mismatches\": \"18\", \"usecontigs\": \"yes\", \"minoverlap\": \"-1\", \"__current_case__\": 0}", "maxhomop": "\"-1\"", "dbkey": "\"hg17\"", "summary": "null", "alignrep": "{\"usealign\": \"no\", \"__current_case__\": 1}", "start": "\"-1\"", "maxambig": "\"0\"", "names": "null", "groups": "null", "minlength": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "qfile": "null", "maxlength": "\"275\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "1890", "id": "071599f87a4de604", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_screen_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"alignrep\|minscore": "100", "maxambig": "0", "alignrep\|usealign": "yes", "maxlength": "275", "alignrep\|alignreport": {"src": "hda", "id": "284b37b92e77841f"}, "fasta": {"src": "hda", "id": "5d1c7a267ee4549c"}}, "job": {"inputs": {"alignreport": {"src": "hda", "id": "284b37b92e77841f", "uuid": "faa386f7-f6d9-4b4e-8eca-e58fa2a6b0e8"}, "fasta": {"src": "hda", "id": "5d1c7a267ee4549c", "uuid": "350eb235-3d69-4cd0-8777-b0c22175248e"}}, "update_time": "2018-02-08T18:22:58.316487", "tool_id": "mothur_screen_seqs", "outputs": {"contigsreport_out": {"src": "hda", "id": "0f56156b04eb5a7c", "uuid": "33739706-afc6-45f6-939c-d47391d38deb"}, "logfile": {"src": "hda", "id": "8efa80d3971b8580", "uuid": "73a8ee94-8fd3-4da6-8134-ab8e859ade40"}, "bad_accnos": {"src": "hda", "id": "fe2332f09b9a6caf", "uuid": "e7738364-47d8-4f27-90f7-b964dcbafbcd"}, "alignreport_out": {"src": "hda", "id": "82c7032da1686dba", "uuid": "146b2158-8170-4ae8-894a-1100daa724f6"}, "fasta_out": {"src": "hda", "id": "e5f17aed15456c1d", "uuid": "8973d539-161c-48e0-947d-0825d21e6336"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > screen.seqs(fasta=fasta.dat,minlength=10,maxlength=275,maxambig=0,align \rreport=alignreport.dat,minsim=-1,minscore=100,maxinsert=-1,processors=1)\n\nUsing 1 processors.\nProcessing sequence: 22\n\nOutput File Names: \nalignreport.good.align.report\nfasta.good.dat\nfasta.bad.accnos\n\n\nIt took 0 secs to screen 22 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2545.dat' fasta.dat && ln -s 'None' names.dat && ln -s 'None' groups.dat && ln -s 'None' qfile.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat && ln -s 'None' summary.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2546.dat' alignreport.dat && echo 'screen.seqs( fasta=fasta.dat ,minlength=10 ,maxlength=275 ,maxambig=0 ,alignreport=alignreport.dat ,minsim=-1 ,minscore=100 ,maxinsert=-1 ,processors='\"${GALAXY_SLOTS:-8}\"' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:22:54.951671", "params": {"count": "null", "criteria": "\"-1\"", "optimize": "null", "end": "\"-1\"", "taxonomy": "null", "contigsrep": "{\"__current_case__\": 1, \"usecontigs\": \"no\"}", "maxhomop": "\"-1\"", "dbkey": "\"hg17\"", "summary": "null", "alignrep": "{\"usealign\": \"yes\", \"alignreport\": {\"values\": [{\"src\": \"hda\", \"id\": 2546}]}, \"__current_case__\": 0, \"minsim\": \"-1\", \"maxinsert\": \"-1\", \"minscore\": \"100\"}", "start": "\"-1\"", "maxambig": "\"0\"", "names": "null", "groups": "null", "minlength": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "qfile": "null", "maxlength": "\"275\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "2022", "id": "8cfece4559d4fc3b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_screen_seqs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"matrix\|method_name\|count": {"src": "hda", "id": "ca5000435bda311d"}, "otu": {"src": "hda", "id": "bb539f073f00812b"}, "matrix\|dist": {"src": "hda", "id": "220cf7d719dd1e3f"}}, "job": {"inputs": {"dist": {"src": "hda", "id": "ca5000435bda311d", "uuid": "e9a28efa-a393-44fa-967f-a0b7bd9ebf71"}, "otu": {"src": "hda", "id": "bb539f073f00812b", "uuid": "ba882201-0e75-49ee-9788-1e4c9eb91022"}, "matrix\|count": {"src": "hda", "id": "ca5000435bda311d", "uuid": "e9a28efa-a393-44fa-967f-a0b7bd9ebf71"}}, "update_time": "2018-02-08T18:23:33.150499", "tool_id": "mothur_sens_spec", "outputs": {"sensspec": {"src": "hda", "id": "cd2710fe9c8e2a0a", "uuid": "f89fcbc4-fb42-49c8-a692-454e7f940363"}, "logfile": {"src": "hda", "id": "a6abaddda864dc74", "uuid": "a7d81a4b-2f77-4699-8769-23850fa276bb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sens.spec(list=otu.dat,column=matrix.dist.dat,count=matrix.method_name. \rcount.dat,precision=100,cutoff=-1.0)\n\nNOTE: sens.spec assumes that only unique sequences were used to generate the distance matrix.\n\nIt took 0 to run sens.spec.\n\nOutput File Names: \notu.sensspec\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2554.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2552.dat' matrix.dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2553.dat' matrix.method_name.count.dat && echo 'sens.spec( list=otu.dat, column=matrix.dist.dat, count=matrix.method_name.count.dat, precision=100, cutoff=-1.0 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:23:29.979676", "params": {"cutoff": "\"-1.0\"", "matrix": "{\"method_name\": {\"count\": {\"values\": [{\"src\": \"hda\", \"id\": 2553}]}, \"method\": \"count\", \"__current_case__\": 0}, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 2552}]}, \"__current_case__\": 0, \"format\": \"column\"}", "precision": "\"100\"", "dbkey": "\"hg17\"", "label": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "2173", "id": "29caadb190f2e006", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sens_spec.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"matrix\|method_name\|count": {"src": "hda", "id": "0b8bf891c9e392c5"}, "cutoff": "0.10", "otu": {"src": "hda", "id": "a770ee5c0aa4752d"}, "matrix\|dist": {"src": "hda", "id": "276a286d69827381"}, "label": ["0.03", "0.05", "0.22"]}, "job": {"inputs": {"dist": {"src": "hda", "id": "0b8bf891c9e392c5", "uuid": "8c1fb6ef-8fb2-4f3b-9e5a-71f302eadb4e"}, "otu": {"src": "hda", "id": "a770ee5c0aa4752d", "uuid": "862748b0-5a4c-4a8e-9ce1-d484f0cea78f"}, "matrix\|count": {"src": "hda", "id": "0b8bf891c9e392c5", "uuid": "8c1fb6ef-8fb2-4f3b-9e5a-71f302eadb4e"}}, "update_time": "2018-02-08T18:23:58.017498", "tool_id": "mothur_sens_spec", "outputs": {"sensspec": {"src": "hda", "id": "13e8a4ab78efa0c3", "uuid": "830b10f1-e3e1-4daf-9543-3a3c84272526"}, "logfile": {"src": "hda", "id": "0e1aeed8734b5624", "uuid": "f309d90b-da0b-488c-8acd-d7c88e5cfcf6"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sens.spec(list=otu.dat,column=matrix.dist.dat,count=matrix.method_name. \rcount.dat,label=0.03-0.05-0.22,label=0.03-0.05-0.22,precision=100,cutoff=0.1)\n\nNOTE: sens.spec assumes that only unique sequences were used to generate the distance matrix.\n\nIt took 0 to run sens.spec.\n\nOutput File Names: \notu.sensspec\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2559.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2557.dat' matrix.dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2558.dat' matrix.method_name.count.dat && echo 'sens.spec( list=otu.dat, column=matrix.dist.dat, count=matrix.method_name.count.dat, label=0.03-0.05-0.22, label=0.03-0.05-0.22, precision=100, cutoff=0.1 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:23:54.921822", "params": {"cutoff": "\"0.1\"", "matrix": "{\"method_name\": {\"count\": {\"values\": [{\"src\": \"hda\", \"id\": 2558}]}, \"method\": \"count\", \"__current_case__\": 0}, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 2557}]}, \"__current_case__\": 0, \"format\": \"column\"}", "precision": "\"100\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\", \"0.22\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "2317", "id": "41cb101ab8c7143d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sens_spec.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"alignment\|template": {"src": "hda", "id": "3d56df3f9910bb65"}, "alignment\|source": "history", "fasta_in": {"src": "hda", "id": "5244dd9a7b7ad1ff"}}, "job": {"inputs": {"fasta_in": {"src": "hda", "id": "5244dd9a7b7ad1ff", "uuid": "3cc67e25-f341-4480-b12f-daccd035f7c0"}, "template": {"src": "hda", "id": "3d56df3f9910bb65", "uuid": "0b126cee-0e8c-4f41-a425-0693293ee426"}}, "update_time": "2018-02-08T18:24:19.878364", "tool_id": "mothur_seq_error", "outputs": {"seq_reverse_out": {"src": "hda", "id": "8b42193f5326fbe1", "uuid": "4e9fe539-3b01-47d8-a593-57f6c554dbd9"}, "seq_forward_out": {"src": "hda", "id": "e18f72b039a3216a", "uuid": "e8c55d65-3633-425b-bbb2-5212ba243e6f"}, "count_out": {"src": "hda", "id": "42d2637b0f6e48e5", "uuid": "feb6bfc7-287a-432e-983b-a699b04999e1"}, "ref_query_out": {"src": "hda", "id": "f4fa5631199a49ea", "uuid": "231a8554-5816-4549-b52c-f67243a6f128"}, "matrix_out": {"src": "hda", "id": "244af713c6fa3d39", "uuid": "74ae8954-8372-4c96-8bd7-b2cdf5ea50da"}, "seq_out": {"src": "hda", "id": "a1cf0baa8d621c92", "uuid": "453d4d7f-fcd1-414d-94b7-dddcefe48909"}, "summary_out": {"src": "hda", "id": "26853ddf806efff5", "uuid": "fbca03a6-37ed-4926-a21a-e907093a45c7"}, "chimera_out": {"src": "hda", "id": "aefbd28d5fee1c64", "uuid": "7197202a-ba63-4414-94d7-83b30b16ff49"}, "logfile": {"src": "hda", "id": "ba0aff7639a35591", "uuid": "3aa03c30-d34e-4efb-9945-d30e19ca5f2f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > seq.error(fasta=fasta_in.dat,reference=alignment.template.dat,ignorechi \rmeras=true,aligned=T,processors=1)\n\nUsing 1 processors.\nIt took 0 to read 32 sequences.\n3\n\nMultiply error rate by 100 to obtain the percent sequencing errors.\nOverall error rate:\t-nan\nErrors\tSequences\n0\t0\n1\t0\n2\t0\n3\t0\n4\t0\n5\t0\n6\t0\n7\t0\n8\t0\n9\t0\n10\t0\nIt took 0 secs to check 3 sequences.\n\nOutput File Names: \nfasta_in.error.summary\nfasta_in.error.seq\nfasta_in.error.chimera\nfasta_in.error.seq.forward\nfasta_in.error.seq.reverse\nfasta_in.error.count\nfasta_in.error.matrix\nfasta_in.error.ref\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2562.dat' fasta_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2563.dat' alignment.template.dat && echo 'seq.error( fasta=fasta_in.dat, reference=alignment.template.dat, ignorechimeras=true, aligned=T, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:24:15.531119", "params": {"count": "null", "ignorechimeras": "\"true\"", "dbkey": "\"hg17\"", "qual": "{\"use\": \"no\", \"__current_case__\": 1}", "alignment": "{\"source\": \"history\", \"template\": {\"values\": [{\"src\": \"hda\", \"id\": 2563}]}, \"__current_case__\": 1}", "threshold": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "2427", "id": "e0b8f8f721986493", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_seq_error.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"alignment\|source": "history", "fasta_in": {"src": "hda", "id": "1b8205f65139cc31"}, "alignment\|template": {"src": "hda", "id": "c7d1feb17824923b"}, "qual\|use": "yes", "qual\|alignreport_in": {"src": "hda", "id": "d8dc82f61882a266"}, "qual\|qfile_in": {"src": "hda", "id": "70da4f87b75aff13"}}, "job": {"inputs": {"fasta_in": {"src": "hda", "id": "1b8205f65139cc31", "uuid": "478ca9d3-322b-4068-b94f-0111b59efb11"}, "qfile_in": {"src": "hda", "id": "70da4f87b75aff13", "uuid": "19cdfb37-ff45-4d94-b11f-71656e9bd677"}, "template": {"src": "hda", "id": "c7d1feb17824923b", "uuid": "8b385164-a043-4860-957f-0c59305bea7d"}, "alignreport_in": {"src": "hda", "id": "d8dc82f61882a266", "uuid": "4248447c-9976-4a7d-9406-4ae5c33c2f2a"}}, "update_time": "2018-02-08T18:24:48.000084", "tool_id": "mothur_seq_error", "outputs": {"seq_reverse_out": {"src": "hda", "id": "3912249166cad271", "uuid": "bfc03af8-1d7c-40bb-97bc-982771be91dd"}, "seq_forward_out": {"src": "hda", "id": "f65e64aaf8a7f10a", "uuid": "2d8976df-abbb-41d7-963b-2cb994e4c835"}, "count_out": {"src": "hda", "id": "be576b0744534969", "uuid": "8826c8d6-32bc-4f2b-9ee6-7726fd2b62c0"}, "ref_query_out": {"src": "hda", "id": "903a94902fe885ed", "uuid": "cb6b9beb-3cd2-42ba-a8b8-ff547586997a"}, "matrix_out": {"src": "hda", "id": "0627c045bdb77024", "uuid": "48e3d2f5-2a04-451e-b40e-a3bed16a281a"}, "seq_out": {"src": "hda", "id": "04dcc2b07f73afca", "uuid": "96970c38-c54c-40e2-8ea7-a6af943ede96"}, "qual_forward_out": {"src": "hda", "id": "9a8ce407cbfa5454", "uuid": "b00274e3-fe1f-4fa9-bb5f-5a113e6d9f0a"}, "qual_reverse_out": {"src": "hda", "id": "73cb3a10e2a8b26b", "uuid": "26cba71c-8da2-4e9c-9584-d55a4b7809f4"}, "quality_out": {"src": "hda", "id": "d1fd239c001b68d8", "uuid": "a06f233b-442f-48a8-99f6-ae776f11dd42"}, "summary_out": {"src": "hda", "id": "87efef17dc7885df", "uuid": "8430a187-be22-468b-87ef-40a39cdcf0b1"}, "chimera_out": {"src": "hda", "id": "48b20c4302f2bed8", "uuid": "0515294f-48ed-461b-a2bc-a9a62c7a63c1"}, "logfile": {"src": "hda", "id": "876ad4f8f38f071f", "uuid": "6f101a55-e289-4b9f-a7f1-fda7481c8de4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > seq.error(fasta=fasta_in.dat,reference=alignment.template.dat,qfile=qfi \rle_in.dat,report=alignreport_in.dat,ignorechimeras=true,aligned=T,processors=1)\n\nUsing 1 processors.\nIt took 0 to read 32 sequences.\n10\n\nMultiply error rate by 100 to obtain the percent sequencing errors.\nOverall error rate:\t0.000790514\nErrors\tSequences\n0\t8\n1\t2\nIt took 0 secs to check 10 sequences.\n\nOutput File Names: \nfasta_in.error.summary\nfasta_in.error.seq\nfasta_in.error.chimera\nfasta_in.error.quality\nfasta_in.error.qual.forward\nfasta_in.error.qual.reverse\nfasta_in.error.seq.forward\nfasta_in.error.seq.reverse\nfasta_in.error.count\nfasta_in.error.matrix\nfasta_in.error.ref\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2573.dat' fasta_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2574.dat' alignment.template.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2575.dat' qfile_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2576.dat' alignreport_in.dat && echo 'seq.error( fasta=fasta_in.dat, reference=alignment.template.dat, qfile=qfile_in.dat, report=alignreport_in.dat, ignorechimeras=true, aligned=T, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:24:42.401874", "params": {"count": "null", "ignorechimeras": "\"true\"", "dbkey": "\"hg17\"", "qual": "{\"use\": \"yes\", \"qfile_in\": {\"values\": [{\"src\": \"hda\", \"id\": 2575}]}, \"__current_case__\": 0, \"alignreport_in\": {\"values\": [{\"src\": \"hda\", \"id\": 2576}]}}", "alignment": "{\"source\": \"history\", \"template\": {\"values\": [{\"src\": \"hda\", \"id\": 2574}]}, \"__current_case__\": 1}", "threshold": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "2599", "id": "a4a6e47454aeba8e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_seq_error.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"sff": {"src": "hda", "id": "47a2e2cdac6d4f80"}, "sfftxt": true}, "job": {"inputs": {"sff": {"src": "hda", "id": "47a2e2cdac6d4f80", "uuid": "393c86c5-5fd7-4df8-a7e6-9f9789495e64"}}, "update_time": "2018-02-08T18:25:02.507559", "tool_id": "mothur_sffinfo", "outputs": {"out_sfftxt": {"src": "hda", "id": "f9c99ed753d12938", "uuid": "68756bfd-384a-4a42-a0c3-9859a7304837"}, "logfile": {"src": "hda", "id": "fd0620ae7484e07b", "uuid": "a5960cd3-cbb6-42ab-9c71-c454b280004e"}, "out_flow": {"src": "hda", "id": "c13713d4e8eb4016", "uuid": "2fb32b74-a179-4597-a87e-53ea9941bf22"}, "out_qfile": {"src": "hda", "id": "503dd82632d4ca26", "uuid": "50ee6fa5-42b8-47e5-ba7a-24dbd3831d13"}, "out_fasta": {"src": "hda", "id": "26a0fe97059939a7", "uuid": "211f0070-6853-4960-bfb8-c26a1873def5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sffinfo(sff=sff.dat,fasta=true,qfile=true,sfftxt=true,flow=true,trim=tr \rue)\nExtracting info from sff.dat ...\n10\nIt took 0 secs to extract 10.\n\nOutput File Names: \nsff.sff.txt\nsff.fasta\nsff.qual\nsff.flow\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2589.dat' sff.dat && ln -s 'None' accnos.dat && echo 'sffinfo( sff=sff.dat, fasta=true, qfile=true, sfftxt=true, flow=true, trim=true )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:24:58.805899", "params": {"trim": "\"true\"", "oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "qfile": "\"true\"", "flow": "\"true\"", "dbkey": "\"hg17\"", "sfftxt": "\"true\"", "fasta": "\"true\"", "accnos": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "2700", "id": "e1d20895c4a97cda", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sffinfo.test_tool_000000", "has_data": true}, {"data": {"status": "failure", "inputs": {"sff": {"src": "hda", "id": "bb0ef3014c567e06"}, "oligo\|add": "yes", "oligo\|oligos": {"src": "hda", "id": "738c1dc0cd2bff09"}}, "output_problems": ["History item different than expected\nOutput checksum [cfb0d0595dde77d45b4127bd3517bb78] does not match expected [f03c422fe364815e7214ad31ad135aca] (using hash algorithm md5)."], "job": {"inputs": {"sff": {"src": "hda", "id": "bb0ef3014c567e06", "uuid": "8d6a579c-7351-47ed-946f-102d71d327a5"}, "oligos": {"src": "hda", "id": "738c1dc0cd2bff09", "uuid": "11525dfc-de8b-495e-be2c-cb171928aa12"}}, "update_time": "2018-02-08T18:25:42.054096", "tool_id": "mothur_sffinfo", "outputs": {"logfile": {"src": "hda", "id": "3623f8401cdd50f2", "uuid": "e895e777-80e3-4570-acac-dc3653a75acf"}, "out_flow": {"src": "hda", "id": "2c561ba9c8e1003b", "uuid": "0d5af101-9f8c-431d-881a-5e3b1f0204c8"}, "out_qfile": {"src": "hda", "id": "1e46021b14d0447d", "uuid": "fad20474-627d-4fd3-bf9c-ea781849e5bc"}, "out_scrap": {"src": "hda", "id": "a3acd9d044b84d2e", "uuid": "13c1edf7-7864-452b-bebf-f91ff2a280f0"}, "out_fasta": {"src": "hda", "id": "9f2c5693ba5a738c", "uuid": "91304043-a44f-4fd7-be45-5a6c526ba7c1"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sffinfo(sff=sff.dat,fasta=true,qfile=true,flow=true,trim=true,oligos=ol \rigo.oligos.dat,bdiffs=0,pdiffs=0,tdiffs=0,ldiffs=0,sdiffs=0)\nExtracting info from sff.dat ...\n10\nIt took 0 secs to extract 10.\n\nOutput File Names: \nsff.fasta\nsff.qual\nsff.flow\nsff.scrap.sff\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2595.dat' sff.dat && ln -s 'None' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2596.dat' oligo.oligos.dat && echo 'sffinfo( sff=sff.dat, fasta=true, qfile=true, flow=true, trim=true ,oligos=oligo.oligos.dat ,bdiffs=0 ,pdiffs=0 ,tdiffs=0 ,ldiffs=0 ,sdiffs=0 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:25:38.219069", "params": {"trim": "\"true\"", "oligo": "{\"bdiffs\": \"0\", \"sdiffs\": \"0\", \"ldiffs\": \"0\", \"pdiffs\": \"0\", \"tdiffs\": \"0\", \"add\": \"yes\", \"__current_case__\": 1, \"oligos\": {\"values\": [{\"src\": \"hda\", \"id\": 2596}]}}", "qfile": "\"true\"", "flow": "\"true\"", "dbkey": "\"hg17\"", "sfftxt": "\"false\"", "fasta": "\"true\"", "accnos": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "2822", "id": "227f734e4aa4c9b2", "user_email": "test@bx.psu.edu"}, "problem_log": "Traceback (most recent call last):\n File \"/usr/lib/python2.7/unittest/case.py\", line 329, in run\n testMethod()\n File \"/tmp/saskia/tmpKSDp0p/galaxy-dev/test/functional/test_toolbox.py\", line 317, in test_tool\n self.do_it(td)\n File \"/tmp/saskia/tmpKSDp0p/galaxy-dev/test/functional/test_toolbox.py\", line 83, in do_it\n raise e\nJobOutputsError: History item different than expected\nOutput checksum [cfb0d0595dde77d45b4127bd3517bb78] does not match expected [f03c422fe364815e7214ad31ad135aca] (using hash algorithm md5).\n", "problem_type": "functional.test_toolbox.JobOutputsError"}, "id": "functional.test_toolbox.TestForTool_mothur_sffinfo.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"prob\|lookup": {"src": "hda", "id": "77320b12e7ef91b5"}, "prob\|source": "hist", "flow": {"src": "hda", "id": "60c9b24d33e5937f"}}, "job": {"inputs": {"flow": {"src": "hda", "id": "60c9b24d33e5937f", "uuid": "8d46123d-b3f3-457f-ad4d-024a7458fd04"}, "lookup": {"src": "hda", "id": "77320b12e7ef91b5", "uuid": "c1a56757-fa60-4089-b4db-9369e2c4a563"}}, "update_time": "2018-02-08T18:26:26.039346", "tool_id": "mothur_shhh_flows", "outputs": {"shhh_qual": {"src": "hda", "id": "8e6e70ad3cbf6f5b", "uuid": "69442f06-4b7a-4d79-9770-a016c935e627"}, "shhh_fasta": {"src": "hda", "id": "d72069b333912103", "uuid": "bf6ce55b-137f-495e-b1c6-ee26b34f831b"}, "logfile": {"src": "hda", "id": "2a9e71b0254082e4", "uuid": "f11c3307-a478-43e9-9cb6-d86d89a9d4a0"}, "shhh_names": {"src": "hda", "id": "fdd8c264ffdf0e15", "uuid": "630abd25-463a-4776-8f78-158cdb5f1f01"}, "shhh_groups": {"src": "hda", "id": "146f0f4a4c131555", "uuid": "047263be-7f66-4515-85df-25d06897dbc5"}, "shhh_counts": {"src": "hda", "id": "818c72f58eb43f6e", "uuid": "2b64f07c-3445-420d-8470-adb7619c2d58"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > shhh.flows(flow=flow.dat,lookup=lookup.dat,maxiter=1000,mindelta=0.0000 \r01000000,cutoff=0.01,sigma=0.06,order=A,large=10000,processors=1)\n\nUsing 1 processors.\n\nDivided flow.dat into 1 files.\n\n\n>>>>>\tProcessing flow.dat0.temp (file 1 of 1)\t<<<<<\nReading flowgrams...\nIdentifying unique flowgrams...\nCalculating distances between flowgrams...\n0\t0\t3e-06\n92\t0\t0.007893\n\nTotal time: 0\t0.016342\n\nClustering flowgrams...\n******************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\n\nDenoising 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08686\n983\t1.80003e-05\t-137.977\t0\t0.008962\n984\t1.7897e-05\t-137.977\t0\t0.008972\n985\t1.77943e-05\t-137.977\t0\t0.008752\n986\t1.76922e-05\t-137.977\t0\t0.008905\n987\t1.75907e-05\t-137.977\t0\t0.008841\n988\t1.74898e-05\t-137.977\t0\t0.008855\n989\t1.73895e-05\t-137.977\t0\t0.008889\n990\t1.72897e-05\t-137.977\t0\t0.008923\n991\t1.71905e-05\t-137.977\t0\t0.008746\n992\t1.70919e-05\t-137.977\t0\t0.008875\n993\t1.69938e-05\t-137.977\t0\t0.008746\n994\t1.68963e-05\t-137.977\t0\t0.008762\n995\t1.67994e-05\t-137.977\t0\t0.008854\n996\t1.6703e-05\t-137.977\t0\t0.008782\n997\t1.66071e-05\t-137.977\t0\t0.008768\n998\t1.65119e-05\t-137.977\t0\t0.0088\n999\t1.64171e-05\t-137.977\t0\t0.008842\n1000\t1.63229e-05\t-137.977\t0\t0.008814\n\nFinalizing...\nTotal time to process flow.dat:\t10\t9.25086\n\nOutput File Names: \nflow.shhh.qual\nflow.shhh.fasta\nflow.shhh.names\nflow.shhh.counts\nflow.shhh.groups\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2602.dat' flow.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2603.dat' lookup.dat && echo 'shhh.flows( flow=flow.dat, lookup=lookup.dat, maxiter=1000, mindelta=0.000001000000, cutoff=0.01, sigma=0.06, order=A, large=10000, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:26:13.200749", "params": {"cutoff": "\"0.01\"", "mindelta": "\"1e-06\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "order": "\"A\"", "large": "\"10000\"", "maxiter": "\"1000\"", "sigma": "\"0.06\"", "prob": "{\"source\": \"hist\", \"lookup\": {\"values\": [{\"src\": \"hda\", \"id\": 2603}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "2971", "id": "0a751ae1f530d3b0", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_shhh_flows.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "5777a6cd586901d1"}, "name": {"src": "hda", "id": "e133ff35d26a8aa1"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "5777a6cd586901d1", "uuid": "1cc6590e-9390-471b-a21c-74538fdc1b4a"}, "name": {"src": "hda", "id": "e133ff35d26a8aa1", "uuid": "cb099a08-1915-49f5-b316-653980bb6909"}}, "update_time": "2018-02-08T18:27:08.235372", "tool_id": "mothur_shhh_seqs", "outputs": {"shhh_fasta": {"src": "hda", "id": "b19ebbe1c1d1e884", "uuid": "d9994bf8-4f31-4d47-96fc-2f72512afb63"}, "logfile": {"src": "hda", "id": "a49605dd668f2992", "uuid": "9cc76af6-07f5-458a-878f-d84c573e7999"}, "shhh_map": {"src": "hda", "id": "e64b5914d8ba7854", "uuid": "5f9bd29b-c4a9-411d-8543-68f262cdc3b8"}, "shhh_names": {"src": "hda", "id": "3e4ace9eb2eabedd", "uuid": "5834d8cb-f75c-4513-9458-3678121edd82"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > shhh.seqs(fasta=fasta.dat,name=name.dat,sigma=0.01,processors=1)\n\nUsing 1 processors.\n\nCalculating distances...\n0\t0\n9\t0\nDone.\n/**************************************/\nRunning command: cluster(phylip=fasta.shhh.dist, method=furthest, cutoff=0.08)\n\nUsing 1 processors.\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\nunique\t2\t8\t1\n0.05\t2\t6\t2\nIt took 0 seconds to cluster\n\nOutput File Names: \nfasta.shhh.fn.sabund\nfasta.shhh.fn.rabund\nfasta.shhh.fn.list\n\n/**************************************/\n\nOutput File Names: \nfasta.shhh_seqs.map\nfasta.shhh_seqs.fasta\nfasta.shhh_seqs.names\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2610.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2611.dat' name.dat && ln -s 'None' group.dat && echo 'shhh.seqs( fasta=fasta.dat, name=name.dat, sigma=0.01, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:27:04.735094", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "group": "null", "sigma": "\"0.01\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "3138", "id": "5bc2b2daf3f5f2ab", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_shhh_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta_in": {"src": "hda", "id": "1cd50e97ce5776f1"}}, "job": {"inputs": {"fasta_in": {"src": "hda", "id": "1cd50e97ce5776f1", "uuid": "9e7a7665-6ca5-4527-a9e9-a63baa6cbfed"}}, "update_time": "2018-02-08T18:27:39.681966", "tool_id": "mothur_sort_seqs", "outputs": {"logfile": {"src": "hda", "id": "346c6a409ca2df72", "uuid": "42f2fa77-d96e-4a9c-8939-d912cb67fc1a"}, "fasta_out": {"src": "hda", "id": "4628ae23f7bf7c59", "uuid": "8900356a-102f-4939-a96f-2d0a8afcf3b9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sort.seqs(fasta=fasta_in.dat,large=false)\n\nUsing fasta_in.dat to determine the order. It contains 98 sequences.\n\nOutput File Names: \nfasta_in.sorted.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2616.dat' fasta_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' flow_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' tax_in.dat && ln -s 'None' accnos.dat && ln -s 'None' count.dat && echo 'sort.seqs( fasta=fasta_in.dat, large=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:27:35.785519", "params": {"count": "null", "accnos": "null", "dbkey": "\"hg17\"", "large": "\"false\"", "group_in": "null", "tax_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "flow_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "3256", "id": "25291f5c38a3933e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sort_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"qfile_in": {"src": "hda", "id": "824743428f8b7c8d"}}, "job": {"inputs": {"qfile_in": {"src": "hda", "id": "824743428f8b7c8d", "uuid": "c9c55f34-7a04-43e3-bb69-ac0f242ccad2"}}, "update_time": "2018-02-08T18:27:59.212444", "tool_id": "mothur_sort_seqs", "outputs": {"logfile": {"src": "hda", "id": "31e158d4a9000232", "uuid": "808de0d3-c1fc-4457-91df-b06e3bcfe3b4"}, "qfile_out": {"src": "hda", "id": "db53bbfda4df48de", "uuid": "cbf4ab99-8973-422b-bd93-f147f201103d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sort.seqs(qfile=qfile_in.dat,large=false)\n\nUsing qfile_in.dat to determine the order. It contains 25 sequences.\n\nOutput File Names: \nqfile_in.sorted.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s 'None' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2619.dat' qfile_in.dat && ln -s 'None' flow_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' tax_in.dat && ln -s 'None' accnos.dat && ln -s 'None' count.dat && echo 'sort.seqs( qfile=qfile_in.dat, large=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:27:56.051824", "params": {"count": "null", "fasta_in": "null", "dbkey": "\"hg17\"", "large": "\"false\"", "group_in": "null", "tax_in": "null", "accnos": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "flow_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "3351", "id": "211e907a60c908e9", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sort_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"group_in": {"src": "hda", "id": "16d880b4edd0df2d"}}, "job": {"inputs": {"group_in": {"src": "hda", "id": "16d880b4edd0df2d", "uuid": "75b739f3-ddc0-4f71-9c88-3d21ab47d1e8"}}, "update_time": "2018-02-08T18:28:18.033002", "tool_id": "mothur_sort_seqs", "outputs": {"group_out": {"src": "hda", "id": "3f996a02633eb191", "uuid": "0dbf0bc4-fcc8-44d2-a46f-0a9215046bf8"}, "logfile": {"src": "hda", "id": "8cbd5613d4a60bc9", "uuid": "405d9f6c-ca17-411f-847c-25be73d2e6a7"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sort.seqs(group=group_in.dat,large=false)\n\nUsing group_in.dat to determine the order. It contains 98 sequences.\n\nOutput File Names: \ngroup_in.sorted.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s 'None' fasta_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' flow_in.dat && ln -s 'None' name_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2622.dat' group_in.dat && ln -s 'None' tax_in.dat && ln -s 'None' accnos.dat && ln -s 'None' count.dat && echo 'sort.seqs( group=group_in.dat, large=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:28:13.805640", "params": {"count": "null", "accnos": "null", "fasta_in": "null", "dbkey": "\"hg17\"", "large": "\"false\"", "tax_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "flow_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "3445", "id": "0a2f8c1113cd2df5", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sort_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"count": {"src": "hda", "id": "8bf06e7b389a0ffb"}, "fasta_in": {"src": "hda", "id": "d1826c27f8cbf4a0"}}, "job": {"inputs": {"count": {"src": "hda", "id": "8bf06e7b389a0ffb", "uuid": "8e56c30e-7b59-4767-991f-d9688891c932"}, "fasta_in": {"src": "hda", "id": "d1826c27f8cbf4a0", "uuid": "98024751-92aa-4a52-aafd-26a9121a53e3"}}, "update_time": "2018-02-08T18:28:40.437807", "tool_id": "mothur_sort_seqs", "outputs": {"logfile": {"src": "hda", "id": "a300c5f999d0cfba", "uuid": "9ca6f143-214e-4fc6-adcc-6162c94689f3"}, "fasta_out": {"src": "hda", "id": "a46cf8d4ce36a708", "uuid": "16dd653a-47fd-4e16-bd9a-591390988f25"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sort.seqs(fasta=fasta_in.dat,count=count.dat,large=false)\n\nUsing fasta_in.dat to determine the order. It contains 98 sequences.\nOrdered 96 sequences from count.dat.\n\nOutput File Names: \nfasta_in.sorted.dat\ncount.sorted.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2625.dat' fasta_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' flow_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' tax_in.dat && ln -s 'None' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2626.dat' count.dat && echo 'sort.seqs( fasta=fasta_in.dat, count=count.dat, large=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:28:37.404630", "params": {"accnos": "null", "dbkey": "\"hg17\"", "large": "\"false\"", "group_in": "null", "tax_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "flow_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "3576", "id": "b2c5ddb42b4715c3", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sort_seqs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"group_in": {"src": "hda", "id": "c76193b10ac0b663"}, "fasta_in": {"src": "hda", "id": "e706d88604ad5bf3"}, "qfile_in": {"src": "hda", "id": "ba12713cb9628bec"}}, "job": {"inputs": {"group_in": {"src": "hda", "id": "c76193b10ac0b663", "uuid": "c6a6d783-c7c1-493d-be2f-a876d6323589"}, "fasta_in": {"src": "hda", "id": "e706d88604ad5bf3", "uuid": "991a3a59-3d83-4fae-b11a-65f430fdd634"}, "qfile_in": {"src": "hda", "id": "ba12713cb9628bec", "uuid": "02124aba-f4fe-4838-ba90-cb365b9e2576"}}, "update_time": "2018-02-08T18:29:05.595883", "tool_id": "mothur_sort_seqs", "outputs": {"fasta_out": {"src": "hda", "id": "c7b310e48f70e08a", "uuid": "b17499bf-c0d5-4d5b-b7c3-9f4f404ec20b"}, "group_out": {"src": "hda", "id": "33554e7d04f7eca7", "uuid": "e3eafd81-6d26-49ba-9f8a-d6c6a9c8ad6e"}, "logfile": {"src": "hda", "id": "ebfc3f08b652b108", "uuid": "97d399d6-1351-47df-900d-f6ffaca100a0"}, "qfile_out": {"src": "hda", "id": "b04e7e1be4882fea", "uuid": "8ddadd71-545d-482b-a95b-0178f6f4931d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sort.seqs(fasta=fasta_in.dat,qfile=qfile_in.dat,group=group_in.dat,larg \re=false)\n\nUsing fasta_in.dat to determine the order. It contains 98 sequences.\nM00967_43_000000000-A3JHG_1_1101_19936_3208 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_15923_3823 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_14010_4122 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_10776_4204 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_22487_4260 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_13293_4703 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_24357_4866 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_23552_5194 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_7326_5417 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_11148_6457 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_7079_6722 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_8607_6805 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_15208_7185 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_4525_7317 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_9121_7358 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_8480_7498 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_11790_7581 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_20566_7622 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_10073_7632 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_5170_7771 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_18966_7778 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_5494_7973 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_10246_8076 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_23931_8157 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_18269_8162 was not in the contained the file which determined the order, adding it to the end.\nOrdered 25 sequences from qfile_in.dat.\nOrdered 98 sequences from group_in.dat.\n\nOutput File Names: \nfasta_in.sorted.dat\nqfile_in.sorted.dat\ngroup_in.sorted.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2629.dat' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2630.dat' qfile_in.dat && ln -s 'None' flow_in.dat && ln -s 'None' name_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2631.dat' group_in.dat && ln -s 'None' tax_in.dat && ln -s 'None' accnos.dat && ln -s 'None' count.dat && echo 'sort.seqs( fasta=fasta_in.dat, qfile=qfile_in.dat, group=group_in.dat, large=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:29:02.185987", "params": {"count": "null", "dbkey": "\"hg17\"", "large": "\"false\"", "tax_in": "null", "accnos": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "flow_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "3731", "id": "0b396aab4382c1fc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sort_seqs.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"search\|input": {"src": "hda", "id": "cdd1b52138ec3e26"}, "cutoff": "1", "fasta": {"src": "hda", "id": "9db5f5afb41f3f39"}, "search\|type": "count", "accnos": true}, "job": {"inputs": {"input": {"src": "hda", "id": "cdd1b52138ec3e26", "uuid": "f97d3777-7d5a-496e-a5b7-7b011b6d852e"}, "fasta": {"src": "hda", "id": "9db5f5afb41f3f39", "uuid": "a7691f15-bd94-4b72-b433-456b92cec73b"}}, "update_time": "2018-02-08T18:29:36.918042", "tool_id": "mothur_split_abund", "outputs": {"rare_accnos": {"src": "hda", "id": "05138872ca68fd64", "uuid": "ea36fba9-61ad-42b7-b35f-5520c9a4d20b"}, "abund_accnos": {"src": "hda", "id": "a35b136816ca4ba6", "uuid": "3c3ae35d-b8cc-416d-9944-0e815e007ca2"}, "abund_count": {"src": "hda", "id": "91276d14d453a3b2", "uuid": "896492f3-c80a-4355-90ba-18c48015365b"}, "rare_count": {"src": "hda", "id": "63060f896ee9403e", "uuid": "2ec8cd6d-b418-41a4-a12f-016c3c9f4dec"}, "logfile": {"src": "hda", "id": "f678f751d18ba8c1", "uuid": "04e53333-620c-42af-bc0e-f31a264d2031"}, "rare_fasta": {"src": "hda", "id": "2efa83e2c9a3aa93", "uuid": "9c58ec60-46e1-467b-8277-c15fb5e74f9d"}, "abund_fasta": {"src": "hda", "id": "61dab379dc68ff95", "uuid": "dc7edc84-60bb-4e28-959e-2e9bbfb5cec4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > split.abund(fasta=fasta.dat,count=search_input.dat,accnos=true,cutoff=1 \r)\nYou cannot pick groups without group info in your count file; I will disregard your groups selection.\nU68620 is not in your names or list file, ignoring.\nU68667 is not in your names or list file, ignoring.\n\nOutput File Names: \nsearch_input.rare.count_table\nsearch_input.abund.count_table\nrare.accnos\nabund.accnos\nfasta.rare.fasta\nfasta.abund.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2636.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2637.dat' search_input.dat && echo 'split.abund( fasta=fasta.dat, count=search_input.dat, accnos=true, cutoff=1 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:29:33.061698", "params": {"cutoff": "\"1\"", "search": "{\"input\": {\"values\": [{\"src\": \"hda\", \"id\": 2637}]}, \"type\": \"count\", \"__current_case__\": 2}", "dbkey": "\"hg17\"", "split": "{\"dosplit\": \"no\", \"__current_case__\": 1}", "accnos": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "3854", "id": "35c110361200e678", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_split_abund.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"search\|input": {"src": "hda", "id": "d7e1f95024c927b1"}, "cutoff": "1", "fasta": {"src": "hda", "id": "9cd1e40020f8e503"}, "search\|type": "name", "accnos": true}, "job": {"inputs": {"input": {"src": "hda", "id": "d7e1f95024c927b1", "uuid": "7dc73945-9565-471d-b4fa-4bd8a597de34"}, "fasta": {"src": "hda", "id": "9cd1e40020f8e503", "uuid": "87d8b73f-3f9f-4a3a-afc6-813cec7c4224"}}, "update_time": "2018-02-08T18:30:27.641772", "tool_id": "mothur_split_abund", "outputs": {"abund_names": {"src": "hda", "id": "f791823f89c6163a", "uuid": "7aa7cb68-2cfc-4c17-9401-c1b551ecf743"}, "rare_names": {"src": "hda", "id": "d1ac60a58050f6ed", "uuid": "e4a6a0c5-eb4c-4d24-8617-1dc1aa54a082"}, "rare_accnos": {"src": "hda", "id": "db502a362bf63aa5", "uuid": "1e51b011-00bb-4ffa-8ccd-a0d66e5e5152"}, "abund_accnos": {"src": "hda", "id": "e3466765404e7b1c", "uuid": "247d27da-0689-4e33-b7d3-4b6235ba0cab"}, "logfile": {"src": "hda", "id": "fc26c44486a936db", "uuid": "19c47713-a360-477c-8985-ed31d2e2c3a4"}, "rare_fasta": {"src": "hda", "id": "ab82f8d568f8fb18", "uuid": "463dd8c9-26dd-4416-9b1a-6a5fd9f4c2df"}, "abund_fasta": {"src": "hda", "id": "11d9965bae4dbe18", "uuid": "efd16a42-3ca0-42c4-9844-963d7cfccc31"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > split.abund(fasta=fasta.dat,name=search_input.dat,accnos=true,cutoff=1) \r\u001b[A\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[K)\nU68620 is not in your names or list file, ignoring.\nU68667 is not in your names or list file, ignoring.\n\nOutput File Names: \nsearch_input.rare.names\nsearch_input.abund.names\nsearch_input.rare.accnos\nsearch_input.abund.accnos\nfasta.rare.fasta\nfasta.abund.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2645.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2646.dat' search_input.dat && echo 'split.abund( fasta=fasta.dat, name=search_input.dat, accnos=true, cutoff=1 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:30:23.593046", "params": {"cutoff": "\"1\"", "search": "{\"input\": {\"values\": [{\"src\": \"hda\", \"id\": 2646}]}, \"type\": \"name\", \"__current_case__\": 0}", "dbkey": "\"hg17\"", "split": "{\"dosplit\": \"no\", \"__current_case__\": 1}", "accnos": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "3979", "id": "3f65e49d411bc75a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_split_abund.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"search\|input": {"src": "hda", "id": "32fe67477db245f3"}, "cutoff": "1", "search\|type": "name", "split\|dosplit": "yes", "split\|groups": ["forest", "pasture"], "split\|group": {"src": "hda", "id": "3d0e97279f557300"}, "fasta": {"src": "hda", "id": "c2087ad656f5fd9b"}, "accnos": true}, "job": {"inputs": {"input": {"src": "hda", "id": "32fe67477db245f3", "uuid": "fdf6e7df-2c44-4074-9c6b-8bd1c696aac9"}, "fasta": {"src": "hda", "id": "c2087ad656f5fd9b", "uuid": "ebbabcec-254a-49dc-b629-f6187045222f"}, "group": {"src": "hda", "id": "3d0e97279f557300", "uuid": "9ea1d5dd-7a33-4e51-b05d-195c622a3e6d"}}, "update_time": "2018-02-08T18:31:24.163950", "tool_id": "mothur_split_abund", "outputs": {"abund_names": {"src": "hda", "id": "3220fd9000201448", "uuid": "1b92abd6-a9e4-443c-9ef2-4fbdce603b9f"}, "__new_primary_file_pasture\|pasture__": {"src": "hda", "id": "b17c01ef6787726a", "uuid": "857bb644-caec-4d2e-a8cc-8c0a5a3a2ef2"}, "rare_accnos": {"src": "hda", "id": "8d1eae6dc7520e79", "uuid": "c3b60632-0579-497d-928e-f5220103ac0c"}, "abund_groups": {"src": "hda", "id": "61f64de29b08b609", "uuid": "bc78c0ea-7561-436d-9d35-d7e9f1f33acd"}, "rare_groups": {"src": "hda", "id": "cd67d5a3e6361697", "uuid": "a95f69ca-b6cc-474e-b34f-5502a685396a"}, "abund_accnos": {"src": "hda", "id": "52716b0ebe92fa96", "uuid": "5f2b1f65-bf25-44a4-8d30-07881af0d9ab"}, "__new_primary_file_pasture\|forest__": {"src": "hda", "id": "546df6a89628ce23", "uuid": "06404d8a-b8cc-4666-b24b-14b417fa99e7"}, "logfile": {"src": "hda", "id": "0b9ed415b6d11582", "uuid": "b0cc327d-b3f1-4227-be98-ca2b7db2f6af"}, "rare_fasta": {"src": "hda", "id": "606329f9408a9a88", "uuid": "3653c7f2-b854-4803-9482-7f99fdaa5890"}, "abund_fasta": {"src": "hda", "id": "8cbfae124c6c8023", "uuid": "d9262219-3839-4331-8094-4823c755ccc1"}, "rare_names": {"src": "hda", "id": "ee2119e1cbbc112d", "uuid": "63d0f8b0-a860-4e54-8784-985282623795"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > split.abund(fasta=fasta.dat,name=search_input.dat,group=split_group.dat \r,groups=forest-pasture,accnos=true,cutoff=1)\nU68620 is not in your names or list file, ignoring.\nU68667 is not in your names or list file, ignoring.\n\nOutput File Names: \nsearch_input.forest.abund.names\nsearch_input.forest.rare.names\nsearch_input.pasture.abund.names\nsearch_input.pasture.rare.names\nsplit_group.forest.abund.groups\nsplit_group.forest.rare.groups\nsplit_group.pasture.abund.groups\nsplit_group.pasture.rare.groups\nsearch_input.forest.abund.accnos\nsearch_input.forest.rare.accnos\nsearch_input.pasture.abund.accnos\nsearch_input.pasture.rare.accnos\nfasta.forest.abund.fasta\nfasta.forest.rare.fasta\nfasta.pasture.abund.fasta\nfasta.pasture.rare.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2654.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2655.dat' search_input.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2656.dat' split_group.dat && echo 'split.abund( fasta=fasta.dat, name=search_input.dat, group=split_group.dat, groups=forest-pasture, accnos=true, cutoff=1 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:31:18.285897", "params": {"cutoff": "\"1\"", "search": "{\"input\": {\"values\": [{\"src\": \"hda\", \"id\": 2655}]}, \"type\": \"name\", \"__current_case__\": 0}", "dbkey": "\"hg17\"", "split": "{\"dosplit\": \"yes\", \"group\": {\"values\": [{\"src\": \"hda\", \"id\": 2656}]}, \"groups\": [\"forest\", \"pasture\"], \"__current_case__\": 0}", "accnos": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n/tmp/saskia/tmpKSDp0p/job_working_directory/000/727/galaxy_727.sh: line 40: [: /tmp/saskia/tmpKSDp0p/job_working_directory/000/727/working/fasta.forest.abund.fasta: binary operator expected\n/tmp/saskia/tmpKSDp0p/job_working_directory/000/727/galaxy_727.sh: line 40: [: /tmp/saskia/tmpKSDp0p/job_working_directory/000/727/working/fasta.forest.rare.fasta: binary operator expected\n/tmp/saskia/tmpKSDp0p/job_working_directory/000/727/galaxy_727.sh: line 40: [: /tmp/saskia/tmpKSDp0p/job_working_directory/000/727/working/search_input.forest.abund.names: binary operator expected\n/tmp/saskia/tmpKSDp0p/job_working_directory/000/727/galaxy_727.sh: line 40: [: /tmp/saskia/tmpKSDp0p/job_working_directory/000/727/working/search_input.forest.rare.names: binary operator expected\n/tmp/saskia/tmpKSDp0p/job_working_directory/000/727/galaxy_727.sh: line 40: [: /tmp/saskia/tmpKSDp0p/job_working_directory/000/727/working/search_input.forest.abund.accnos: binary operator expected\n/tmp/saskia/tmpKSDp0p/job_working_directory/000/727/galaxy_727.sh: line 40: [: /tmp/saskia/tmpKSDp0p/job_working_directory/000/727/working/search_input.forest.rare.accnos: binary operator expected\n", "job_metrics": [], "model_class": "Job", "external_id": "4120", "id": "8398b6d40e2a8a5d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_split_abund.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"search\|input": {"src": "hda", "id": "a91c1fc0bea9aceb"}, "cutoff": "2", "search\|type": "list", "split\|dosplit": "yes", "split\|groups": ["forest", "pasture"], "split\|group": {"src": "hda", "id": "38625663880471ee"}, "fasta": {"src": "hda", "id": "9d6afbc2e4d51931"}, "accnos": true}, "job": {"inputs": {"input": {"src": "hda", "id": "a91c1fc0bea9aceb", "uuid": "e90e80a1-a39b-4caa-a737-1cc3a752ad15"}, "fasta": {"src": "hda", "id": "9d6afbc2e4d51931", "uuid": "077c9849-0f47-47e2-b871-4e78e1e080e4"}, "group": {"src": "hda", "id": "38625663880471ee", "uuid": "34f1049d-d4a0-4016-8bb1-9624460bac3f"}}, "update_time": "2018-02-08T18:33:04.548476", "tool_id": "mothur_split_abund", "outputs": 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"__new_primary_file_unique.pasture\|0.18.pasture__": {"src": "hda", "id": "88c3e2aa0e098102", "uuid": "95c4c608-e0c5-4599-8129-a991a9bc9944"}, "__new_primary_file_unique.pasture\|0.03.pasture__": {"src": "hda", "id": "41eb5160056d0dd7", "uuid": "5f5146d2-30ef-45c6-a740-48c6088b5c36"}, "__new_primary_file_pasture.unique\|forest.0.06__": {"src": "hda", "id": "f1735000ceaa96c7", "uuid": "fd647ae7-3a87-4b2a-8bb5-fd12cd5d3c03"}, "__new_primary_file_unique.pasture\|0.17.forest__": {"src": "hda", "id": "e92007f01f461c3b", "uuid": "b5d29455-87c4-4b8b-ab60-c669a45f14ff"}, "__new_primary_file_unique.pasture\|0.21.forest__": {"src": "hda", "id": "a72cfe8d7dc00791", "uuid": "40c6c7b4-ea5f-4c18-8cd7-10323eeae6ef"}, "__new_primary_file_unique.pasture\|unique.forest__": {"src": "hda", "id": "67eef77c2f9bcaa2", "uuid": "d1d40e8c-eaf0-4454-8797-f71a5b0b4460"}, "__new_primary_file_unique.pasture\|0.26.forest__": {"src": "hda", "id": "a1ccf4ae9b8614ff", "uuid": "4a7e4482-82ac-4fcf-a4ad-235db114182c"}, "__new_primary_file_pasture.unique\|pasture.0.21__": {"src": "hda", "id": "606e3ef8eac308b5", "uuid": "47dd1200-1fdc-415a-9e18-fb12611da2b0"}, "__new_primary_file_unique.pasture\|0.45.forest__": {"src": "hda", "id": "22cb5fc644c58a5a", "uuid": "df612a46-d11d-4ecf-af77-e9e4d16d9fed"}, "__new_primary_file_unique.pasture\|0.33.pasture__": {"src": "hda", "id": "0e56755c1543e19a", "uuid": "81f52878-1f03-4a9a-8fb8-7f1da327a7ee"}, "__new_primary_file_unique.pasture\|0.08.pasture__": {"src": "hda", "id": "ad0ff5ee11869c5b", "uuid": "6e07bc5b-9d87-4e60-961e-42a684cb80c5"}, "__new_primary_file_unique.pasture\|0.11.pasture__": {"src": "hda", "id": "e0c9f8fa9e2a9a1f", "uuid": "84475843-31c2-4274-87a6-6239685b92a6"}, "__new_primary_file_unique.pasture\|0.29.forest__": {"src": "hda", "id": "ed0f3d9d31cb16f5", "uuid": "51a716d4-b71d-4f70-8129-46144cf47b3e"}, "__new_primary_file_pasture.unique\|pasture.0.04__": {"src": "hda", "id": "4afaca0e255a3fe7", "uuid": "c4d2c701-31c8-414c-9352-4d520978ea7a"}, "__new_primary_file_pasture.unique\|forest.0.10__": {"src": "hda", "id": "5ff6f23d86855864", "uuid": "7dd79160-7908-48f3-bc7c-20af82f4f5ca"}, "__new_primary_file_pasture.unique\|pasture.0.17__": {"src": "hda", "id": "3b764b52f1bd148c", "uuid": "41f2de98-340b-4b87-ad59-ddd9294b5d4a"}, "__new_primary_file_unique.pasture\|0.16.forest__": {"src": "hda", "id": "f5edbdc74c048cb7", "uuid": "e6497537-42bd-4fb0-ab43-566a25a3d7d5"}, "__new_primary_file_unique.pasture\|0.09.forest__": {"src": "hda", "id": "3ad46d0876505527", "uuid": "38cb5145-ce69-4a7f-b0f8-abc2c2cd59d9"}, "__new_primary_file_pasture.unique\|pasture.0.11__": {"src": "hda", "id": "642c89e257077ace", "uuid": "a8b01cdd-73eb-4c36-a64f-7eae63b450f9"}, "__new_primary_file_unique.pasture\|0.07.forest__": {"src": "hda", "id": "b7ab6693497f1546", "uuid": "a7760d4a-8331-480b-985e-6ede1a474803"}, "__new_primary_file_pasture.unique\|forest.0.33__": {"src": "hda", "id": "9b721d17ce9398bd", "uuid": "9a19302c-584b-4e8f-9737-200cc5504d5f"}, "__new_primary_file_pasture.unique\|pasture.0.27__": {"src": "hda", "id": "a7f9f960bf14b912", "uuid": "de677757-63a9-4c9a-a31a-7ba42d194c30"}, "__new_primary_file_unique.pasture\|0.13.pasture__": {"src": "hda", "id": "cb22b884c09c9a4a", "uuid": "0ef4646b-df13-47c4-95d5-92e341c1ed9a"}, "__new_primary_file_pasture.unique\|pasture.0.13__": {"src": "hda", "id": "77c59cb779645430", "uuid": "0fb2e472-7021-4f76-959f-7f0c93577af2"}, "__new_primary_file_pasture.unique\|pasture.0.09__": {"src": "hda", "id": "e9a0109cf14053bb", "uuid": "920261f9-8b79-4e21-84b1-a31638d23eff"}, "__new_primary_file_unique.pasture\|0.15.forest__": {"src": "hda", "id": "3e23ba40b1da2c39", "uuid": "4825aede-38ba-4462-bde9-90ee0c91c263"}, "__new_primary_file_unique.pasture\|0.38.forest__": {"src": "hda", "id": "f1dd4f7bf6c1b572", "uuid": "c0cefec2-aa56-49ca-a8fb-58a8eeaf8596"}, "__new_primary_file_pasture.unique\|forest.0.05__": {"src": "hda", "id": "27120e02373f6774", "uuid": "256e47e3-bb06-4757-9c3f-051b94801ea4"}, "__new_primary_file_unique.pasture\|0.14.forest__": {"src": "hda", "id": "ca9771e82e1e81c0", "uuid": "10b40e6f-aa2a-4bba-b371-2fee16151cd1"}, "__new_primary_file_unique.pasture\|0.23.pasture__": {"src": "hda", "id": "28a3d07ded47537c", "uuid": "d427bbdb-c901-4ae8-9221-882014b34fd8"}, "__new_primary_file_pasture.unique\|forest.0.22__": {"src": "hda", "id": "acc1e364ecb5d595", "uuid": "d75870b8-fc57-46db-a12b-f0912b17eda1"}, "__new_primary_file_unique.pasture\|0.22.forest__": {"src": "hda", "id": "d7df3153d415bfb1", "uuid": "5d36b538-f42a-4d1b-b005-4c30f8ccb016"}, "__new_primary_file_pasture.unique\|forest.0.03__": {"src": "hda", "id": "9c2ad00c99c65fad", "uuid": "da1e4bad-6d4f-4b5d-998e-dbbb759c89ac"}, "__new_primary_file_unique.pasture\|0.55.forest__": {"src": "hda", "id": "0ffa75d02bcbec96", "uuid": "8af734ca-679b-49d0-856b-c8bd0d7bc56a"}, "__new_primary_file_unique.pasture\|0.20.pasture__": {"src": "hda", "id": "7e19a36c8d7f6ccd", "uuid": "d92904d4-9498-49c7-bd5d-82fa5d7a0c3c"}, "__new_primary_file_unique.pasture\|0.32.pasture__": {"src": "hda", "id": "226ed7c9e7c4dde3", "uuid": "345e7498-4b17-4b44-a53a-e727a3ea3e69"}, "__new_primary_file_pasture.unique\|pasture.0.01__": {"src": "hda", "id": "9d880b6fef8dd1a7", "uuid": "25dc2cde-c472-4650-8f7b-404c88bf6aca"}, "__new_primary_file_unique.pasture\|0.05.forest__": {"src": "hda", "id": "f4c6523a3f3132e1", "uuid": "cbbdf025-f779-4d69-9f55-e2d6d024256f"}, "__new_primary_file_pasture.unique\|forest.0.01__": {"src": "hda", "id": "733d33a681415efe", "uuid": "998de589-eeb4-4eaf-ac51-5935afdafa59"}, "__new_primary_file_pasture.unique\|forest.unique__": {"src": "hda", "id": "164f6a2d7032da6e", "uuid": "6d946417-d1b0-4d1e-b4f1-320ecc9a70f9"}, "__new_primary_file_unique.pasture\|0.08.forest__": {"src": "hda", "id": "c9bfc8877335e3a8", "uuid": "2f9981d8-4e3c-492e-8b6a-b348809cb939"}, "__new_primary_file_pasture.unique\|forest.0.07__": {"src": "hda", "id": "1dc5ab55aa6b887f", "uuid": "86f55ec4-3914-49d1-8d04-d76b7944fae9"}, "__new_primary_file_pasture.unique\|pasture.0.32__": {"src": "hda", "id": "26c0054211fe320f", "uuid": "08e089c0-49df-42b7-8e4b-77a493ed56d9"}, "__new_primary_file_unique.pasture\|0.32.forest__": {"src": "hda", "id": "0c5bf0fee2c9f2f2", "uuid": "54703ca7-1b6b-425e-99e3-9b443b9dc764"}, "__new_primary_file_unique.pasture\|0.26.pasture__": {"src": "hda", "id": "ed3993a642a536c2", "uuid": "55fda38d-9035-46c3-9479-4ba397cd8e96"}, "__new_primary_file_pasture.unique\|forest.0.25__": {"src": "hda", "id": "d4e6425fff4b7b44", "uuid": "dbaa8103-4e50-4ccc-a63d-d6f071d35ec8"}, "__new_primary_file_unique.pasture\|0.15.pasture__": {"src": "hda", "id": "e07ab57151a51654", "uuid": "f0ea7182-bb30-4012-bf7e-06f2c98ecff8"}, "__new_primary_file_unique.pasture\|0.36.pasture__": {"src": "hda", "id": "aaff7b2db40e0f9b", "uuid": "bde40b31-480e-43fc-b06c-90caf6fa0966"}, "__new_primary_file_unique.pasture\|0.24.forest__": {"src": "hda", "id": "d7b4881ce8f2a650", "uuid": "403d4138-0734-4e0e-beb8-37b8fed1c9a5"}, "__new_primary_file_pasture.unique\|forest.0.11__": {"src": "hda", "id": "0f9d27ef44328c88", "uuid": "4f8c9396-37ca-4d86-bbf6-3af3f9bd3514"}, "__new_primary_file_unique.pasture\|0.14.pasture__": {"src": "hda", "id": "d7384c1e0a3adbb9", "uuid": "224cc942-84dc-4272-ae33-0ffd664c3469"}, "__new_primary_file_pasture.unique\|forest.0.36__": {"src": "hda", "id": "786cdb8512e719d3", "uuid": "29a13eb1-237f-4fb9-8de7-2b92ba28252f"}, "__new_primary_file_pasture.unique\|forest.0.17__": {"src": "hda", "id": "80bae1ac661749cb", "uuid": "8d07c84c-4f29-4ffb-ae7b-c98646daf9a6"}, "__new_primary_file_unique.pasture\|0.41.pasture__": {"src": "hda", "id": "cdd00c2f56d70d8c", "uuid": "263e2a70-b626-454e-b16e-4d7bc06ff47d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > split.abund(fasta=fasta.dat,list=search_input.dat,group=split_group.dat \r,groups=forest-pasture,accnos=true,cutoff=2)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \nsearch_input.forest.unique.rare.list\nsearch_input.forest.unique.abund.list\nsearch_input.pasture.unique.rare.list\nsearch_input.pasture.unique.abund.list\nsplit_group.unique.forest.abund.groups\nsplit_group.unique.forest.rare.groups\nsplit_group.unique.pasture.abund.groups\nsplit_group.unique.pasture.rare.groups\nsearch_input.unique.forest.abund.accnos\nsearch_input.unique.forest.rare.accnos\nsearch_input.unique.pasture.abund.accnos\nsearch_input.unique.pasture.rare.accnos\nfasta.unique.forest.abund.fasta\nfasta.unique.forest.rare.fasta\nfasta.unique.pasture.abund.fasta\nfasta.unique.pasture.rare.fasta\nsearch_input.forest.0.01.rare.list\nsearch_input.forest.0.01.abund.list\nsearch_input.pasture.0.01.rare.list\nsearch_input.pasture.0.01.abund.list\nsplit_group.0.01.forest.abund.groups\nsplit_group.0.01.forest.rare.groups\nsplit_group.0.01.pasture.abund.groups\nsplit_group.0.01.pasture.rare.groups\nsearch_input.0.01.forest.abund.accnos\nsearch_input.0.01.forest.rare.accnos\nsearch_input.0.01.pasture.abund.accnos\nsearch_input.0.01.pasture.rare.accnos\nfasta.0.01.forest.abund.fasta\nfasta.0.01.forest.rare.fasta\nfasta.0.01.pasture.abund.fasta\nfasta.0.01.pasture.rare.fasta\nsearch_input.forest.0.02.rare.list\nsearch_input.forest.0.02.abund.list\nsearch_input.pasture.0.02.rare.list\nsearch_input.pasture.0.02.abund.list\nsplit_group.0.02.forest.abund.groups\nsplit_group.0.02.forest.rare.groups\nsplit_group.0.02.pasture.abund.groups\nsplit_group.0.02.pasture.rare.groups\nsearch_input.0.02.forest.abund.accnos\nsearch_input.0.02.forest.rare.accnos\nsearch_input.0.02.pasture.abund.accnos\nsearch_input.0.02.pasture.rare.accnos\nfasta.0.02.forest.abund.fasta\nfasta.0.02.forest.rare.fasta\nfasta.0.02.pasture.abund.fasta\nfasta.0.02.pasture.rare.fasta\nsearch_input.forest.0.03.rare.list\nsearch_input.forest.0.03.abund.list\nsearch_input.pasture.0.03.rare.list\nsearch_input.pasture.0.03.abund.list\nsplit_group.0.03.forest.abund.groups\nsplit_group.0.03.forest.rare.groups\nsplit_group.0.03.pasture.abund.groups\nsplit_group.0.03.pasture.rare.groups\nsearch_input.0.03.forest.abund.accnos\nsearch_input.0.03.forest.rare.accnos\nsearch_input.0.03.pasture.abund.accnos\nsearch_input.0.03.pasture.rare.accnos\nfasta.0.03.forest.abund.fasta\nfasta.0.03.forest.rare.fasta\nfasta.0.03.pasture.abund.fasta\nfasta.0.03.pasture.rare.fasta\nsearch_input.forest.0.04.rare.list\nsearch_input.forest.0.04.abund.list\nsearch_input.pasture.0.04.rare.list\nsearch_input.pasture.0.04.abund.list\nsplit_group.0.04.forest.abund.groups\nsplit_group.0.04.forest.rare.groups\nsplit_group.0.04.pasture.abund.groups\nsplit_group.0.04.pasture.rare.groups\nsearch_input.0.04.forest.abund.accnos\nsearch_input.0.04.forest.rare.accnos\nsearch_input.0.04.pasture.abund.accnos\nsearch_input.0.04.pasture.rare.accnos\nfasta.0.04.forest.abund.fasta\nfasta.0.04.forest.rare.fasta\nfasta.0.04.pasture.abund.fasta\nfasta.0.04.pasture.rare.fasta\nsearch_input.forest.0.05.rare.list\nsearch_input.forest.0.05.abund.list\nsearch_input.pasture.0.05.rare.list\nsearch_input.pasture.0.05.abund.list\nsplit_group.0.05.forest.abund.groups\nsplit_group.0.05.forest.rare.groups\nsplit_group.0.05.pasture.abund.groups\nsplit_group.0.05.pasture.rare.groups\nsearch_input.0.05.forest.abund.accnos\nsearch_input.0.05.forest.rare.accnos\nsearch_input.0.05.pasture.abund.accnos\nsearch_input.0.05.pasture.rare.accnos\nfasta.0.05.forest.abund.fasta\nfasta.0.05.forest.rare.fasta\nfasta.0.05.pasture.abund.fasta\nfasta.0.05.pasture.rare.fasta\nsearch_input.forest.0.06.rare.list\nsearch_input.forest.0.06.abund.list\nsearch_input.pasture.0.06.rare.list\nsearch_input.pasture.0.06.abund.list\nsplit_group.0.06.forest.abund.groups\nsplit_group.0.06.forest.rare.groups\nsplit_group.0.06.pasture.abund.groups\nsplit_group.0.06.pasture.rare.groups\nsearch_input.0.06.forest.abund.accnos\nsearch_input.0.06.forest.rare.accnos\nsearch_input.0.06.pasture.abund.accnos\nsearch_input.0.06.pasture.rare.accnos\nfasta.0.06.forest.abund.fasta\nfasta.0.06.forest.rare.fasta\nfasta.0.06.pasture.abund.fasta\nfasta.0.06.pasture.rare.fasta\nsearch_input.forest.0.07.rare.list\nsearch_input.forest.0.07.abund.list\nsearch_input.pasture.0.07.rare.list\nsearch_input.pasture.0.07.abund.list\nsplit_group.0.07.forest.abund.groups\nsplit_group.0.07.forest.rare.groups\nsplit_group.0.07.pasture.abund.groups\nsplit_group.0.07.pasture.rare.groups\nsearch_input.0.07.forest.abund.accnos\nsearch_input.0.07.forest.rare.accnos\nsearch_input.0.07.pasture.abund.accnos\nsearch_input.0.07.pasture.rare.accnos\nfasta.0.07.forest.abund.fasta\nfasta.0.07.forest.rare.fasta\nfasta.0.07.pasture.abund.fasta\nfasta.0.07.pasture.rare.fasta\nsearch_input.forest.0.08.rare.list\nsearch_input.forest.0.08.abund.list\nsearch_input.pasture.0.08.rare.list\nsearch_input.pasture.0.08.abund.list\nsplit_group.0.08.forest.abund.groups\nsplit_group.0.08.forest.rare.groups\nsplit_group.0.08.pasture.abund.groups\nsplit_group.0.08.pasture.rare.groups\nsearch_input.0.08.forest.a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e.abund.groups\nsplit_group.0.45.pasture.rare.groups\nsearch_input.0.45.forest.abund.accnos\nsearch_input.0.45.forest.rare.accnos\nsearch_input.0.45.pasture.abund.accnos\nsearch_input.0.45.pasture.rare.accnos\nfasta.0.45.forest.abund.fasta\nfasta.0.45.forest.rare.fasta\nfasta.0.45.pasture.abund.fasta\nfasta.0.45.pasture.rare.fasta\nsearch_input.forest.0.55.rare.list\nsearch_input.forest.0.55.abund.list\nsearch_input.pasture.0.55.rare.list\nsearch_input.pasture.0.55.abund.list\nsplit_group.0.55.forest.abund.groups\nsplit_group.0.55.forest.rare.groups\nsplit_group.0.55.pasture.abund.groups\nsplit_group.0.55.pasture.rare.groups\nsearch_input.0.55.forest.abund.accnos\nsearch_input.0.55.forest.rare.accnos\nsearch_input.0.55.pasture.abund.accnos\nsearch_input.0.55.pasture.rare.accnos\nfasta.0.55.forest.abund.fasta\nfasta.0.55.forest.rare.fasta\nfasta.0.55.pasture.abund.fasta\nfasta.0.55.pasture.rare.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2682.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2683.dat' search_input.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2684.dat' split_group.dat && echo 'split.abund( fasta=fasta.dat, list=search_input.dat, group=split_group.dat, groups=forest-pasture, accnos=true, cutoff=2 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:32:21.857882", "params": {"cutoff": "\"2\"", "search": "{\"input\": {\"values\": [{\"src\": \"hda\", \"id\": 2683}]}, \"type\": \"list\", \"__current_case__\": 1, \"label\": null}", "dbkey": "\"hg17\"", "split": "{\"dosplit\": \"yes\", \"group\": {\"values\": [{\"src\": \"hda\", \"id\": 2684}]}, \"groups\": [\"forest\", \"pasture\"], \"__current_case__\": 0}", "accnos": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "4268", "id": "a97fae24847b82ef", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_split_abund.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"search\|input": {"src": "hda", "id": "38360e2d3ab06177"}, "cutoff": "2", "search\|type": "list", "split\|dosplit": "yes", "split\|group": {"src": "hda", "id": "7fd9dcdabb947ccd"}, "split\|groups": ["forest", "pasture"], "search\|label": ["0.05", "0.22"], "fasta": {"src": "hda", "id": "5a062b1ff6cc9d5a"}, "accnos": true}, "job": {"inputs": {"input": {"src": "hda", "id": "38360e2d3ab06177", "uuid": "d0b2ed14-9037-4dd5-ae88-b7585e53d01d"}, "fasta": {"src": "hda", "id": "5a062b1ff6cc9d5a", "uuid": "a5a3ef3b-52e9-49cc-a4fc-8c86ccf0771e"}, "group": {"src": "hda", "id": "7fd9dcdabb947ccd", "uuid": "fd5545e9-1c74-45f8-afdb-aac61299fd9c"}}, "update_time": "2018-02-08T18:34:21.332942", "tool_id": "mothur_split_abund", "outputs": {"__new_primary_file_0.22.pasture\|0.22.pasture__": {"src": "hda", "id": "d16be2ae47deec72", "uuid": "e0e1bc85-d362-4c10-99ed-37f4e5dc12a9"}, "__new_primary_file_pasture.0.22\|forest.0.05__": {"src": "hda", "id": "ab54917a7131c881", "uuid": "6d56c002-39f5-47ab-8a9c-09b75b732005"}, "__new_primary_file_pasture.0.22\|forest.0.22__": {"src": "hda", "id": "8e584b6d1dcf6293", "uuid": "377f5b7d-fdf7-477e-ba68-467ec6554408"}, "__new_primary_file_0.22.pasture\|0.05.pasture__": {"src": "hda", "id": "b9aa8dda8024d3ce", "uuid": "daaa40c3-883f-47f0-95d1-33311618cfc4"}, "__new_primary_file_pasture.0.22\|pasture.0.22__": {"src": "hda", "id": "28b0a5b79d875620", "uuid": "e01a2820-65d9-403c-9adf-6c096bd2a8eb"}, "__new_primary_file_0.22.pasture\|0.05.forest__": {"src": "hda", "id": "44d57fb3b86c5aae", "uuid": "be5f6fb8-3477-45f8-b5cc-be9589ef8d22"}, "__new_primary_file_pasture.0.22\|pasture.0.05__": {"src": "hda", "id": "bb320b551226491d", "uuid": "50a0d19c-a9cb-4bf5-9cc5-0347397aa46b"}, "logfile": {"src": "hda", "id": "90c7d1a0099e9a76", "uuid": "2419fe03-fbd8-4951-971c-a1e31e00592b"}, "__new_primary_file_0.22.pasture\|0.22.forest__": {"src": "hda", "id": "51ecdd8f7307fd69", "uuid": "6819aa98-7c97-4468-a665-c3b4033568b5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > split.abund(fasta=fasta.dat,list=search_input.dat,label=0.05-0.22,group \r=split_group.dat,groups=forest-pasture,accnos=true,cutoff=2)\n0.05\n0.22\n\nOutput File Names: \nsearch_input.forest.0.05.rare.list\nsearch_input.forest.0.05.abund.list\nsearch_input.pasture.0.05.rare.list\nsearch_input.pasture.0.05.abund.list\nsplit_group.0.05.forest.abund.groups\nsplit_group.0.05.forest.rare.groups\nsplit_group.0.05.pasture.abund.groups\nsplit_group.0.05.pasture.rare.groups\nsearch_input.0.05.forest.abund.accnos\nsearch_input.0.05.forest.rare.accnos\nsearch_input.0.05.pasture.abund.accnos\nsearch_input.0.05.pasture.rare.accnos\nfasta.0.05.forest.abund.fasta\nfasta.0.05.forest.rare.fasta\nfasta.0.05.pasture.abund.fasta\nfasta.0.05.pasture.rare.fasta\nsearch_input.forest.0.22.rare.list\nsearch_input.forest.0.22.abund.list\nsearch_input.pasture.0.22.rare.list\nsearch_input.pasture.0.22.abund.list\nsplit_group.0.22.forest.abund.groups\nsplit_group.0.22.forest.rare.groups\nsplit_group.0.22.pasture.abund.groups\nsplit_group.0.22.pasture.rare.groups\nsearch_input.0.22.forest.abund.accnos\nsearch_input.0.22.forest.rare.accnos\nsearch_input.0.22.pasture.abund.accnos\nsearch_input.0.22.pasture.rare.accnos\nfasta.0.22.forest.abund.fasta\nfasta.0.22.forest.rare.fasta\nfasta.0.22.pasture.abund.fasta\nfasta.0.22.pasture.rare.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3262.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3263.dat' search_input.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3264.dat' split_group.dat && echo 'split.abund( fasta=fasta.dat, list=search_input.dat, label=0.05-0.22, group=split_group.dat, groups=forest-pasture, accnos=true, cutoff=2 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:34:15.959750", "params": {"cutoff": "\"2\"", "search": "{\"input\": {\"values\": [{\"src\": \"hda\", \"id\": 3263}]}, \"type\": \"list\", \"__current_case__\": 1, \"label\": [\"0.05\", \"0.22\"]}", "dbkey": "\"hg17\"", "split": "{\"dosplit\": \"yes\", \"group\": {\"values\": [{\"src\": \"hda\", \"id\": 3264}]}, \"groups\": [\"forest\", \"pasture\"], \"__current_case__\": 0}", "accnos": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "4425", "id": "9ecc9b17e1423ee8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_split_abund.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "94e36d9344f4dff1"}, "group": {"src": "hda", "id": "77055d672d3dfc70"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "94e36d9344f4dff1", "uuid": "bcb0a685-26a1-473e-8db2-731290c2d71a"}, "group": {"src": "hda", "id": "77055d672d3dfc70", "uuid": "2f686bf5-cc63-4dac-bacd-d82878b6663b"}}, "update_time": "2018-02-08T18:35:19.336599", "tool_id": "mothur_split_groups", "outputs": {"__new_primary_file_pasture\|forest__": {"src": "hda", "id": "086a78d5d6cf5d6e", "uuid": "1f832a18-6aee-4670-a3a9-1d87ce78cfa1"}, "logfile": {"src": "hda", "id": "2ea441e22c11eebd", "uuid": "331204e8-c42f-4b25-b488-c5e55ea91543"}, "__new_primary_file_pasture\|pasture__": {"src": "hda", "id": "ace7c95418a0de52", "uuid": "d11fd81b-73bd-4f17-9c52-a544e8145683"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > split.groups(fasta=fasta.dat,group=group.dat)\n\nProcessing group: forest\nProcessing group: pasture\n\nOutput File Names: \nfasta.forest.fasta\nfasta.pasture.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s 'None' name.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3298.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3299.dat' group.dat && echo 'split.groups( fasta=fasta.dat, group=group.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:35:16.412552", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groups": "null", "name": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "4550", "id": "7ec799cf0545a3b8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_split_groups.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|format": "list", "input\|otu": {"src": "hda", "id": "2e7cb023461a16f4"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "2e7cb023461a16f4", "uuid": "838e9592-03b6-4a6c-836c-502754f9c3a1"}}, "update_time": "2018-02-08T18:35:43.597787", "tool_id": "mothur_sub_sample", "outputs": {"__new_primary_file_unique\|0.10__": {"src": "hda", "id": "fd4a4a3fe46f280b", "uuid": "bc41ab14-c9f3-427b-a331-7c36da5d7dc7"}, "__new_primary_file_unique\|0.05__": {"src": "hda", "id": "c64ee5ee7f79f0a6", "uuid": "cb5eb702-6ca0-43ff-add9-b7f2b7cf3450"}, "__new_primary_file_unique\|0.17__": {"src": "hda", "id": "ec09a227354975ff", "uuid": "836f92e1-34ba-41e9-a565-3f77bde0324e"}, "__new_primary_file_unique\|0.02__": {"src": "hda", "id": "45a337b5db97ab85", "uuid": "08901a22-bd50-4fb3-b244-041281afb8ff"}, "__new_primary_file_unique\|0.21__": {"src": "hda", "id": "94fd33d364fcc131", "uuid": "107a3582-b007-4093-aa74-592e23bbd511"}, "__new_primary_file_unique\|0.16__": {"src": "hda", "id": "c7c45b9b7153b04b", "uuid": "0c5d48a4-d3c2-4bbe-a53d-02a47be5b02e"}, "__new_primary_file_unique\|0.45__": {"src": "hda", "id": "4c2ab93933e14931", "uuid": "91077f83-fe87-4f99-9827-17b0f990d620"}, "__new_primary_file_unique\|0.03__": {"src": "hda", "id": "041847c37ff1f11d", "uuid": "15225a6a-10ef-4e9a-8a01-5bd335636c72"}, "__new_primary_file_unique\|0.15__": {"src": "hda", "id": "fd10df936e5a6ffd", "uuid": "0595e1fb-4082-4417-af63-833df5b63f82"}, "__new_primary_file_unique\|0.08__": {"src": "hda", "id": "db7b606431d708fd", "uuid": "7ad15d11-b0e7-41b9-99f3-b46a4628a7e8"}, "__new_primary_file_unique\|0.14__": {"src": "hda", "id": "fedc92590bf7a1e3", "uuid": "036ed503-f693-4973-b57d-00786b4027ca"}, "__new_primary_file_unique\|0.13__": {"src": "hda", "id": "fa68b0f5b7e3310f", "uuid": "1bb4262c-7f17-487d-b369-6fd216bdb468"}, "__new_primary_file_unique\|0.09__": {"src": "hda", "id": "becaa11690574381", "uuid": "a5b3a3f3-3c59-44c0-b930-3e8db1d85e9d"}, "__new_primary_file_unique\|0.12__": {"src": "hda", "id": "2b8bcf1bee106508", "uuid": "17439678-5ed0-4a85-a4d6-fa15666f7590"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "ca918f436c0404da", "uuid": "dd2c7108-a96c-4100-8d96-2785d0ffa2c7"}, "__new_primary_file_unique\|0.11__": {"src": "hda", "id": "52ae354051a713cf", "uuid": "3ce96159-82e0-4e0e-a644-1522dd4ab280"}, "__new_primary_file_unique\|0.41__": {"src": "hda", "id": "a21f6630d51aa237", "uuid": "6b2c9e56-d4b3-4deb-8f52-bee0305572cf"}, "__new_primary_file_unique\|0.06__": {"src": "hda", "id": "e88c34232705ba65", "uuid": "81cafa7f-41d0-429e-8038-58cab8fc431b"}, "__new_primary_file_unique\|0.25__": {"src": "hda", "id": "7c3a3946772cd3a5", "uuid": "9ac59227-fa48-4d82-85ad-75448bbced38"}, "__new_primary_file_unique\|0.22__": {"src": "hda", "id": "25c2f28094be3e4a", "uuid": "a56e8353-e761-45df-820e-fb3342713ea7"}, "__new_primary_file_unique\|0.36__": {"src": "hda", "id": "610851f8602f4f94", "uuid": "035d59ef-d1d7-4967-bb23-4fb16e3b5ed2"}, "__new_primary_file_unique\|0.04__": {"src": "hda", "id": "3883bbf3e69f96c4", "uuid": "a42088ee-667c-44a9-b5ad-dd6b80141c6c"}, "__new_primary_file_unique\|0.23__": {"src": "hda", "id": "c53c947799f8d062", "uuid": "0f9e30d9-8dbf-4829-8584-0bbdce6be1e1"}, "__new_primary_file_unique\|0.33__": {"src": "hda", "id": "dccae4d18ce46393", "uuid": "1e44f7be-25ed-43b2-a1c1-205fbafe265f"}, "logfile": {"src": "hda", "id": "bf85b7bcdfa19ca1", "uuid": "38f29163-266b-48b0-9624-8bfd516f73e7"}, "__new_primary_file_unique\|0.20__": {"src": "hda", "id": "eb14a43b730af9b0", "uuid": "a031af33-4cd8-4e5b-926c-a31e5bd60efc"}, "__new_primary_file_unique\|0.29__": {"src": "hda", "id": "783cb8e61a95c257", "uuid": "a233e3ce-f9cb-41e7-ba68-4fbef3cc7031"}, "__new_primary_file_unique\|0.38__": {"src": "hda", "id": "77520fba82154a85", "uuid": "6683bbc2-c8eb-4caa-b5c0-175565aaef41"}, "__new_primary_file_unique\|0.55__": {"src": "hda", "id": "07494a3104a83c58", "uuid": "867eb8e2-805b-43b8-a020-254c764a27c4"}, "__new_primary_file_unique\|0.07__": {"src": "hda", "id": "1bd4fe964f1633ec", "uuid": "3d529eea-171f-42bc-9ee7-b2b5ee04b27c"}, "__new_primary_file_unique\|0.26__": {"src": "hda", "id": "c0e32004680aebdc", "uuid": "19c1897d-da47-4cbe-9aaf-a2402357915d"}, "__new_primary_file_unique\|0.32__": {"src": "hda", "id": "8191b8e06b896e17", "uuid": "ff6c896b-e40b-4ba4-a214-237c1c89323c"}, "__new_primary_file_unique\|0.27__": {"src": "hda", "id": "59b498d849471e88", "uuid": "20a0b8de-3faa-4698-afe3-cbf5e32ec68c"}, "__new_primary_file_unique\|0.19__": {"src": "hda", "id": "713308dcadc7b298", "uuid": "81cc846e-6e1e-40ce-8928-d283c86af865"}, "__new_primary_file_unique\|0.01__": {"src": "hda", "id": "94a9be080ede912f", "uuid": "2c99ebe0-181a-4ed9-a6d1-fcff02f1f95d"}, "__new_primary_file_unique\|0.24__": {"src": "hda", "id": "8cd99efd35c03f63", "uuid": "df0df989-9b8f-4e8e-9656-364cbf999132"}, "__new_primary_file_unique\|0.18__": {"src": "hda", "id": "098690efcaf79838", "uuid": "fea1943c-c4b0-4b4a-8939-b46a3b520e28"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sub.sample(list=input_otu.dat)\nSampling 9 from 98.\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu.unique.subsample.dat\ninput_otu.0.01.subsample.dat\ninput_otu.0.02.subsample.dat\ninput_otu.0.03.subsample.dat\ninput_otu.0.04.subsample.dat\ninput_otu.0.05.subsample.dat\ninput_otu.0.06.subsample.dat\ninput_otu.0.07.subsample.dat\ninput_otu.0.08.subsample.dat\ninput_otu.0.09.subsample.dat\ninput_otu.0.10.subsample.dat\ninput_otu.0.11.subsample.dat\ninput_otu.0.12.subsample.dat\ninput_otu.0.13.subsample.dat\ninput_otu.0.14.subsample.dat\ninput_otu.0.15.subsample.dat\ninput_otu.0.16.subsample.dat\ninput_otu.0.17.subsample.dat\ninput_otu.0.18.subsample.dat\ninput_otu.0.19.subsample.dat\ninput_otu.0.20.subsample.dat\ninput_otu.0.21.subsample.dat\ninput_otu.0.22.subsample.dat\ninput_otu.0.23.subsample.dat\ninput_otu.0.24.subsample.dat\ninput_otu.0.25.subsample.dat\ninput_otu.0.26.subsample.dat\ninput_otu.0.27.subsample.dat\ninput_otu.0.29.subsample.dat\ninput_otu.0.32.subsample.dat\ninput_otu.0.33.subsample.dat\ninput_otu.0.36.subsample.dat\ninput_otu.0.38.subsample.dat\ninput_otu.0.41.subsample.dat\ninput_otu.0.45.subsample.dat\ninput_otu.0.55.subsample.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3303.dat' input_otu.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat && echo 'sub.sample( list=input_otu.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:35:38.794951", "params": {"count": "null", "taxonomy": "null", "dbkey": "\"hg17\"", "input": "{\"label\": null, \"use_group\": {\"to_filter\": \"no\", \"__current_case__\": 0}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3303}]}, \"__current_case__\": 1, \"format\": \"list\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "4648", "id": "25d0f693a44d3b63", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sub_sample.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|use_group\|to_filter": "yes", "input\|format": "list", "input\|label": ["0.20", "0.45", "0.55"], "input\|use_group\|group_in": {"src": "hda", "id": "6c33be6b38ca33c8"}, "input\|otu": {"src": "hda", "id": "a6914750373c5dca"}, "input\|use_group\|groups": ["forest", "pasture"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "a6914750373c5dca", "uuid": "273992d2-624e-4e47-9e79-53149cf7489e"}, "input\|group_in": {"src": "hda", "id": "6c33be6b38ca33c8", "uuid": "4e6343ec-eef2-4ddf-870e-9f1771d9160f"}}, "update_time": "2018-02-08T18:36:06.787393", "tool_id": "mothur_sub_sample", "outputs": {"group_out": {"src": "hda", "id": "e1d9bb3f99cf6cdf", "uuid": "71c9c6f1-8226-4835-9d0e-0aac8d68b7cb"}, "__new_primary_file_0.55\|0.45__": {"src": "hda", "id": "9ae55fc576dc60f1", "uuid": "47707b9a-c6e9-4112-8550-b72d078f5d33"}, "logfile": {"src": "hda", "id": "124f3cdfbbd95fda", "uuid": "14a1fcc8-3c6c-4dcb-b91b-f5f92ea6b31a"}, "__new_primary_file_0.55\|0.20__": {"src": "hda", "id": "d7fb8460258b019b", "uuid": "034a36b0-49a6-4c55-a60f-4ec36e35a084"}, "__new_primary_file_0.55\|0.55__": {"src": "hda", "id": "68ee566869d6b1ed", "uuid": "670a77ac-fda5-46e2-a978-5fcd0bad7785"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sub.sample(list=input_otu.dat,label=0.20-0.45-0.55,group=input_use_grou \rp_group_in.dat,groups=forest-pasture,persample=false)\nSampling 9 from 98.\n0.20\n0.45\n0.55\n\nOutput File Names: \ninput_use_group_group_in.subsample.dat\ninput_otu.0.20.subsample.dat\ninput_otu.0.45.subsample.dat\ninput_otu.0.55.subsample.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3341.dat' input_otu.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3342.dat' input_use_group_group_in.dat && echo 'sub.sample( list=input_otu.dat ,label=0.20-0.45-0.55 ,group=input_use_group_group_in.dat ,groups=forest-pasture ,persample=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:36:03.484357", "params": {"count": "null", "taxonomy": "null", "dbkey": "\"hg17\"", "input": "{\"label\": [\"0.20\", \"0.45\", \"0.55\"], \"use_group\": {\"groups\": [\"forest\", \"pasture\"], \"group_in\": {\"values\": [{\"src\": \"hda\", \"id\": 3342}]}, \"to_filter\": \"yes\", \"__current_case__\": 1, \"persample\": \"false\"}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3341}]}, \"__current_case__\": 1, \"format\": \"list\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "4799", "id": "5d14d4d6e1b26e70", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sub_sample.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"taxonomy": {"src": "hda", "id": "1f575f6909f01a06"}, "input\|format": "fasta", "input\|otu": {"src": "hda", "id": "bece6f670e32e3b2"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "1f575f6909f01a06", "uuid": "6e828b79-1871-4f06-bc3b-31124c33f80f"}, "otu": {"src": "hda", "id": "bece6f670e32e3b2", "uuid": "45d3232c-e01f-434b-baf0-a36f8911e6d7"}}, "update_time": "2018-02-08T18:36:27.157284", "tool_id": "mothur_sub_sample", "outputs": {"logfile": {"src": "hda", "id": "08fc905d422a8de9", "uuid": "50b3fb39-3176-4b2a-8d7d-56affc461bdb"}, "taxonomy_out": {"src": "hda", "id": "94b1487945e42c0e", "uuid": "ca5f7679-1915-4578-95cb-044a508074d0"}, "fasta_out": {"src": "hda", "id": "4ea647ba3b7d95df", "uuid": "071973e8-c400-49ef-b9a5-6657b427e0ae"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sub.sample(fasta=input_otu.dat,taxonomy=taxonomy.dat)\nSampling 9 from 98.\n\nOutput File Names: \ntaxonomy.subsample.dat\ninput_otu.subsample.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3348.dat' input_otu.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3349.dat' taxonomy.dat && ln -s 'None' input_name_in.dat && echo 'sub.sample( fasta=input_otu.dat ,taxonomy=taxonomy.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:36:23.949610", "params": {"count": "null", "input": "{\"name_in\": null, \"use_group\": {\"to_filter\": \"no\", \"__current_case__\": 0}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3348}]}, \"__current_case__\": 0, \"format\": \"fasta\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "4910", "id": "3299fdcb51cc47eb", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sub_sample.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|use_group\|to_filter": "yes", "input\|format": "fasta", "input\|use_group\|group_in": {"src": "hda", "id": "eee039b20a991e3a"}, "input\|name_in": {"src": "hda", "id": "b5720c569f7288b1"}, "input\|otu": {"src": "hda", "id": "ee0ce12141350359"}, "input\|use_group\|groups": ["forest", "pasture"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "ee0ce12141350359", "uuid": "42469f25-5708-4222-8760-ff76e6d4d9c3"}, "name_in": {"src": "hda", "id": "b5720c569f7288b1", "uuid": "e240f77e-5836-449b-9fb9-ee9ed7a7aa34"}, "input\|group_in": {"src": "hda", "id": "eee039b20a991e3a", "uuid": "a42c8f9c-d99a-48c9-a576-c8456e430272"}}, "update_time": "2018-02-08T18:36:57.127387", "tool_id": "mothur_sub_sample", "outputs": {"group_out": {"src": "hda", "id": "23aff3aec83edf3b", "uuid": "154fd6b1-2176-4bd8-ba50-bf69094a6a5d"}, "logfile": {"src": "hda", "id": "e05ecd771fc816b3", "uuid": "217b049f-b60a-4381-babb-7d066d4f80e9"}, "names_out": {"src": "hda", "id": "26cbd2176813479a", "uuid": "98e02803-23f3-4b1e-9643-8f39ea708d6a"}, "fasta_out": {"src": "hda", "id": "91ae72a932583c4d", "uuid": "3f0fd802-fd00-4559-820b-2a76a91912d9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sub.sample(fasta=input_otu.dat,name=input_name_in.dat,group=input_use_g \rroup_group_in.dat,groups=forest-pasture,persample=false)\nSampling 9 from 98.\nDeconvoluting subsampled fasta file... \n/**************************************/\nRunning command: unique.seqs(fasta=input_otu.subsample.dat)\n9\t9\n\nOutput File Names: \ninput_otu.subsample.names\ninput_otu.subsample.unique.dat\n\n/***************************************/\nDone.\n\nOutput File Names: \ninput_name_in.subsample.dat\ninput_otu.subsample.dat\ninput_use_group_group_in.subsample.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3353.dat' input_otu.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3354.dat' input_name_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3355.dat' input_use_group_group_in.dat && echo 'sub.sample( fasta=input_otu.dat ,name=input_name_in.dat ,group=input_use_group_group_in.dat ,groups=forest-pasture ,persample=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:36:53.756809", "params": {"count": "null", "taxonomy": "null", "dbkey": "\"hg17\"", "input": "{\"name_in\": {\"values\": [{\"src\": \"hda\", \"id\": 3354}]}, \"use_group\": {\"groups\": [\"forest\", \"pasture\"], \"group_in\": {\"values\": [{\"src\": \"hda\", \"id\": 3355}]}, \"to_filter\": \"yes\", \"__current_case__\": 1, \"persample\": \"false\"}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3353}]}, \"__current_case__\": 0, \"format\": \"fasta\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5043", "id": "8ef1d4aff90ec17a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sub_sample.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|label": ["unique", "0.20"], "input\|groups": "forest", "input\|format": "shared", "input\|otu": {"src": "hda", "id": "ef698126cba35364"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "ef698126cba35364", "uuid": "e59a69f6-ea54-4896-a614-6a30742cb504"}}, "update_time": "2018-02-08T18:37:24.623961", "tool_id": "mothur_sub_sample", "outputs": {"__new_primary_file_unique\|0.20__": {"src": "hda", "id": "8197278eca4fd946", "uuid": "b6bbe5af-0df4-4784-b8e0-d1b94535fff7"}, "__new_primary_file_unique\|unique__": {"src": "hda", "id": "3ed661d3927e064a", "uuid": "ce0d0dd6-a206-4810-9de8-2bc82dd76873"}, "logfile": {"src": "hda", "id": "85326d390990318f", "uuid": "1e3805df-515e-4e08-8f96-1e000697d674"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sub.sample(shared=input_otu.dat,groups=forest,label=unique-0.20)\nSampling 49 from each group.\nunique\n0.20\n\nOutput File Names: \ninput_otu.unique.subsample.dat\ninput_otu.0.20.subsample.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3360.dat' input_otu.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat && echo 'sub.sample( shared=input_otu.dat ,groups=forest ,label=unique-0.20 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:37:21.465530", "params": {"count": "null", "taxonomy": "null", "dbkey": "\"hg17\"", "input": "{\"groups\": \"forest\", \"label\": [\"unique\", \"0.20\"], \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3360}]}, \"__current_case__\": 2, \"format\": \"shared\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5144", "id": "28ff0d67f20f4379", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sub_sample.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|format": "rabund", "input\|otu": {"src": "hda", "id": "edee4d329f8f498b"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "edee4d329f8f498b", "uuid": "d7a3be04-025a-4ede-a135-079084fb394f"}}, "update_time": "2018-02-08T18:37:42.101206", "tool_id": "mothur_sub_sample", "outputs": {"rabund_out": {"src": "hda", "id": "d7f196f58f1b0b71", "uuid": "d6cfb504-3504-4392-bf5e-7afcb080ec67"}, "logfile": {"src": "hda", "id": "46e41148fd1dda0c", "uuid": "011d4c74-d116-42a0-b8a6-a250368b8f9a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sub.sample(rabund=input_otu.dat)\nSampling 9 from 98.\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu.subsample.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3364.dat' input_otu.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat && echo 'sub.sample( rabund=input_otu.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:37:38.974213", "params": {"count": "null", "taxonomy": "null", "dbkey": "\"hg17\"", "input": "{\"label\": null, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3364}]}, \"__current_case__\": 4, \"format\": \"rabund\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5235", "id": "45a4f11c8f7e7223", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sub_sample.test_tool_000005", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|format": "sabund", "input\|otu": {"src": "hda", "id": "10d4ec46a6dab525"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "10d4ec46a6dab525", "uuid": "485908f3-8e8b-4984-a10e-f9718499bf14"}}, "update_time": "2018-02-08T18:37:59.562528", "tool_id": "mothur_sub_sample", "outputs": {"sabund_out": {"src": "hda", "id": "edb9aecf4037cd61", "uuid": "844b4d73-8677-45ee-93cf-9da60b83311f"}, "logfile": {"src": "hda", "id": "78353c3ca164fa23", "uuid": "30f65e57-bb1f-4dbb-9cfe-e552341c898a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sub.sample(sabund=input_otu.dat)\nSampling 9 from 98.\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu.subsample.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3367.dat' input_otu.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat && echo 'sub.sample( sabund=input_otu.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:37:56.411698", "params": {"count": "null", "taxonomy": "null", "dbkey": "\"hg17\"", "input": "{\"label\": null, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3367}]}, \"__current_case__\": 3, \"format\": \"sabund\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5329", "id": "973cca1598618f36", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sub_sample.test_tool_000006", "has_data": true}, {"data": {"status": "success", "inputs": {"qfile": {"src": "hda", "id": "997fdd605baf4477"}}, "job": {"inputs": {"qfile": {"src": "hda", "id": "997fdd605baf4477", "uuid": "b13158ea-6190-42e6-a8ae-3a5c21ead029"}}, "update_time": "2018-02-08T18:38:17.046071", "tool_id": "mothur_summary_qual", "outputs": {"logfile": {"src": "hda", "id": "be79454c845000eb", "uuid": "75a6e837-a714-412f-8804-367ca29718e0"}, "out_summary": {"src": "hda", "id": "c4be6070688ee40e", "uuid": "b3c138ce-bf0f-42a9-827e-bd29523e12e1"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.qual(qfile=qfile.dat)\n\nUsing 1 processors.\n\nPosition\tNumSeqs\tAverageQ\n0\t25\t31.760000\n100\t25\t29.719999\n200\t25\t28.799999\n\nIt took 0 secs to create the summary file for 25 sequences.\n\n\nOutput File Names: \nqfile.qual.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3370.dat' qfile.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && echo 'summary.qual( qfile=qfile.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:38:13.919763", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name": "null", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5418", "id": "76bb1b91489711f4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_qual.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "56ac79356c05acc8"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "56ac79356c05acc8", "uuid": "6f0d83d5-f9ac-46f9-9ace-50ad5ceeb974"}}, "update_time": "2018-02-08T18:38:29.506638", "tool_id": "mothur_summary_seqs", "outputs": {"logfile": {"src": "hda", "id": "d5f96994fda893d3", "uuid": "75fbfa36-0d67-4a1f-abbe-68f632470429"}, "out_summary": {"src": "hda", "id": "08a03081f5d556bd", "uuid": "cef79172-0f84-4dc6-a21a-226ca0d18391"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.seqs(fasta=fasta.dat,processors=1)\n\nUsing 1 processors.\n\n\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs\nMinimum:\t1\t252\t252\t0\t3\t1\n2.5%-tile:\t1\t252\t252\t0\t3\t1\n25%-tile:\t1\t253\t253\t0\t4\t7\nMedian: \t1\t253\t253\t0\t4\t13\n75%-tile:\t1\t253\t253\t0\t5\t19\n97.5%-tile:\t1\t254\t254\t8\t6\t25\nMaximum:\t1\t254\t254\t8\t6\t25\nMean:\t1\t252.92\t252.92\t0.4\t4.24\n# of Seqs:\t25\n\nOutput File Names: \nfasta.summary\n\nIt took 0 secs to summarize 25 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3373.dat' fasta.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && echo 'summary.seqs( fasta=fasta.dat, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:38:26.369792", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name": "null", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5507", "id": "40537184298763b3", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "bfbf916ea0862825"}, "name": {"src": "hda", "id": "a1bca696e6338746"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "bfbf916ea0862825", "uuid": "441d697c-304b-48b5-b977-c692f16ebf90"}, "name": {"src": "hda", "id": "a1bca696e6338746", "uuid": "fd30122b-1410-4d81-a9c9-06d3623f37cf"}}, "update_time": "2018-02-08T18:38:50.021600", "tool_id": "mothur_summary_seqs", "outputs": {"logfile": {"src": "hda", "id": "d308ef85a2ecdd63", "uuid": "8d77bc24-c3a9-476a-a08f-88dcc3f16174"}, "out_summary": {"src": "hda", "id": "bd5984605556083f", "uuid": "97a18d25-524f-41a4-9f71-b5db69e2a367"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.seqs(fasta=fasta.dat,name=name.dat,processors=1)\n\nUsing 1 processors.\n\n\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs\nMinimum:\t1\t422\t422\t0\t4\t1\n2.5%-tile:\t1\t436\t436\t0\t4\t3\n25%-tile:\t1\t507\t507\t1\t5\t25\nMedian: \t1\t530\t530\t3\t5\t50\n75%-tile:\t1\t961\t961\t6\t6\t74\n97.5%-tile:\t1\t973\t973\t15\t8\t96\nMaximum:\t1\t978\t978\t20\t9\t98\nMean:\t1\t678.235\t678.235\t4.54082\t5.44898\n# of unique seqs:\t96\ntotal # of seqs:\t98\n\nOutput File Names: \nfasta.summary\n\nIt took 0 secs to summarize 98 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3376.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3377.dat' name.dat && ln -s 'None' count.dat && echo 'summary.seqs( fasta=fasta.dat, name=name.dat, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:38:46.918829", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5627", "id": "0cc52239f966e8d8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"count": {"src": "hda", "id": "d32f8d2680587f70"}, "fasta": {"src": "hda", "id": "561fb224c4db80ce"}}, "job": {"inputs": {"count": {"src": "hda", "id": "d32f8d2680587f70", "uuid": "89db742d-5a41-4b17-8121-7d7990cac273"}, "fasta": {"src": "hda", "id": "561fb224c4db80ce", "uuid": "82f53e55-3751-4359-9711-7e6d49e40902"}}, "update_time": "2018-02-08T18:39:10.818528", "tool_id": "mothur_summary_seqs", "outputs": {"logfile": {"src": "hda", "id": "183b6b1fd8567283", "uuid": "f98a65a4-a5af-44c6-901d-c2870b7e17a4"}, "out_summary": {"src": "hda", "id": "309dfc9ec023321e", "uuid": "88e59858-87d0-4485-813c-2060acf87822"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.seqs(fasta=fasta.dat,count=count.dat,processors=1)\n\nUsing 1 processors.\n\n\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs\nMinimum:\t1\t422\t422\t0\t4\t1\n2.5%-tile:\t1\t436\t436\t0\t4\t3\n25%-tile:\t1\t507\t507\t1\t5\t25\nMedian: \t1\t530\t530\t3\t5\t50\n75%-tile:\t1\t961\t961\t6\t6\t74\n97.5%-tile:\t1\t973\t973\t15\t8\t96\nMaximum:\t1\t978\t978\t20\t9\t98\nMean:\t1\t678.235\t678.235\t4.54082\t5.44898\n# of unique seqs:\t96\ntotal # of seqs:\t98\n\nOutput File Names: \nfasta.summary\n\nIt took 0 secs to summarize 98 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3380.dat' fasta.dat && ln -s 'None' name.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3381.dat' count.dat && echo 'summary.seqs( fasta=fasta.dat, count=count.dat, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:39:07.731295", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name": "null", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5738", "id": "20daa85480c5e233", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "0426109cd781ead0"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "0426109cd781ead0", "uuid": "bdb3a54a-e140-44c2-9d09-1eea16f2634a"}}, "update_time": "2018-02-08T18:39:28.523455", "tool_id": "mothur_summary_shared", "outputs": {"logfile": {"src": "hda", "id": "66e1b7e2cc1eadad", "uuid": "98586141-b915-4211-8008-76ce467ce6fa"}, "summary": {"src": "hda", "id": "3cd2bed6e83f9950", "uuid": "59846e5d-4dc2-4cfb-9db0-7d6977934fe4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.shared(shared=otu.dat,calc=sharedsobs-sharedchao-sharedace-jcla \rss-jest-sorclass-sorest-jabund-sorabund-thetan-thetayc,all=false,distance=false, \routput=lt,processors=1)\n\nUsing 1 processors.\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3384.dat' otu.dat && echo 'summary.shared( shared=otu.dat, calc=sharedsobs-sharedchao-sharedace-jclass-jest-sorclass-sorest-jabund-sorabund-thetan-thetayc, all=false, distance=false, output=lt, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:39:25.392601", "params": {"distance": "\"false\"", "all": "\"false\"", "dbkey": "\"hg17\"", "label": "null", "subsample": "{\"use\": \"no\", \"__current_case__\": 1}", "groups": "null", "output": "\"lt\"", "calc": "[\"sharedsobs\", \"sharedchao\", \"sharedace\", \"jclass\", \"jest\", \"sorclass\", \"sorest\", \"jabund\", \"sorabund\", \"thetan\", \"thetayc\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5829", "id": "68b1b014e79dbbac", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_shared.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"subsample\|use": "yes", "otu": {"src": "hda", "id": "254a819efefe8354"}, "subsample\|iters": "42", "subsample\|subsample": "10"}, "job": {"inputs": {"otu": {"src": "hda", "id": "254a819efefe8354", "uuid": "aaf98054-0ba0-481b-91bf-9da58d5967e4"}}, "update_time": "2018-02-08T18:39:46.006201", "tool_id": "mothur_summary_shared", "outputs": {"logfile": {"src": "hda", "id": "cded715b2eb96d19", "uuid": "daa6c625-e03b-4735-8b46-013ba527ad23"}, "summary": {"src": "hda", "id": "c6fdefa03add2afa", "uuid": "95ec8fed-62b1-4cc9-8287-621a7afac31e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.shared(shared=otu.dat,calc=sharedsobs-sharedchao-sharedace-jcla \rss-jest-sorclass-sorest-jabund-sorabund-thetan-thetayc,all=false,distance=false, \rsubsample=10,iters=42,output=lt,processors=1)\n\nUsing 1 processors.\n0.10\n\nOutput File Names: \notu.summary\notu.sharedsobs.0.10.lt.dist\notu.sharedchao.0.10.lt.dist\notu.sharedace.0.10.lt.dist\notu.jclass.0.10.lt.dist\notu.jest.0.10.lt.dist\notu.sorclass.0.10.lt.dist\notu.sorest.0.10.lt.dist\notu.jabund.0.10.lt.dist\notu.sorabund.0.10.lt.dist\notu.thetan.0.10.lt.dist\notu.thetayc.0.10.lt.dist\notu.sharedsobs.0.10.lt.ave.dist\notu.sharedsobs.0.10.lt.std.dist\notu.sharedchao.0.10.lt.ave.dist\notu.sharedchao.0.10.lt.std.dist\notu.sharedace.0.10.lt.ave.dist\notu.sharedace.0.10.lt.std.dist\notu.jclass.0.10.lt.ave.dist\notu.jclass.0.10.lt.std.dist\notu.jest.0.10.lt.ave.dist\notu.jest.0.10.lt.std.dist\notu.sorclass.0.10.lt.ave.dist\notu.sorclass.0.10.lt.std.dist\notu.sorest.0.10.lt.ave.dist\notu.sorest.0.10.lt.std.dist\notu.jabund.0.10.lt.ave.dist\notu.jabund.0.10.lt.std.dist\notu.sorabund.0.10.lt.ave.dist\notu.sorabund.0.10.lt.std.dist\notu.thetan.0.10.lt.ave.dist\notu.thetan.0.10.lt.std.dist\notu.thetayc.0.10.lt.ave.dist\notu.thetayc.0.10.lt.std.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3387.dat' otu.dat && echo 'summary.shared( shared=otu.dat, calc=sharedsobs-sharedchao-sharedace-jclass-jest-sorclass-sorest-jabund-sorabund-thetan-thetayc, all=false, distance=false, subsample=10, iters=42, output=lt, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:39:42.829423", "params": {"distance": "\"false\"", "all": "\"false\"", "dbkey": "\"hg17\"", "label": "null", "subsample": "{\"iters\": \"42\", \"subsample\": \"10\", \"use\": \"yes\", \"__current_case__\": 0}", "groups": "null", "output": "\"lt\"", "calc": "[\"sharedsobs\", \"sharedchao\", \"sharedace\", \"jclass\", \"jest\", \"sorclass\", \"sorest\", \"jabund\", \"sorabund\", \"thetan\", \"thetayc\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5925", "id": "71eba17e79d46ea5", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_shared.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"calc": ["sharedsobs", "sharedchao", "sharedace", "anderberg", "jclass", "jest", "kulczynski", "kulczynskicody", "kstest", "lennon", "ochiai", "sorclass", "sorest", "whittaker", "hamming", "memchi2", "memchord", "memeuclidean", "mempearson", "braycurtis", "jabund", "morisitahorn", "sorabund", "thetan", "thetayc", "canberra", "gower", "hellinger", "manhattan", "odum", "soergel", "spearman", "speciesprofile", "structchi2", "structchord", "structeuclidean", "structkulczynski", "structpearson", "sharednseqs", "sharedobserved"], "otu": {"src": "hda", "id": "e747dd9ffcf57168"}, "groups": ["forest", "pasture"], "label": ["0.05", "0.22", "0.32"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "e747dd9ffcf57168", "uuid": "59d81e55-859a-492b-aa87-40e647394b7e"}}, "update_time": "2018-02-08T18:40:03.413375", "tool_id": "mothur_summary_shared", "outputs": {"logfile": {"src": "hda", "id": "75d696f5e8005428", "uuid": "d3c6f0a0-fa22-4672-94c1-da0bf5ab2f46"}, "summary": {"src": "hda", "id": "da7a9cd1bf67613c", "uuid": "d24a67fa-9b8b-4683-becf-e5e71f369043"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.shared(shared=otu.dat,label=0.05-0.22-0.32,groups=forest-pastur \re,calc=sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczyns \rkicody-kstest-lennon-ochiai-sorclass-sorest-whittaker-hamming-memchi2-memchord-m \remeuclidean-mempearson-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc-ca \rnberra-gower-hellinger-manhattan-odum-soergel-spearman-speciesprofile-structchi2 \r-structchord-structeuclidean-structkulczynski-structpearson-sharednseqs-sharedob \rserved,all=false,distance=false,output=lt,processors=1)\n\nUsing 1 processors.\nsharedobserved is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are anderberg, braycurtis, canberra, default, gower, hamming, hellinger, jabund, jclass, jest, jsd, kstest, kulczynski, kulczynskicody, lennon, manhattan, memchi2, memchord, memeuclidean, mempearson, morisitahorn, ochiai, odum, rjsd, sharedace, sharedchao, sharednseqs, sharedsobs, soergel, sorabund, sorclass, sorest, spearman, speciesprofile, structchi2, structchord, structeuclidean, structkulczynski, structpearson, thetan, thetayc, whittaker, \n0.05\n0.22\n0.32\n\nOutput File Names: \notu.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3390.dat' otu.dat && echo 'summary.shared( shared=otu.dat, label=0.05-0.22-0.32, groups=forest-pasture, calc=sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-kstest-lennon-ochiai-sorclass-sorest-whittaker-hamming-memchi2-memchord-memeuclidean-mempearson-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc-canberra-gower-hellinger-manhattan-odum-soergel-spearman-speciesprofile-structchi2-structchord-structeuclidean-structkulczynski-structpearson-sharednseqs-sharedobserved, all=false, distance=false, output=lt, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:40:00.489517", "params": {"distance": "\"false\"", "all": "\"false\"", "dbkey": "\"hg17\"", "label": "[\"0.05\", \"0.22\", \"0.32\"]", "subsample": "{\"use\": \"no\", \"__current_case__\": 1}", "groups": "[\"forest\", \"pasture\"]", "output": "\"lt\"", "calc": "[\"sharedsobs\", \"sharedchao\", \"sharedace\", \"anderberg\", \"jclass\", \"jest\", \"kulczynski\", \"kulczynskicody\", \"kstest\", \"lennon\", \"ochiai\", \"sorclass\", \"sorest\", \"whittaker\", \"hamming\", \"memchi2\", \"memchord\", \"memeuclidean\", \"mempearson\", \"braycurtis\", \"jabund\", \"morisitahorn\", \"sorabund\", \"thetan\", \"thetayc\", \"canberra\", \"gower\", \"hellinger\", \"manhattan\", \"odum\", \"soergel\", \"spearman\", \"speciesprofile\", \"structchi2\", \"structchord\", \"structeuclidean\", \"structkulczynski\", \"structpearson\", \"sharednseqs\", \"sharedobserved\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6045", "id": "617cf9f340bd6e86", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_shared.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"distance": true, "calc": "sorclass", "otu": {"src": "hda", "id": "b443405669a58394"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "b443405669a58394", "uuid": "9c2927b2-b6be-4c3d-9f35-e3ffb0ed545c"}}, "update_time": "2018-02-08T18:40:22.695570", "tool_id": "mothur_summary_shared", "outputs": {"__new_primary_file_sorclass.unique.lt\|sorclass.0.20.lt__": {"src": "hda", "id": "c6b272724420a0c3", "uuid": "c3c3c914-e794-404a-8ae6-c5f927315eb3"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.16.lt__": {"src": "hda", "id": "fbf13bbace0e382f", "uuid": "ced285e3-693a-4653-8054-29c1e871b8c8"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.38.lt__": {"src": "hda", "id": "a9b933fa687d9518", "uuid": "d34cfb4c-ae40-41e5-8925-4955c6f0d4b7"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.41.lt__": {"src": "hda", "id": "5a3d96751cec6e3e", "uuid": "4446d774-e6cc-44d6-92a3-17aa2eb4a61e"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.15.lt__": {"src": "hda", "id": "7b9f8b98c4ffad77", "uuid": "7516dc4e-4037-4c88-9afd-cf7ff670952e"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.12.lt__": {"src": "hda", "id": "3282233258f0f7fb", "uuid": "fc7b66ab-3c8a-4ab3-9496-ba84db2f0731"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.08.lt__": {"src": "hda", "id": "549fe069f41f5e42", "uuid": "365bffa5-59d1-44fa-b958-25b05b357828"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.11.lt__": {"src": "hda", "id": "feb74fd2f7fd44fb", "uuid": "5537588f-6aa0-4c34-86b9-bcac45e7c8ef"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.36.lt__": {"src": "hda", "id": "6c0029535d6b5111", "uuid": "1aaea491-b9b1-4052-b65a-c98cfab6ed52"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.33.lt__": {"src": "hda", "id": "fca77c5af4471e3e", "uuid": "e9edeb83-266d-4fe6-8160-86a967b21ddb"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.25.lt__": {"src": "hda", "id": "710299148e65bdb4", "uuid": "db0a5fc7-2f8d-4eb4-9dc2-e57635ca41ab"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.19.lt__": {"src": "hda", "id": "1e9f3a99da895dd5", "uuid": "08b73e49-5643-466c-86c6-23ce58861812"}, "__new_primary_file_sorclass.unique.lt\|sorclass.unique.lt__": {"src": "hda", "id": "fc51f4aebb0d65c0", "uuid": "8fa6fbcb-a7f8-4800-a968-a4911976e902"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.32.lt__": {"src": "hda", "id": "bec9e7f6333d2f36", "uuid": "156b9944-86bc-45ef-ac41-9d5291dd252d"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.26.lt__": {"src": "hda", "id": "bf875c8c7ae3c4c1", "uuid": "90d2df26-0a4e-4e6d-ac1c-81cb840c3761"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.03.lt__": {"src": "hda", "id": "9e4763fe06d09ee1", "uuid": "cebd135c-c029-42e4-8a13-edcf9f7fa2a8"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.04.lt__": {"src": "hda", "id": "a3a91b9854e528c1", "uuid": "8c3d70ea-ac21-4191-9e66-60bb499d8e46"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.14.lt__": {"src": "hda", "id": "6b308095f18dba3b", "uuid": "9ba48b4e-d989-467d-adfb-5583f91b0f62"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.01.lt__": {"src": "hda", "id": "d0f92696983585f3", "uuid": "3836c464-9fa2-42ab-8f7a-98eeae340704"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.18.lt__": {"src": "hda", "id": "b97c4dee7d66e350", "uuid": "beca01d7-5288-44c6-ba13-8d6bce14c1fc"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.09.lt__": {"src": "hda", "id": "c57e8cad56a6ff2a", "uuid": "cfc4ffbc-8b06-4608-9448-6e8bdbbee96a"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.29.lt__": {"src": "hda", "id": "49b04723a575686c", "uuid": "efac65e1-b627-4685-960b-021dc4682f49"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.22.lt__": {"src": "hda", "id": "10b3c1fe38490935", "uuid": "d7be3e40-f86a-41e5-9cbd-bebc6ca8a987"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.21.lt__": {"src": "hda", "id": "30b2b5ef7167ced6", "uuid": "50d3ac63-53e2-43bd-966c-0dbf3b34fa53"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.05.lt__": {"src": "hda", "id": "8031952532462a13", "uuid": "d9dfc3e0-370d-42a5-a4b9-a7fc39506fab"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.23.lt__": {"src": "hda", "id": "0dea4abf9bb0415a", "uuid": "c692dc6d-b5db-4d53-a90d-d7f162177c91"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.02.lt__": {"src": "hda", "id": "5936ec972cea4795", "uuid": "0a08ca9f-39b2-44b1-a5f4-f422a557ddb3"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.06.lt__": {"src": "hda", "id": "4efb683e59835243", "uuid": "ff63daba-f9ac-495b-9c99-004a47c23bc6"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.27.lt__": {"src": "hda", "id": "777dd7569c196c76", "uuid": "956fcdce-a6d3-4d84-b713-c35ab476121b"}, "logfile": {"src": "hda", "id": "10212f8402b2f379", "uuid": "93761f5c-938e-46a6-adcb-511c4a7d4032"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.45.lt__": {"src": "hda", "id": "0d3149843a425eae", "uuid": "ed2d13b5-f26e-454d-86a4-956bcea163d6"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.24.lt__": {"src": "hda", "id": "bfd4ea23a1e8bbdd", "uuid": "b2d06a53-2ec3-4e5b-be3c-6a27f2d87d0f"}, "summary": {"src": "hda", "id": "8747915bc2bfc819", "uuid": "05e4e93c-2242-4fff-85b0-37eebcd5fd19"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.13.lt__": {"src": "hda", "id": "5fc0b50ca858f8c5", "uuid": "95c1eeb0-1d07-468a-a70a-883db948f832"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.10.lt__": {"src": "hda", "id": "f8ccb799d73ec3dd", "uuid": "548923ee-863b-4120-a0dd-2d27df2d49c2"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.17.lt__": {"src": "hda", "id": "74bd528cdd946582", "uuid": "c3f23ca4-9d84-4027-9dc2-e7f85a80fcd7"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.07.lt__": {"src": "hda", "id": "f241b8715eaa6b7a", "uuid": "e60417f2-c85b-4b50-ae86-feb13f49d5a5"}, "__new_primary_file_sorclass.unique.lt\|sorclass.0.55.lt__": {"src": "hda", "id": "af41e4fac73960a1", "uuid": "90ea88dc-ea36-4b42-a782-e4d6556864b8"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.shared(shared=otu.dat,calc=sorclass,all=false,distance=true,out \rput=lt,processors=1)\n\nUsing 1 processors.\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.summary\notu.sorclass.unique.lt.dist\notu.sorclass.0.01.lt.dist\notu.sorclass.0.02.lt.dist\notu.sorclass.0.03.lt.dist\notu.sorclass.0.04.lt.dist\notu.sorclass.0.05.lt.dist\notu.sorclass.0.06.lt.dist\notu.sorclass.0.07.lt.dist\notu.sorclass.0.08.lt.dist\notu.sorclass.0.09.lt.dist\notu.sorclass.0.10.lt.dist\notu.sorclass.0.11.lt.dist\notu.sorclass.0.12.lt.dist\notu.sorclass.0.13.lt.dist\notu.sorclass.0.14.lt.dist\notu.sorclass.0.15.lt.dist\notu.sorclass.0.16.lt.dist\notu.sorclass.0.17.lt.dist\notu.sorclass.0.18.lt.dist\notu.sorclass.0.19.lt.dist\notu.sorclass.0.20.lt.dist\notu.sorclass.0.21.lt.dist\notu.sorclass.0.22.lt.dist\notu.sorclass.0.23.lt.dist\notu.sorclass.0.24.lt.dist\notu.sorclass.0.25.lt.dist\notu.sorclass.0.26.lt.dist\notu.sorclass.0.27.lt.dist\notu.sorclass.0.29.lt.dist\notu.sorclass.0.32.lt.dist\notu.sorclass.0.33.lt.dist\notu.sorclass.0.36.lt.dist\notu.sorclass.0.38.lt.dist\notu.sorclass.0.41.lt.dist\notu.sorclass.0.45.lt.dist\notu.sorclass.0.55.lt.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3393.dat' otu.dat && echo 'summary.shared( shared=otu.dat, calc=sorclass, all=false, distance=true, output=lt, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:40:17.726109", "params": {"distance": "\"true\"", "all": "\"false\"", "dbkey": "\"hg17\"", "label": "null", "subsample": "{\"use\": \"no\", \"__current_case__\": 1}", "groups": "null", "output": "\"lt\"", "calc": "\"sorclass\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6135", "id": "e033f1f6a16a5fdb", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_shared.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "bcc40440bc682f91"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "bcc40440bc682f91", "uuid": "cfb793d1-0a5b-4fb0-8348-342f73d77406"}}, "update_time": "2018-02-08T18:40:47.563664", "tool_id": "mothur_summary_single", "outputs": {"subsample_summary": {"src": "hda", "id": "8223d3aea03f91a3", "uuid": "5013c585-03ac-4702-934b-1120f0e54c2b"}, "logfile": {"src": "hda", "id": "a8b76ec0d8bb9cbb", "uuid": "0121e22c-dc77-450e-b2b8-d470c1e949cd"}, "summary": {"src": "hda", "id": "e75c6e7fd38a1506", "uuid": "498bcf3f-59f1-4df3-9878-5b7e881d6eef"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.single(shared=otu.dat,groupmode=true,calc=ace-chao-jack-sobs-si \rmpson-shannon-npshannon,abund=10)\n\nProcessing group forest\n\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nProcessing group pasture\n\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.groups.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3432.dat' otu.dat && echo 'summary.single( shared=otu.dat, groupmode=true ,calc=ace-chao-jack-sobs-simpson-shannon-npshannon ,abund=10 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:40:44.372596", "params": {"abund": "\"10\"", "groupmode": "\"true\"", "dbkey": "\"hg17\"", "label": "null", "subsample": "{\"use\": \"no\", \"__current_case__\": 1}", "calc": "[\"ace\", \"chao\", \"jack\", \"sobs\", \"simpson\", \"shannon\", \"npshannon\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6237", "id": "f691a5951523571b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_single.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"calc": ["ace", "bootstrap", "chao", "jack", "sobs", "simpsoneven", "shannoneven", "heip", "smithwilson", "bergerparker", "coverage", "goodscoverage", "simpson", "invsimpson", "qstat", "shannon", "npshannon", "boneh", "efron", "shen", "solow", "logseries", "geometric", "bstick", "nseqs"], "otu": {"src": "hda", "id": "7d4fdaa4731a0a66"}, "label": ["0.05", "0.22", "0.32"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "7d4fdaa4731a0a66", "uuid": "d335fa95-0e14-4417-ac8d-7dda122edf81"}}, "update_time": "2018-02-08T18:41:05.019830", "tool_id": "mothur_summary_single", "outputs": {"subsample_summary": {"src": "hda", "id": "7058e5df1feb4870", "uuid": "6677b51b-6194-4588-9305-54a602c6e0d8"}, "logfile": {"src": "hda", "id": "3c8c6806cad72b43", "uuid": "98646530-a51f-40f7-bfe0-dfb9c1d72bd1"}, "summary": {"src": "hda", "id": "97e0cfb4245121c2", "uuid": "a6b1aaa8-0a10-4db0-9562-c5b664054a9e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.single(shared=otu.dat,groupmode=true,label=0.05-0.22-0.32,calc= \race-bootstrap-chao-jack-sobs-simpsoneven-shannoneven-heip-smithwilson-bergerpark \rer-coverage-goodscoverage-simpson-invsimpson-qstat-shannon-npshannon-boneh-efron \r-shen-solow-logseries-geometric-bstick-nseqs,abund=10)\n\nProcessing group forest\n\n0.05\n0.22\n0.32\n\nProcessing group pasture\n\n0.05\n0.22\n0.32\n\nOutput File Names: \notu.groups.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3436.dat' otu.dat && echo 'summary.single( shared=otu.dat, groupmode=true ,label=0.05-0.22-0.32 ,calc=ace-bootstrap-chao-jack-sobs-simpsoneven-shannoneven-heip-smithwilson-bergerparker-coverage-goodscoverage-simpson-invsimpson-qstat-shannon-npshannon-boneh-efron-shen-solow-logseries-geometric-bstick-nseqs ,abund=10 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:41:01.859227", "params": {"abund": "\"10\"", "groupmode": "\"true\"", "dbkey": "\"hg17\"", "label": "[\"0.05\", \"0.22\", \"0.32\"]", "subsample": "{\"use\": \"no\", \"__current_case__\": 1}", "calc": "[\"ace\", \"bootstrap\", \"chao\", \"jack\", \"sobs\", \"simpsoneven\", \"shannoneven\", \"heip\", \"smithwilson\", \"bergerparker\", \"coverage\", \"goodscoverage\", \"simpson\", \"invsimpson\", \"qstat\", \"shannon\", \"npshannon\", \"boneh\", \"efron\", \"shen\", \"solow\", \"logseries\", \"geometric\", \"bstick\", \"nseqs\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6322", "id": "824db84bb730ff40", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_single.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "046dc814339ceff4"}, "groupmode": false}, "job": {"inputs": {"otu": {"src": "hda", "id": "046dc814339ceff4", "uuid": "5d866346-b6e2-40e8-aa7f-21a7a7ca52b8"}}, "update_time": "2018-02-08T18:41:22.364406", "tool_id": "mothur_summary_single", "outputs": {"__new_primary_file_pasture\|forest__": {"src": "hda", "id": "10280f41f2c7c752", "uuid": "280db29e-fa14-46cb-b8eb-b36a5103e501"}, "logfile": {"src": "hda", "id": "7ecd6e9675e139a5", "uuid": "c199174e-86c5-4c48-929e-045952aea5da"}, "__new_primary_file_pasture\|pasture__": {"src": "hda", "id": "09457d21386fcba3", "uuid": "134660e0-0e9f-41d3-8967-863d43c77492"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.single(shared=otu.dat,groupmode=false,calc=ace-chao-jack-sobs-s \rimpson-shannon-npshannon,abund=10)\n\nProcessing group forest\n\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nProcessing group pasture\n\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.forest.summary\notu.pasture.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3440.dat' otu.dat && echo 'summary.single( shared=otu.dat, groupmode=false ,calc=ace-chao-jack-sobs-simpson-shannon-npshannon ,abund=10 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:41:19.336102", "params": {"abund": "\"10\"", "groupmode": "\"false\"", "dbkey": "\"hg17\"", "label": "null", "subsample": "{\"use\": \"no\", \"__current_case__\": 1}", "calc": "[\"ace\", \"chao\", \"jack\", \"sobs\", \"simpson\", \"shannon\", \"npshannon\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6407", "id": "030656b247de0efe", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_single.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"subsample\|use": "yes", "otu": {"src": "hda", "id": "637ab171f9780706"}, "subsample\|iters": "42", "subsample\|subsample": "10"}, "job": {"inputs": {"otu": {"src": "hda", "id": "637ab171f9780706", "uuid": "50d44bc0-2460-415c-b57b-6488b6c68d87"}}, "update_time": "2018-02-08T18:41:39.911044", "tool_id": "mothur_summary_single", "outputs": {"subsample_summary": {"src": "hda", "id": "bd8bdd2a2038a190", "uuid": "153e4833-9b1e-4ebb-9b30-3edeb40fd930"}, "logfile": {"src": "hda", "id": "7822d21d2c1efd0f", "uuid": "6e7de8a6-23f3-48b9-a297-f29da3fa89e3"}, "summary": {"src": "hda", "id": "1bf84afd7b930518", "uuid": "ab83ce62-5f57-4e0c-b7e4-e6a3017d55a6"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.single(rabund=otu.dat,calc=ace-chao-jack-sobs-simpson-shannon-n \rpshannon,abund=10,subsample=10,iters=42)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.summary\notu.ave_std.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3444.dat' otu.dat && echo 'summary.single( rabund=otu.dat ,calc=ace-chao-jack-sobs-simpson-shannon-npshannon ,abund=10 ,subsample=10 ,iters=42 )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv otu.ave_std.summary otu.ave-std", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:41:36.674896", "params": {"abund": "\"10\"", "groupmode": "\"true\"", "dbkey": "\"hg17\"", "label": "null", "subsample": "{\"iters\": \"42\", \"subsample\": \"10\", \"use\": \"yes\", \"__current_case__\": 0}", "calc": "[\"ace\", \"chao\", \"jack\", \"sobs\", \"simpson\", \"shannon\", \"npshannon\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6495", "id": "35610b944eae1662", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_single.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"tax\|source": "hist", "tax\|taxonomy": {"src": "hda", "id": "97f081ffc622334b"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "97f081ffc622334b", "uuid": "94641a0d-5fcd-4a33-9735-80ca65bbce70"}}, "update_time": "2018-02-08T18:42:02.367553", "tool_id": "mothur_summary_tax", "outputs": {"logfile": {"src": "hda", "id": "ef827ef9990b2a18", "uuid": "637cc626-75b4-4632-8123-48e27a7d16d9"}, "taxsummary": {"src": "hda", "id": "13bed055b69c3f53", "uuid": "013032a7-b3f4-4148-b0c5-5d9301e501f5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.tax(taxonomy=tax.taxonomy.dat,relabund=false)\n\nIt took 0 secs to create the summary file for 242 sequences.\n\n\nOutput File Names: \ntax.taxonomy.tax.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3448.dat' tax.taxonomy.dat && ln -s 'None' name.dat && ln -s 'None' group.dat && ln -s 'None' count.dat && echo 'summary.tax( taxonomy=tax.taxonomy.dat, relabund=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:41:59.440341", "params": {"count": "null", "group": "null", "name": "null", "relabund": "\"false\"", "tax": "{\"source\": \"hist\", \"__current_case__\": 1, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 3448}]}}", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6584", "id": "0f7bfbeda1808692", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_tax.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"tax\|source": "hist", "tax\|taxonomy": {"src": "hda", "id": "5703175d6b845ade"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "5703175d6b845ade", "uuid": "523cfa41-689b-48c1-84d2-c6b4b8fabf74"}}, "update_time": "2018-02-08T18:42:19.745721", "tool_id": "mothur_summary_tax", "outputs": {"logfile": {"src": "hda", "id": "a062654a409016a9", "uuid": "afd4ff3b-f29e-4de1-b3ad-9effa990ef5b"}, "taxsummary": {"src": "hda", "id": "498b124981096150", "uuid": "7794df82-88d4-4f07-a14c-5237fa5da76a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.tax(taxonomy=tax.taxonomy.dat,relabund=false)\n\nIt took 0 secs to create the summary file for 242 sequences.\n\n\nOutput File Names: \ntax.taxonomy.tax.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3451.dat' tax.taxonomy.dat && ln -s 'None' name.dat && ln -s 'None' group.dat && ln -s 'None' count.dat && echo 'summary.tax( taxonomy=tax.taxonomy.dat, relabund=false )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:42:16.663062", "params": {"count": "null", "group": "null", "name": "null", "relabund": "\"false\"", "tax": "{\"source\": \"hist\", \"__current_case__\": 1, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 3451}]}}", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6673", "id": "32e4cd7ce068c585", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_tax.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|dist": {"src": "hda", "id": "6201901e7bcadfb4"}, "input\|source": "phylip"}, "job": {"inputs": {"dist": {"src": "hda", "id": "6201901e7bcadfb4", "uuid": "62a2698a-0ed3-4ecb-8d7d-3a9ac80d514e"}}, "update_time": "2018-02-08T18:42:37.247942", "tool_id": "mothur_tree_shared", "outputs": {"logfile": {"src": "hda", "id": "231281dccddcf77b", "uuid": "d331c62c-2528-404b-8d3e-fae0d559cbb2"}, "tre": {"src": "hda", "id": "bcdc79e6d8f62c6d", "uuid": "3b6a726e-e127-40bb-b982-64d8d017cb9b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > tree.shared(phylip=input_dist.dat,calc=jclass-thetayc,processors=1)\n\nUsing 1 processors.\n******************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n*******************************************************************\nTree complete. \n\nOutput File Names: \ninput_dist.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3454.dat' input_dist.dat && ln -s 'None' input_name.dat && echo 'tree.shared( phylip=input_dist.dat, calc=jclass-thetayc, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:42:34.145621", "params": {"input": "{\"source\": \"phylip\", \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 3454}]}, \"name\": null, \"__current_case__\": 1}", "calc": "[\"jclass\", \"thetayc\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6772", "id": "d1ff5636c3d156c1", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_tree_shared.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": 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"__new_primary_file_jclass.unique.cons\|jclass.0.13.ave__": {"src": "hda", "id": "4f2303e786a8aa1a", "uuid": "05fbb359-b5d6-4e10-b176-206719d56439"}, "__new_primary_file_jclass.unique.cons\|jclass.0.41.ave__": {"src": "hda", "id": "9a9674f3715775b8", "uuid": "8929b193-8790-4e65-af9c-70218bb24ad2"}, "__new_primary_file_jclass.unique.cons\|jclass.0.27.all__": {"src": "hda", "id": "7a877928f08a37f2", "uuid": "97805f61-2c09-4220-8d5c-110ef998d7f7"}, "__new_primary_file_jclass.unique.cons\|jclass.0.32.cons__": {"src": "hda", "id": "f67920aad2a3bc05", "uuid": "ad781555-3c40-41fc-bb18-4e5724944ce0"}, "__new_primary_file_jclass.unique.cons\|jclass.0.10.all__": {"src": "hda", "id": "22a81c9c4e0c0ce1", "uuid": "4cd2e75f-07d9-4088-a744-ce71d66692ca"}, "__new_primary_file_jclass.unique.cons\|jclass.0.24.all__": {"src": "hda", "id": "30e1dc3b30d9883e", "uuid": "256c0c2d-f1c6-4310-8864-35c2639ee2da"}, "__new_primary_file_jclass.unique.cons\|jclass.0.05.ave__": {"src": "hda", "id": "82c91c59d67b5472", "uuid": "8e5f97bc-4c65-43c7-946d-3af8694c2f93"}, "__new_primary_file_jclass.unique.cons\|jclass.0.29.ave__": {"src": "hda", "id": "ba55981b7d786ccd", "uuid": "25c46b16-8b69-4209-9039-608684d18c03"}, "__new_primary_file_jclass.unique.cons\|jclass.0.38.ave__": {"src": "hda", "id": "f1ffd5138cc4a01d", "uuid": "474884c6-2d98-4793-834f-4fbf5d185cfb"}, "__new_primary_file_jclass.unique.cons\|jclass.0.01.ave__": {"src": "hda", "id": "583e03b410a3a90a", "uuid": "10f34357-ee4b-40e7-b505-bc143ee08ddf"}, "__new_primary_file_jclass.unique.cons\|jclass.0.11.ave__": {"src": "hda", "id": "dd278f0ade637866", "uuid": "1c31c901-a39a-48f0-be29-65d0d7569071"}, "__new_primary_file_jclass.unique.cons\|jclass.0.32.all__": {"src": "hda", "id": "90768a1b9728ba37", "uuid": "8b50ad5a-d301-4e58-8a01-77f6580dbe9e"}, "__new_primary_file_jclass.unique.cons\|jclass.0.19.ave__": {"src": "hda", "id": "15e4d725538ff507", "uuid": "2dd16816-6d80-4dba-83f5-b379d52adb8e"}, "__new_primary_file_jclass.unique.cons\|jclass.0.07.cons__": {"src": "hda", "id": "78a5ef7657ea1833", "uuid": "22407272-1b16-44aa-be16-25e717daf1b7"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > tree.shared(shared=input_dist.dat,subsample=T,calc=jclass,processors=1) \r\u001b[A\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[K)\n\nUsing 1 processors.\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_dist.jclass.unique.ave.tre\ninput_dist.jclass.unique.all.tre\ninput_dist.jclass.unique.cons.tre\ninput_dist.jclass.0.01.ave.tre\ninput_dist.jclass.0.01.all.tre\ninput_dist.jclass.0.01.cons.tre\ninput_dist.jclass.0.02.ave.tre\ninput_dist.jclass.0.02.all.tre\ninput_dist.jclass.0.02.cons.tre\ninput_dist.jclass.0.03.ave.tre\ninput_dist.jclass.0.03.all.tre\ninput_dist.jclass.0.03.cons.tre\ninput_dist.jclass.0.04.ave.tre\ninput_dist.jclass.0.04.all.tre\ninput_dist.jclass.0.04.cons.tre\ninput_dist.jclass.0.05.ave.tre\ninput_dist.jclass.0.05.all.tre\ninput_dist.jclass.0.05.cons.tre\ninput_dist.jclass.0.06.ave.tre\ninput_dist.jclass.0.06.all.tre\ninput_dist.jclass.0.06.cons.tre\ninput_dist.jclass.0.07.ave.tre\ninput_dist.jclass.0.07.all.tre\ninput_dist.jclass.0.07.cons.tre\ninput_dist.jclass.0.08.ave.tre\ninput_dist.jclass.0.08.all.tre\ninput_dist.jclass.0.08.cons.tre\ninput_dist.jclass.0.09.ave.tre\ninput_dist.jclass.0.09.all.tre\ninput_dist.jclass.0.09.cons.tre\ninput_dist.jclass.0.10.ave.tre\ninput_dist.jclass.0.10.all.tre\ninput_dist.jclass.0.10.cons.tre\ninput_dist.jclass.0.11.ave.tre\ninput_dist.jclass.0.11.all.tre\ninput_dist.jclass.0.11.cons.tre\ninput_dist.jclass.0.12.ave.tre\ninput_dist.jclass.0.12.all.tre\ninput_dist.jclass.0.12.cons.tre\ninput_dist.jclass.0.13.ave.tre\ninput_dist.jclass.0.13.all.tre\ninput_dist.jclass.0.13.cons.tre\ninput_dist.jclass.0.14.ave.tre\ninput_dist.jclass.0.14.all.tre\ninput_dist.jclass.0.14.cons.tre\ninput_dist.jclass.0.15.ave.tre\ninput_dist.jclass.0.15.all.tre\ninput_dist.jclass.0.15.cons.tre\ninput_dist.jclass.0.16.ave.tre\ninput_dist.jclass.0.16.all.tre\ninput_dist.jclass.0.16.cons.tre\ninput_dist.jclass.0.17.ave.tre\ninput_dist.jclass.0.17.all.tre\ninput_dist.jclass.0.17.cons.tre\ninput_dist.jclass.0.18.ave.tre\ninput_dist.jclass.0.18.all.tre\ninput_dist.jclass.0.18.cons.tre\ninput_dist.jclass.0.19.ave.tre\ninput_dist.jclass.0.19.all.tre\ninput_dist.jclass.0.19.cons.tre\ninput_dist.jclass.0.20.ave.tre\ninput_dist.jclass.0.20.all.tre\ninput_dist.jclass.0.20.cons.tre\ninput_dist.jclass.0.21.ave.tre\ninput_dist.jclass.0.21.all.tre\ninput_dist.jclass.0.21.cons.tre\ninput_dist.jclass.0.22.ave.tre\ninput_dist.jclass.0.22.all.tre\ninput_dist.jclass.0.22.cons.tre\ninput_dist.jclass.0.23.ave.tre\ninput_dist.jclass.0.23.all.tre\ninput_dist.jclass.0.23.cons.tre\ninput_dist.jclass.0.24.ave.tre\ninput_dist.jclass.0.24.all.tre\ninput_dist.jclass.0.24.cons.tre\ninput_dist.jclass.0.25.ave.tre\ninput_dist.jclass.0.25.all.tre\ninput_dist.jclass.0.25.cons.tre\ninput_dist.jclass.0.26.ave.tre\ninput_dist.jclass.0.26.all.tre\ninput_dist.jclass.0.26.cons.tre\ninput_dist.jclass.0.27.ave.tre\ninput_dist.jclass.0.27.all.tre\ninput_dist.jclass.0.27.cons.tre\ninput_dist.jclass.0.29.ave.tre\ninput_dist.jclass.0.29.all.tre\ninput_dist.jclass.0.29.cons.tre\ninput_dist.jclass.0.32.ave.tre\ninput_dist.jclass.0.32.all.tre\ninput_dist.jclass.0.32.cons.tre\ninput_dist.jclass.0.33.ave.tre\ninput_dist.jclass.0.33.all.tre\ninput_dist.jclass.0.33.cons.tre\ninput_dist.jclass.0.36.ave.tre\ninput_dist.jclass.0.36.all.tre\ninput_dist.jclass.0.36.cons.tre\ninput_dist.jclass.0.38.ave.tre\ninput_dist.jclass.0.38.all.tre\ninput_dist.jclass.0.38.cons.tre\ninput_dist.jclass.0.41.ave.tre\ninput_dist.jclass.0.41.all.tre\ninput_dist.jclass.0.41.cons.tre\ninput_dist.jclass.0.45.ave.tre\ninput_dist.jclass.0.45.all.tre\ninput_dist.jclass.0.45.cons.tre\ninput_dist.jclass.0.55.ave.tre\ninput_dist.jclass.0.55.all.tre\ninput_dist.jclass.0.55.cons.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3457.dat' input_dist.dat && echo 'tree.shared( shared=input_dist.dat, subsample=T, calc=jclass, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:42:51.798862", "params": {"input": "{\"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 3457}]}, \"__current_case__\": 2, \"label\": null, \"source\": \"shared\", \"groups\": null, \"subsampling\": {\"iters\": \"\", \"subsample\": \"\", \"use\": \"yes\", \"__current_case__\": 0}}", "calc": "\"jclass\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6867", "id": "1380d0b9d445228e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_tree_shared.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|label": ["0.05", "0.22", "0.32"], "input\|dist": {"src": "hda", "id": "30d3d99850e82b58"}, "input\|source": "shared", "input\|groups": ["forest", "pasture"], "calc": ["sharedsobs", "sharedchao", "sharedace", "anderberg", "jclass", "jest", "kulczynski", "kulczynskicody", "kstest", "lennon", "ochiai", "sorclass", "sorest", "whittaker", "hamming", "memchi2", "memchord", "memeuclidean", "mempearson", "braycurtis", "jabund", "morisitahorn", "sorabund", "thetan", "thetayc", "canberra", "gower", "hellinger", "manhattan", "odum", "soergel", "spearman", 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"f50a00f8ed6bd0a3", "uuid": "9aaa5e0b-1f5c-4306-a5f3-ec10d41a04ed"}, "__new_primary_file_whittaker.0.32\|jabund.0.22__": {"src": "hda", "id": "44266e3275225d0f", "uuid": "c7212309-3124-44eb-b5c9-57310160f93b"}, "__new_primary_file_whittaker.0.32\|thetayc.0.32__": {"src": "hda", "id": "d1445ecd5410041e", "uuid": "9159e8ff-0cd1-43ae-9972-d4a1049942a8"}, "__new_primary_file_whittaker.0.32\|sharedsobs.0.22__": {"src": "hda", "id": "c9da000ecda07245", "uuid": "30f528df-ae4c-4d66-adb6-498a60e6e525"}, "__new_primary_file_whittaker.0.32\|odum.0.22__": {"src": "hda", "id": "d018ac0d94e012e8", "uuid": "7b13e8fd-df14-4be5-a637-f14b98e467b2"}, "__new_primary_file_whittaker.0.32\|sorest.0.32__": {"src": "hda", "id": "e746dd872753a042", "uuid": "3533d097-f86e-4f80-bab4-0612e4278c8b"}, "__new_primary_file_whittaker.0.32\|memchord.0.32__": {"src": "hda", "id": "735efd674719e24f", "uuid": "5469f970-b958-4b90-9d86-8c9a36f7b790"}, "__new_primary_file_whittaker.0.32\|hellinger.0.22__": {"src": "hda", "id": "0a8b6862ab30b456", "uuid": "d4170f76-cc41-4a80-937e-d4ea5bf479a1"}, "__new_primary_file_whittaker.0.32\|gower.0.05__": {"src": "hda", "id": "4903012a42643751", "uuid": "e8191da1-6091-473a-8708-ade1fb227c27"}, "__new_primary_file_whittaker.0.32\|structchi2.0.22__": {"src": "hda", "id": "4396493fbfdb6ad4", "uuid": "3b7e4011-fdb8-484a-a21e-f908efa2acd5"}, "__new_primary_file_whittaker.0.32\|hellinger.0.32__": {"src": "hda", "id": "baadb50d03c0b826", "uuid": "b3c0803f-91a9-44eb-8db5-0baba4aa198a"}, "__new_primary_file_whittaker.0.32\|hamming.0.05__": {"src": "hda", "id": "6dd4d5ec7dea33a8", "uuid": "511e6489-e5d0-4de6-bb53-87987add5d12"}, "__new_primary_file_whittaker.0.32\|kulczynski.0.05__": {"src": "hda", "id": "cd687c1796d12cc6", "uuid": "d1af4501-b106-4652-8931-fc7694dbb0d8"}, "__new_primary_file_whittaker.0.32\|jclass.0.05__": {"src": "hda", "id": "a7a6eb5dd94f4973", "uuid": "943c4406-a903-4000-8924-e8680ca58d6a"}, "__new_primary_file_whittaker.0.32\|thetayc.0.05__": {"src": "hda", "id": "cd1051f5597a9f45", "uuid": "cc6a47f8-4f98-4a6a-a8ac-c29b7de64308"}, "__new_primary_file_whittaker.0.32\|speciesprofile.0.22__": {"src": "hda", "id": "0b9b6fba2374f3e4", "uuid": "3333c796-64f4-4ac5-8b6d-d559be3ede6c"}, "__new_primary_file_whittaker.0.32\|soergel.0.22__": {"src": "hda", "id": "d398ff86b62273ad", "uuid": "07795010-5665-45ad-8658-2b809e99f259"}, "__new_primary_file_whittaker.0.32\|memchi2.0.05__": {"src": "hda", "id": "a6cfc510c05ff9d2", "uuid": "a923406d-adac-4875-aa54-92355c3da3ff"}, "__new_primary_file_whittaker.0.32\|soergel.0.05__": {"src": "hda", "id": "5668ef31ed2adf25", "uuid": "fb53a96f-159d-4383-a215-1500951f3df8"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > tree.shared(shared=input_dist.dat,groups=forest-pasture,label=0.05-0.22 \r-0.32,calc=sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulc \rzynskicody-kstest-lennon-ochiai-sorclass-sorest-whittaker-hamming-memchi2-memcho \rrd-memeuclidean-mempearson-braycurtis-jabund-morisitahorn-sorabund-thetan-thetay \rc-canberra-gower-hellinger-manhattan-odum-soergel-spearman-speciesprofile-struct \rchi2-structchord-structeuclidean-structkulczynski-structpearson-sharednseqs-shar \redobserved,processors=1)\n\nUsing 1 processors.\nsharedobserved is not a valid estimator for the tree.shared command and will be disregarded. Valid estimators are anderberg, braycurtis, canberra, gower, hamming, hellinger, jabund, jclass, jest, jsd, kstest, kulczynski, kulczynskicody, lennon, manhattan, memchi2, memchord, memeuclidean, mempearson, morisitahorn, ochiai, odum, rjsd, sharedace, sharedchao, sharednseqs, sharedsobs, soergel, sorabund, sorclass, sorest, spearman, speciesprofile, structchi2, structchord, structeuclidean, structkulczynski, structpearson, thetan, thetayc, whittaker, \n0.05\n0.22\n0.32\n\nOutput File Names: \ninput_dist.sharedsobs.0.05.tre\ninput_dist.sharedchao.0.05.tre\ninput_dist.sharedace.0.05.tre\ninput_dist.anderberg.0.05.tre\ninput_dist.jclass.0.05.tre\ninput_dist.jest.0.05.tre\ninput_dist.kulczynski.0.05.tre\ninput_dist.kulczynskicody.0.05.tre\ninput_dist.kstest.0.05.tre\ninput_dist.lennon.0.05.tre\ninput_dist.ochiai.0.05.tre\ninput_dist.sorclass.0.05.tre\ninput_dist.sorest.0.05.tre\ninput_dist.whittaker.0.05.tre\ninput_dist.hamming.0.05.tre\ninput_dist.memchi2.0.05.tre\ninput_dist.memchord.0.05.tre\ninput_dist.memeuclidean.0.05.tre\ninput_dist.mempearson.0.05.tre\ninput_dist.braycurtis.0.05.tre\ninput_dist.jabund.0.05.tre\ninput_dist.morisitahorn.0.05.tre\ninput_dist.sorabund.0.05.tre\ninput_dist.thetan.0.05.tre\ninput_dist.thetayc.0.05.tre\ninput_dist.canberra.0.05.tre\ninput_dist.gower.0.05.tre\ninput_dist.hellinger.0.05.tre\ninput_dist.manhattan.0.05.tre\ninput_dist.odum.0.05.tre\ninput_dist.soergel.0.05.tre\ninput_dist.spearman.0.05.tre\ninput_dist.speciesprofile.0.05.tre\ninput_dist.structchi2.0.05.tre\ninput_dist.structchord.0.05.tre\ninput_dist.structeuclidean.0.05.tre\ninput_dist.structkulczynski.0.05.tre\ninput_dist.structpearson.0.05.tre\ninput_dist.sharednseqs.0.05.tre\ninput_dist.sharedsobs.0.22.tre\ninput_dist.sharedchao.0.22.tre\ninput_dist.sharedace.0.22.tre\ninput_dist.anderberg.0.22.tre\ninput_dist.jclass.0.22.tre\ninput_dist.jest.0.22.tre\ninput_dist.kulczynski.0.22.tre\ninput_dist.kulczynskicody.0.22.tre\ninput_dist.kstest.0.22.tre\ninput_dist.lennon.0.22.tre\ninput_dist.ochiai.0.22.tre\ninput_dist.sorclass.0.22.tre\ninput_dist.sorest.0.22.tre\ninput_dist.whittaker.0.22.tre\ninput_dist.hamming.0.22.tre\ninput_dist.memchi2.0.22.tre\ninput_dist.memchord.0.22.tre\ninput_dist.memeuclidean.0.22.tre\ninput_dist.mempearson.0.22.tre\ninput_dist.braycurtis.0.22.tre\ninput_dist.jabund.0.22.tre\ninput_dist.morisitahorn.0.22.tre\ninput_dist.sorabund.0.22.tre\ninput_dist.thetan.0.22.tre\ninput_dist.thetayc.0.22.tre\ninput_dist.canberra.0.22.tre\ninput_dist.gower.0.22.tre\ninput_dist.hellinger.0.22.tre\ninput_dist.manhattan.0.22.tre\ninput_dist.odum.0.22.tre\ninput_dist.soergel.0.22.tre\ninput_dist.spearman.0.22.tre\ninput_dist.speciesprofile.0.22.tre\ninput_dist.structchi2.0.22.tre\ninput_dist.structchord.0.22.tre\ninput_dist.structeuclidean.0.22.tre\ninput_dist.structkulczynski.0.22.tre\ninput_dist.structpearson.0.22.tre\ninput_dist.sharednseqs.0.22.tre\ninput_dist.sharedsobs.0.32.tre\ninput_dist.sharedchao.0.32.tre\ninput_dist.sharedace.0.32.tre\ninput_dist.anderberg.0.32.tre\ninput_dist.jclass.0.32.tre\ninput_dist.jest.0.32.tre\ninput_dist.kulczynski.0.32.tre\ninput_dist.kulczynskicody.0.32.tre\ninput_dist.kstest.0.32.tre\ninput_dist.lennon.0.32.tre\ninput_dist.ochiai.0.32.tre\ninput_dist.sorclass.0.32.tre\ninput_dist.sorest.0.32.tre\ninput_dist.whittaker.0.32.tre\ninput_dist.hamming.0.32.tre\ninput_dist.memchi2.0.32.tre\ninput_dist.memchord.0.32.tre\ninput_dist.memeuclidean.0.32.tre\ninput_dist.mempearson.0.32.tre\ninput_dist.braycurtis.0.32.tre\ninput_dist.jabund.0.32.tre\ninput_dist.morisitahorn.0.32.tre\ninput_dist.sorabund.0.32.tre\ninput_dist.thetan.0.32.tre\ninput_dist.thetayc.0.32.tre\ninput_dist.canberra.0.32.tre\ninput_dist.gower.0.32.tre\ninput_dist.hellinger.0.32.tre\ninput_dist.manhattan.0.32.tre\ninput_dist.odum.0.32.tre\ninput_dist.soergel.0.32.tre\ninput_dist.spearman.0.32.tre\ninput_dist.speciesprofile.0.32.tre\ninput_dist.structchi2.0.32.tre\ninput_dist.structchord.0.32.tre\ninput_dist.structeuclidean.0.32.tre\ninput_dist.structkulczynski.0.32.tre\ninput_dist.structpearson.0.32.tre\ninput_dist.sharednseqs.0.32.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3567.dat' input_dist.dat && echo 'tree.shared( shared=input_dist.dat, groups=forest-pasture, label=0.05-0.22-0.32, calc=sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-kstest-lennon-ochiai-sorclass-sorest-whittaker-hamming-memchi2-memchord-memeuclidean-mempearson-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc-canberra-gower-hellinger-manhattan-odum-soergel-spearman-speciesprofile-structchi2-structchord-structeuclidean-structkulczynski-structpearson-sharednseqs-sharedobserved, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:43:20.325320", "params": {"input": "{\"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 3567}]}, \"__current_case__\": 2, \"label\": [\"0.05\", \"0.22\", \"0.32\"], \"source\": \"shared\", \"groups\": [\"forest\", \"pasture\"], \"subsampling\": {\"use\": \"no\", \"__current_case__\": 1}}", "calc": "[\"sharedsobs\", \"sharedchao\", \"sharedace\", \"anderberg\", \"jclass\", \"jest\", \"kulczynski\", \"kulczynskicody\", \"kstest\", \"lennon\", \"ochiai\", \"sorclass\", \"sorest\", \"whittaker\", \"hamming\", \"memchi2\", \"memchord\", \"memeuclidean\", \"mempearson\", \"braycurtis\", \"jabund\", \"morisitahorn\", \"sorabund\", \"thetan\", \"thetayc\", \"canberra\", \"gower\", \"hellinger\", \"manhattan\", \"odum\", \"soergel\", \"spearman\", \"speciesprofile\", \"structchi2\", \"structchord\", \"structeuclidean\", \"structkulczynski\", \"structpearson\", \"sharednseqs\", \"sharedobserved\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6951", "id": "0127e3e8a6471eea", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_tree_shared.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|dist": {"src": "hda", "id": "961a47c559285244"}, "input\|name": {"src": "hda", "id": "e579f508f7c68ef6"}, "input\|source": "column"}, "job": {"inputs": {"dist": {"src": "hda", "id": "961a47c559285244", "uuid": "8963264e-8c2d-4832-9118-cc2c994c738d"}, "name": {"src": "hda", "id": "e579f508f7c68ef6", "uuid": "f87a42d3-ec48-433f-a653-b4dba9c5f380"}}, "update_time": "2018-02-08T18:43:56.010151", "tool_id": "mothur_tree_shared", "outputs": {"logfile": {"src": "hda", "id": "b96b0bc03c50c213", "uuid": "589355b7-6228-416e-b93d-65ca3f1de74b"}, "tre": {"src": "hda", "id": "1e52af9f521721f4", "uuid": "1e557f11-db81-450e-b091-beb0cf5e8852"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > tree.shared(column=input_dist.dat,name=input_name.dat,calc=jclass-theta \ryc,processors=1)\n\nUsing 1 processors.\n****************###########\nReading matrix: \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n********************************************************************\nTree complete. \n\nOutput File Names: \ninput_dist.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3686.dat' input_dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3687.dat' input_name.dat && echo 'tree.shared( column=input_dist.dat, name=input_name.dat, calc=jclass-thetayc, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:43:52.868228", "params": {"input": "{\"source\": \"column\", \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 3686}]}, \"name\": {\"values\": [{\"src\": \"hda\", \"id\": 3687}]}, \"__current_case__\": 0}", "calc": "[\"jclass\", \"thetayc\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7076", "id": "d2877f6f2610c2e2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_tree_shared.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"flow": {"src": "hda", "id": "113cebc66d7029f4"}}, "job": {"inputs": {"flow": {"src": "hda", "id": "113cebc66d7029f4", "uuid": "32937a76-7eb0-4ba2-bcf4-1501f91e7efa"}}, "update_time": "2018-02-08T18:44:13.674069", "tool_id": "mothur_trim_flows", "outputs": {"flow_files": {"src": "hda", "id": "656ec4006d660f1e", "uuid": "eb3a4ea6-f598-49c0-bf7d-cc8aa974ac37"}, "logfile": {"src": "hda", "id": "0586ab56d27d9ba2", "uuid": "1fa27a7f-c65a-4225-b91f-1713116e6299"}, "scrap_flow": {"src": "hda", "id": "ea6e776dce59738c", "uuid": "6b64a2db-fc47-4543-8e5a-a8a6129bfeb2"}, "trim_flow": {"src": "hda", "id": "2d34558476a1163b", "uuid": "82fba6fd-ea8d-404e-b6b2-af259e0287dc"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > trim.flows(flow=flow.dat,minflows=450,maxflows=450,order=A,signal=0.5,n \roise=0.7,fasta=false,processors=1)\n\nUsing 1 processors.\n107\n\nOutput File Names: \nflow.trim.flow\nflow.scrap.flow\nflow.flow.files\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3690.dat' flow.dat && echo 'trim.flows( flow=flow.dat, minflows=450, maxflows=450, order=A, signal=0.5, noise=0.7, fasta=false, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv flow.trim.flow flow.trim && mv flow.scrap.flow flow.scrap", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:44:10.318502", "params": {"maxflows": "\"450\"", "noise": "\"0.7\"", "oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "signal": "\"0.5\"", "maxhomop": "\"\"", "dbkey": "\"hg17\"", "minflows": "\"450\"", "fasta": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "order": "\"A\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7167", "id": "8cd4beb5cf8a2f93", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_trim_flows.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"oligo\|oligos": {"src": "hda", "id": "7435327024c6ed38"}, "oligo\|add": "yes", "flow": {"src": "hda", "id": "52fb102da68a2516"}, "order": "I", "oligo\|pdiffs": "10", "fasta": true, "oligo\|bdiffs": "10"}, "job": {"inputs": {"oligos": {"src": "hda", "id": "7435327024c6ed38", "uuid": "b3794253-1136-4bc9-b98d-f61f8a8f4e68"}, "flow": {"src": "hda", "id": "52fb102da68a2516", "uuid": "f0a94d84-d7b8-463c-b0d4-1611c0a29b56"}}, "update_time": "2018-02-08T18:44:45.030422", "tool_id": "mothur_trim_flows", "outputs": {"flow_fasta": {"src": "hda", "id": "1702773de504f46c", "uuid": "4723a1d9-19fe-468b-8190-f08f237f591b"}, "__new_primary_file_F003D142\|F003D142__": {"src": "hda", "id": "796a3be2ad26f064", "uuid": "49605ed7-4690-4303-9aee-95d244e32c93"}, "flow_files": {"src": "hda", "id": "ad3afa20e990c280", "uuid": "9180f164-b852-41fc-91c9-fbf5ca513c65"}, "scrap_flow": {"src": "hda", "id": "f30cdc880e9c60f1", "uuid": "7674ae26-298a-4877-afed-884feb505159"}, "__new_primary_file_F003D142\|F003D006__": {"src": "hda", "id": "d5d52d49034f5895", "uuid": "fabe0c37-7373-4c45-91cd-9a0761242e9c"}, "logfile": {"src": "hda", "id": "25d2b0eb25240170", "uuid": "ada424ee-49fc-442d-9250-9544ffac7042"}, "trim_flow": {"src": "hda", "id": "d1dd3aa4c719e98f", "uuid": "e8f92f6e-4297-48b2-a305-ec469967806b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > trim.flows(flow=flow.dat,minflows=450,maxflows=450,order=I,signal=0.5,n \roise=0.7,oligos=oligo.oligos.dat,bdiffs=10,pdiffs=10,tdiffs=0,ldiffs=0,sdiffs=0, \rfasta=true,processors=1)\n\nUsing 1 processors.\n2\n\nOutput File Names: \nflow.flow.fasta\nflow.trim.flow\nflow.scrap.flow\nflow.F003D142.flow\nflow.F003D006.flow\nflow.flow.files\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3695.dat' flow.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3696.dat' oligo.oligos.dat && echo 'trim.flows( flow=flow.dat, minflows=450, maxflows=450, order=I, signal=0.5, noise=0.7, oligos=oligo.oligos.dat, bdiffs=10, pdiffs=10, tdiffs=0, ldiffs=0, sdiffs=0, fasta=true, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv flow.trim.flow flow.trim && mv flow.scrap.flow flow.scrap", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:44:41.443491", "params": {"maxflows": "\"450\"", "noise": "\"0.7\"", "oligo": "{\"bdiffs\": \"10\", \"sdiffs\": \"0\", \"ldiffs\": \"0\", \"pdiffs\": \"10\", \"tdiffs\": \"0\", \"add\": \"yes\", \"__current_case__\": 1, \"oligos\": {\"values\": [{\"src\": \"hda\", \"id\": 3696}]}}", "signal": "\"0.5\"", "maxhomop": "\"\"", "dbkey": "\"hg17\"", "minflows": "\"450\"", "fasta": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "order": "\"I\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7283", "id": "e400af07ae3fa77f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_trim_flows.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "a4a75edff1315423"}, "maxhomop": "4", "names": {"src": "hda", "id": "a19ac8ddc9ec0357"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "a4a75edff1315423", "uuid": "ca78d74b-119e-4138-8c09-5663b94e6bc0"}, "names": {"src": "hda", "id": "a19ac8ddc9ec0357", "uuid": "45c1b563-5ca5-4cf5-802c-c4387f6c28f8"}}, "update_time": "2018-02-08T18:45:30.049751", "tool_id": "mothur_trim_seqs", "outputs": {"trim_fasta": {"src": "hda", "id": "086eda3627b4c383", "uuid": "263d8389-3ec0-45e9-ab3d-6d8a8254cbf5"}, "logfile": {"src": "hda", "id": "4de4e57b6b68d2e8", "uuid": "d9665fcc-9bf4-475a-a4ba-d22174ec9158"}, "trim_names": {"src": "hda", "id": "9590c041f0c58cb5", "uuid": "a15a909d-8f7f-4af5-b173-bcfa30cd0d35"}, "scrap_names": {"src": "hda", "id": "0c5e32c449987b70", "uuid": "f132f816-1a4e-43df-b749-4b6331cb38bf"}, "scrap_fasta": {"src": "hda", "id": "c7132f326e1735c5", "uuid": "083cb5a8-083b-4990-9ecd-f9ad635bc74e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > trim.seqs(fasta=fasta.dat,minlength=0,maxlength=0,maxambig=-1,maxhomop= \r4,keepfirst=0,removelast=0,flip=false,name=names.dat,logtransform=false,checkori \rent=false,processors=1)\n\nUsing 1 processors.\n98\n\n\nOutput File Names: \nfasta.trim.fasta\nfasta.scrap.fasta\nnames.trim.names\nnames.scrap.names\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3704.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3705.dat' names.dat && ln -s 'None' count.dat && echo 'trim.seqs( fasta=fasta.dat, minlength=0, maxlength=0, maxambig=-1, maxhomop=4, keepfirst=0, removelast=0, flip=false, name=names.dat, logtransform=false, checkorient=false, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv fasta.trim.fasta fasta.trim && mv fasta.scrap.fasta fasta.scrap", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:45:26.324404", "params": {"count": "null", "oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "logtransform": "\"false\"", "checkorient": "\"false\"", "minlength": "\"0\"", "maxhomop": "\"4\"", "flip": "\"false\"", "dbkey": "\"hg17\"", "qual": "{\"add2\": \"no\", \"__current_case__\": 0}", "removelast": "\"0\"", "maxlength": "\"0\"", "maxambig": "\"-1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "keepfirst": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7398", "id": "d9eeaf6b2b0ea17f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_trim_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"count": {"src": "hda", "id": "643ecb59a2c3ee18"}, "fasta": {"src": "hda", "id": "411acc63c278eae0"}, "maxhomop": "4"}, "job": {"inputs": {"count": {"src": "hda", "id": "643ecb59a2c3ee18", "uuid": "c3b13bbf-04f4-43f2-87c3-258a8c2718cf"}, "fasta": {"src": "hda", "id": "411acc63c278eae0", "uuid": "3ac2bbb5-576b-4119-aa0e-b61708b757f4"}}, "update_time": "2018-02-08T18:46:09.845777", "tool_id": "mothur_trim_seqs", "outputs": {"trim_fasta": {"src": "hda", "id": "d18b75b0ada0b975", "uuid": "46585795-839f-49f6-9413-87cf07bc4dd8"}, "trim_count": {"src": "hda", "id": "b89907572eef89bb", "uuid": "6a33eeca-8a62-421f-9259-f5c9bb6d75cc"}, "logfile": {"src": "hda", "id": "4a2d02ae29134135", "uuid": "d82b14b6-7d65-4ed0-b8c7-43cab53059bc"}, "scrap_count": {"src": "hda", "id": "0eb01516e0bf5413", "uuid": "1f5a0f89-e35a-4281-9785-c973be1cd403"}, "scrap_fasta": {"src": "hda", "id": "0a20b5e39a223282", "uuid": "9fb65e6d-7f2a-47bb-9c71-a66ebbcc10dd"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > trim.seqs(fasta=fasta.dat,minlength=0,maxlength=0,maxambig=-1,maxhomop= \r4,keepfirst=0,removelast=0,flip=false,logtransform=false,checkorient=false,count \r=count.dat,processors=1)\n\nUsing 1 processors.\n98\n\n\nOutput File Names: \nfasta.trim.fasta\nfasta.scrap.fasta\ncount.trim.count_table\ncount.scrap.count_table\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3711.dat' fasta.dat && ln -s 'None' names.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3712.dat' count.dat && echo 'trim.seqs( fasta=fasta.dat, minlength=0, maxlength=0, maxambig=-1, maxhomop=4, keepfirst=0, removelast=0, flip=false, logtransform=false, checkorient=false, count=count.dat, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv fasta.trim.fasta fasta.trim && mv fasta.scrap.fasta fasta.scrap", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:46:05.717799", "params": {"oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "logtransform": "\"false\"", "checkorient": "\"false\"", "minlength": "\"0\"", "maxhomop": "\"4\"", "flip": "\"false\"", "dbkey": "\"hg17\"", "qual": "{\"add2\": \"no\", \"__current_case__\": 0}", "removelast": "\"0\"", "names": "null", "maxlength": "\"0\"", "maxambig": "\"-1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "keepfirst": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7519", "id": "92afd254baae3cac", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_trim_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"oligo\|pdiffs": "100", "oligo\|add": "yes", "fasta": {"src": "hda", "id": "e3535752753237cc"}, "oligo\|oligos": {"src": "hda", "id": "449b1393f148b461"}, "oligo\|bdiffs": "100"}, "job": {"inputs": {"oligos": {"src": "hda", "id": "449b1393f148b461", "uuid": "d3ecfbe3-82d7-4653-91b3-0dc533243380"}, "fasta": {"src": "hda", "id": "e3535752753237cc", "uuid": "038e784b-9ef9-41ca-be9c-3cd1ca3b8d1e"}}, "update_time": "2018-02-08T18:46:49.872573", "tool_id": "mothur_trim_seqs", "outputs": {"trim_fasta": {"src": "hda", "id": "58247062b75fcc28", "uuid": "7ed9fab5-b057-4f16-98d9-fcc76b26eaf7"}, "groups_file": {"src": "hda", "id": "51245ff49e713d95", "uuid": "f1155b05-066a-42b0-b884-3f16249b6e09"}, "logfile": {"src": "hda", "id": "72a0b075a3958e20", "uuid": "9c442237-3f36-4b3c-88fa-befa7ad3ccc2"}, "scrap_fasta": {"src": "hda", "id": "3aa93502f78ca78e", "uuid": "cc655219-5ebe-4c48-8b2a-5a3d198e6869"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > trim.seqs(fasta=fasta.dat,minlength=0,maxlength=0,maxambig=-1,maxhomop= \r0,keepfirst=0,removelast=0,oligos=oligo.oligos.dat,bdiffs=100,pdiffs=100,tdiffs= \r0,ldiffs=0,sdiffs=0,keepforward=false,allfiles=false,flip=false,logtransform=fal \rse,checkorient=false,processors=1)\n\nUsing 1 processors.\n98\n\nGroup count: \nF003D000\t32\nF003D006\t1\nF003D008\t3\nF003D142\t7\nF003D144\t8\nF003D146\t4\nF003D148\t33\nF003D150\t1\nMOCK.GQY1XT001\t2\nTotal of all groups is 91\n\nOutput File Names: \nfasta.trim.fasta\nfasta.scrap.fasta\nfasta.groups\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3718.dat' fasta.dat && ln -s 'None' names.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3719.dat' oligo.oligos.dat && echo 'trim.seqs( fasta=fasta.dat, minlength=0, maxlength=0, maxambig=-1, maxhomop=0, keepfirst=0, removelast=0, oligos=oligo.oligos.dat, bdiffs=100, pdiffs=100, tdiffs=0, ldiffs=0, sdiffs=0, keepforward=false, allfiles=false, flip=false, logtransform=false, checkorient=false, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv fasta.trim.fasta fasta.trim && mv fasta.scrap.fasta fasta.scrap", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:46:46.434270", "params": {"count": "null", "oligo": "{\"bdiffs\": \"100\", \"sdiffs\": \"0\", \"allfiles\": \"false\", \"ldiffs\": \"0\", \"pdiffs\": \"100\", \"tdiffs\": \"0\", \"keepforward\": \"false\", \"add\": \"yes\", \"__current_case__\": 1, \"oligos\": {\"values\": [{\"src\": \"hda\", \"id\": 3719}]}}", "logtransform": "\"false\"", "checkorient": "\"false\"", "minlength": "\"0\"", "maxhomop": "\"0\"", "flip": "\"false\"", "dbkey": "\"hg17\"", "qual": "{\"add2\": \"no\", \"__current_case__\": 0}", "removelast": "\"0\"", "names": "null", "maxlength": "\"0\"", "maxambig": "\"-1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "keepfirst": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7643", "id": "ab005d4cdb71cef2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_trim_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"oligo\|oligos": {"src": "hda", "id": "4fa21a2ab98d6a11"}, "oligo\|add": "yes", "oligo\|allfiles": true, "oligo\|pdiffs": "100", "fasta": {"src": "hda", "id": "8f862e98c671efbc"}, "oligo\|bdiffs": "100"}, "job": {"inputs": {"oligos": {"src": "hda", "id": "4fa21a2ab98d6a11", "uuid": "4f8eff6d-55e5-415a-bc0d-c2d29719aeba"}, "fasta": {"src": "hda", "id": "8f862e98c671efbc", "uuid": "4db73f9a-c8d2-4412-a03a-1e97a9d88de9"}}, "update_time": "2018-02-08T18:47:24.871409", "tool_id": "mothur_trim_seqs", "outputs": {"__new_primary_file_MOCK.GQY1XT001\|F003D142__": {"src": "hda", "id": "e2a4c2b0e0ee29b7", "uuid": "a6fdc088-e73a-40f8-bf55-e4e6b05e6df6"}, "__new_primary_file_MOCK.GQY1XT001\|F003D008__": {"src": "hda", "id": "d3e37e974b33cd78", "uuid": "326975c6-ec31-4566-bdf9-992bf271f3fb"}, "trim_fasta": {"src": "hda", "id": "d3b573d52d73e766", "uuid": "aac454ae-8526-4fd9-814b-a1fcd172b940"}, "__new_primary_file_MOCK.GQY1XT001\|F003D006__": {"src": "hda", "id": "bc7fa00e824e36c4", "uuid": "60d14df6-432d-4d0f-8313-f0ae7c23a9fe"}, "__new_primary_file_MOCK.GQY1XT001\|F003D144__": {"src": "hda", "id": "0476296d69f55ec7", "uuid": "800f3e5c-b564-4b05-8b4e-10393cf64eb5"}, "groups_file": {"src": "hda", "id": "521e581659a1db8a", "uuid": "7d8467df-a299-4ab5-981c-809d2c955ab8"}, "__new_primary_file_MOCK.GQY1XT001\|MOCK.GQY1XT001__": {"src": "hda", "id": "6bedfbc6c2ea7489", "uuid": "e0de8a75-b145-4e48-8be9-bd44ba70fa91"}, "scrap_fasta": {"src": "hda", "id": "f5a3628d40cdc020", "uuid": "2daaa7dd-b657-4bab-9daf-774b27ed03d1"}, "__new_primary_file_MOCK.GQY1XT001\|F003D000__": {"src": "hda", "id": "e55fe44fe41229c1", "uuid": "e20e9144-4c6b-4fc7-88ab-0c7752e46b6c"}, "__new_primary_file_MOCK.GQY1XT001\|F003D150__": {"src": "hda", "id": "ea11db34dbe66961", "uuid": "0973157d-fa0f-4060-b1d7-9fbbcc01ee45"}, "logfile": {"src": "hda", "id": "227335580a9b176b", "uuid": "da08afb2-6cc3-4c9d-a89c-ac1d2243af70"}, "__new_primary_file_MOCK.GQY1XT001\|F003D146__": {"src": "hda", "id": "2e2129d42462228f", "uuid": "617ed727-566c-4679-83a7-3c1e15e38d8f"}, "__new_primary_file_MOCK.GQY1XT001\|F003D148__": {"src": "hda", "id": "b2e57fd9cecc5aab", "uuid": "5ebc12ad-7f12-47b2-871c-d84ee6e05504"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > trim.seqs(fasta=fasta.dat,minlength=0,maxlength=0,maxambig=-1,maxhomop= \r0,keepfirst=0,removelast=0,oligos=oligo.oligos.dat,bdiffs=100,pdiffs=100,tdiffs= \r0,ldiffs=0,sdiffs=0,keepforward=false,allfiles=true,flip=false,logtransform=fals \re,checkorient=false,processors=1)\n\nUsing 1 processors.\n98\n\nGroup count: \nF003D000\t32\nF003D006\t1\nF003D008\t3\nF003D142\t7\nF003D144\t8\nF003D146\t4\nF003D148\t33\nF003D150\t1\nMOCK.GQY1XT001\t2\nTotal of all groups is 91\n\nOutput File Names: \nfasta.trim.fasta\nfasta.scrap.fasta\nfasta.MOCK.GQY1XT001.fasta\nfasta.F003D144.fasta\nfasta.F003D000.fasta\nfasta.F003D148.fasta\nfasta.F003D142.fasta\nfasta.F003D146.fasta\nfasta.F003D150.fasta\nfasta.F003D008.fasta\nfasta.F003D006.fasta\nfasta.groups\nfasta.F003D000.groups\nfasta.F003D006.groups\nfasta.F003D008.groups\nfasta.F003D142.groups\nfasta.F003D144.groups\nfasta.F003D146.groups\nfasta.F003D148.groups\nfasta.F003D150.groups\nfasta.MOCK.GQY1XT001.groups\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3724.dat' fasta.dat && ln -s 'None' names.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3725.dat' oligo.oligos.dat && echo 'trim.seqs( fasta=fasta.dat, minlength=0, maxlength=0, maxambig=-1, maxhomop=0, keepfirst=0, removelast=0, oligos=oligo.oligos.dat, bdiffs=100, pdiffs=100, tdiffs=0, ldiffs=0, sdiffs=0, keepforward=false, allfiles=true, flip=false, logtransform=false, checkorient=false, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv fasta.trim.fasta fasta.trim && mv fasta.scrap.fasta fasta.scrap", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:47:20.369148", "params": {"count": "null", "oligo": "{\"bdiffs\": \"100\", \"sdiffs\": \"0\", \"allfiles\": \"true\", \"ldiffs\": \"0\", \"pdiffs\": \"100\", \"tdiffs\": \"0\", \"keepforward\": \"false\", \"add\": \"yes\", \"__current_case__\": 1, \"oligos\": {\"values\": [{\"src\": \"hda\", \"id\": 3725}]}}", "logtransform": "\"false\"", "checkorient": "\"false\"", "minlength": "\"0\"", "maxhomop": "\"0\"", "flip": "\"false\"", "dbkey": "\"hg17\"", "qual": "{\"add2\": \"no\", \"__current_case__\": 0}", "removelast": "\"0\"", "names": "null", "maxlength": "\"0\"", "maxambig": "\"-1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "keepfirst": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7764", "id": "093ebc9d412c603b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_trim_seqs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"qual\|qfile": {"src": "hda", "id": "7934594c89e91a33"}, "fasta": {"src": "hda", "id": "fc95eb28ec7fe06a"}, "maxhomop": "4", "qual\|add2": "yes"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "fc95eb28ec7fe06a", "uuid": "0211fde4-c693-40d3-9b5b-5912e37414d7"}, "qfile": {"src": "hda", "id": "7934594c89e91a33", "uuid": "8b3f866a-c0fe-4a8b-bfe7-af9154ac6314"}}, "update_time": "2018-02-08T18:48:03.759616", "tool_id": "mothur_trim_seqs", "outputs": {"trim_fasta": {"src": "hda", "id": "815697d3d9eb26cb", "uuid": "caf56444-922f-4eee-bc2a-ff2fa5851073"}, "logfile": {"src": "hda", "id": "44f0746e84939f78", "uuid": "34d43e05-0980-4046-97ba-0ed5252d8e66"}, "scrap_qual": {"src": "hda", "id": "7ddeb7c19c1d7c5a", "uuid": "da3e9833-2cb7-4b2d-a02b-2c6b2cec0918"}, "scrap_fasta": {"src": "hda", "id": "454e9e805ca4077a", "uuid": "d7dd29ef-d688-476f-b7a7-05bf9d8715e8"}, "trim_qual": {"src": "hda", "id": "676dc9710b90c439", "uuid": "7ca5b932-3be9-4b70-8274-32b64dc5e60e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > trim.seqs(fasta=fasta.dat,minlength=0,maxlength=0,maxambig=-1,maxhomop= \r4,keepfirst=0,removelast=0,qfile=qual.qfile.dat,qaverage=0,qthreshold=0,qwindowa \rverage=0,qwindowsize=50,rollaverage=0,qstepsize=1,qtrim=false,flip=false,logtran \rsform=false,checkorient=false,processors=1)\n\nUsing 1 processors.\n10\n\n\nOutput File Names: \nfasta.trim.fasta\nfasta.scrap.fasta\nfasta.trim.qual\nfasta.scrap.qual\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3748.dat' fasta.dat && ln -s 'None' names.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3749.dat' qual.qfile.dat && echo 'trim.seqs( fasta=fasta.dat, minlength=0, maxlength=0, maxambig=-1, maxhomop=4, keepfirst=0, removelast=0, qfile=qual.qfile.dat, qaverage=0, qthreshold=0, qwindowaverage=0, qwindowsize=50, rollaverage=0, qstepsize=1, qtrim=false, flip=false, logtransform=false, checkorient=false, processors='${GALAXY_SLOTS:-8}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv fasta.trim.fasta fasta.trim && mv fasta.scrap.fasta fasta.scrap", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:48:00.227292", "params": {"count": "null", "oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "logtransform": "\"false\"", "checkorient": "\"false\"", "minlength": "\"0\"", "maxhomop": "\"4\"", "flip": "\"false\"", "dbkey": "\"hg17\"", "qual": "{\"qaverage\": \"0\", \"add2\": \"yes\", \"rollaverage\": \"0\", \"qfile\": {\"values\": [{\"src\": \"hda\", \"id\": 3749}]}, \"qwindowaverage\": \"0\", \"qthreshold\": \"0\", \"__current_case__\": 1, \"qstepsize\": \"1\", \"qtrim\": \"false\", \"qwindowsize\": \"50\"}", "removelast": "\"0\"", "names": "null", "maxlength": "\"0\"", "maxambig": "\"-1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "keepfirst": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7890", "id": "ef11ae9dd5e1ab5d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_trim_seqs.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"tree": {"src": "hda", "id": "6df0b8642431f7cc"}}, "job": {"inputs": {"tree": {"src": "hda", "id": "6df0b8642431f7cc", "uuid": "6b1c9231-0e1e-4386-a8c2-c68780fddaad"}}, "update_time": "2018-02-08T18:48:36.539810", "tool_id": "mothur_unifrac_unweighted", "outputs": {"logfile": {"src": "hda", "id": "4b2a9422f173d099", "uuid": "22237f41-b2fc-4fcc-9f91-ad1c58ef660d"}, "dist": {"src": "hda", "id": "8ade91c37a8a22e4", "uuid": "1521df49-9e17-4089-af80-1e8cde0e428c"}, "summary": {"src": "hda", "id": "369c1a55ae4ea50a", "uuid": "f5953986-44ae-4b23-8259-a72c04e04771"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unifrac.unweighted(tree=tree.dat,iters=1000,random=false,distance=lt,ro \rot=false,processors=1)\n\nUsing 1 processors.\nTree#\tGroups\tUWScore\t\n1\t\t1\nIt took 0 secs to run unifrac.unweighted.\n\nOutput File Names: \ntree.uwsummary\ntree.dat1.unweighted.phylip.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3755.dat' tree.dat && ln -s 'None' group.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && echo 'unifrac.unweighted( tree=tree.dat, iters=1000, random=false, distance=lt, root=false, processors='${GALAXY_SLOTS:-1}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:48:33.297630", "params": {"count": "null", "distance": "\"lt\"", "group": "null", "name": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "random": "\"false\"", "dbkey": "\"hg17\"", "groups": "null", "subsampling": "{\"use\": \"no\", \"__current_case__\": 1}", "root": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7995", "id": "72b2b39740f9703c", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unifrac_unweighted.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"random": true, "tree": {"src": "hda", "id": "a42959d25b93204d"}}, "job": {"inputs": {"tree": {"src": "hda", "id": "a42959d25b93204d", "uuid": "cc159f63-71d4-43f6-bb06-ca3860641095"}}, "update_time": "2018-02-08T18:48:59.691564", "tool_id": "mothur_unifrac_unweighted", "outputs": {"unweighted": {"src": "hda", "id": "1afbdcbd8124b81c", "uuid": "bd550cfe-d7f3-4576-afbc-732ed1cd0ad1"}, "logfile": {"src": "hda", "id": "5882c2146ac78717", "uuid": "4d57d082-d71e-4cea-aced-050026f1cbb0"}, "dist": {"src": "hda", "id": "ebca56f6202f73d0", "uuid": "d80f9213-4452-4e9e-8cc3-89354629bf11"}, "summary": {"src": "hda", "id": "17941f39887c26fe", "uuid": "70d01ba9-c07d-42e9-93d0-36bfe05590eb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unifrac.unweighted(tree=tree.dat,iters=1000,random=true,distance=lt,roo \rt=false,processors=1)\n\nUsing 1 processors.\nTree#\tGroups\tUWScore\tUWSig\n1\t\t1\t1\nIt took 0 secs to run unifrac.unweighted.\n\nOutput File Names: \ntree.uwsummary\ntree.dat1.unweighted\ntree.dat1.unweighted.phylip.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3759.dat' tree.dat && ln -s 'None' group.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && echo 'unifrac.unweighted( tree=tree.dat, iters=1000, random=true, distance=lt, root=false, processors='${GALAXY_SLOTS:-1}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:48:55.837836", "params": {"count": "null", "distance": "\"lt\"", "group": "null", "name": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "random": "\"true\"", "dbkey": "\"hg17\"", "groups": "null", "subsampling": "{\"use\": \"no\", \"__current_case__\": 1}", "root": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8087", "id": "957ab5f6bc45f41a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unifrac_unweighted.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"group": {"src": "hda", "id": "216531b9838bcc19"}, "tree": {"src": "hda", "id": "13cac33be07cea40"}, "groups": ["A", "B"], "distance": "square"}, "job": {"inputs": {"group": {"src": "hda", "id": "216531b9838bcc19", "uuid": "8ec7f52a-4be6-4ffd-b896-9fdc0e76d0d5"}, "tree": {"src": "hda", "id": "13cac33be07cea40", "uuid": "7a20c32c-6646-4271-b2a1-f89e11ae55fa"}}, "update_time": "2018-02-08T18:49:28.670980", "tool_id": "mothur_unifrac_unweighted", "outputs": {"logfile": {"src": "hda", "id": "832ffb62535b10da", "uuid": "17c0f6f4-784c-44e5-8c94-f6f13fe4f737"}, "dist": {"src": "hda", "id": "91be6474cef830ab", "uuid": "95704f3c-80a0-4fbf-83c7-65d4cbabf9bf"}, "summary": {"src": "hda", "id": "28795f877f71134f", "uuid": "83719290-947c-48da-99fc-95049a661051"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unifrac.unweighted(tree=tree.dat,group=group.dat,groups=A-B,iters=1000, \rrandom=false,distance=square,root=false,processors=1)\n\nUsing 1 processors.\nTree#\tGroups\tUWScore\t\n1\tA-B\t0.697429\nIt took 0 secs to run unifrac.unweighted.\n\nOutput File Names: \ntree.uwsummary\ntree.dat1.unweighted.phylip.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3764.dat' tree.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3765.dat' group.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && echo 'unifrac.unweighted( tree=tree.dat, group=group.dat, groups=A-B, iters=1000, random=false, distance=square, root=false, processors='${GALAXY_SLOTS:-1}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:49:25.419654", "params": {"count": "null", "distance": "\"square\"", "name": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "random": "\"false\"", "dbkey": "\"hg17\"", "groups": "[\"A\", \"B\"]", "subsampling": "{\"use\": \"no\", \"__current_case__\": 1}", "root": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8200", "id": "dd4d919ea4ea0b29", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unifrac_unweighted.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"distance": "column", "group": {"src": "hda", "id": "5e10cd539f2a6619"}, "tree": {"src": "hda", "id": "9aac823dc8c01e16"}, "subsampling\|subsample": "10", "groups": ["A", "B", "C"], "subsampling\|consensus": true, "subsampling\|use": "yes"}, "job": {"inputs": {"group": {"src": "hda", "id": "5e10cd539f2a6619", "uuid": "9afe7468-0185-4855-a9d4-68c0b8ebeb85"}, "tree": {"src": "hda", "id": "9aac823dc8c01e16", "uuid": "5b6b7751-6143-41bc-9921-39b157b4c9e2"}}, "update_time": "2018-02-08T18:49:55.348485", "tool_id": "mothur_unifrac_unweighted", "outputs": {"logfile": {"src": "hda", "id": "5c1603539e28a1c0", "uuid": "08ea5982-30fa-4993-8384-32ab676d85a2"}, "dist": {"src": "hda", "id": "fe4fbad99aec603a", "uuid": "662ee7f3-d3d3-47b0-ab8b-0e3bb348a1ec"}, "cons_tree": {"src": "hda", "id": "c0615e4cb678cabf", "uuid": "bf2192d8-30bc-410c-baca-9ca1823a491c"}, "all_tree": {"src": "hda", "id": "727b1362191da7aa", "uuid": "9a7fe375-9d3f-41dc-9620-cd3e0ac5daa9"}, "ave_dist": {"src": "hda", "id": "ac3107c78c55b210", "uuid": "e16d304c-a86d-4ca0-ab05-32078b53e0f2"}, "std_dist": {"src": "hda", "id": "a04ba41073d3fea6", "uuid": "2319c776-e083-4364-9b61-aba0a91cd913"}, "summary": {"src": "hda", "id": "1cc9930f120e2a4c", "uuid": "9077764c-0952-4a37-a295-7dff1491718f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unifrac.unweighted(tree=tree.dat,group=group.dat,groups=A-B-C,iters=100 \r0,subsample=10,consensus=true,distance=column,root=false,processors=1)\n\nUsing 1 processors.\nTree#\tGroups\tUWScore\t\n100\n200\n300\n400\n500\n600\n700\n800\n900\n1000\nIt took 1 secs to run the subsampling.\n1\tA-B\t0.697429\n1\tA-C\t0.745247\n1\tB-C\t0.779964\nIt took 1 secs to run unifrac.unweighted.\n\nOutput File Names: \ntree.uwsummary\ntree.1.unweighted.ave.dist\ntree.1.unweighted.std.dist\ntree.1.unweighted.all.tre\ntree.1.unweighted.cons.tre\ntree.dat1.unweighted.column.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3769.dat' tree.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3770.dat' group.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && echo 'unifrac.unweighted( tree=tree.dat, group=group.dat, groups=A-B-C, iters=1000, subsample=10, consensus=true, distance=column, root=false, processors='${GALAXY_SLOTS:-1}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:49:51.083299", "params": {"count": "null", "distance": "\"column\"", "name": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "random": "\"false\"", "dbkey": "\"hg17\"", "groups": "[\"A\", \"B\", \"C\"]", "subsampling": "{\"consensus\": \"true\", \"subsample\": \"10\", \"use\": \"yes\", \"__current_case__\": 0}", "root": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8325", "id": "025a944d63daedd1", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unifrac_unweighted.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"group": {"src": "hda", "id": "0838a9bd40f5c4ce"}, "tree": {"src": "hda", "id": "b3462b19f4f15b33"}, "groups": ["A", "B", "C"]}, "job": {"inputs": {"group": {"src": "hda", "id": "0838a9bd40f5c4ce", "uuid": "8c75c923-d3db-4d38-9bb8-0bbfc949fa33"}, "tree": {"src": "hda", "id": "b3462b19f4f15b33", "uuid": "b462b4a8-88cf-41dc-bdb9-05a127fd8063"}}, "update_time": "2018-02-08T18:50:45.499239", "tool_id": "mothur_unifrac_weighted", "outputs": {"logfile": {"src": "hda", "id": "3fa7183d0a1b019b", "uuid": "08246390-a6be-4f84-ad75-9fa451c35c8a"}, "dist": {"src": "hda", "id": "79e7be5d12af6385", "uuid": "cfb6f0a5-f72a-4422-a72c-54e43dcbcd92"}, "summary": {"src": "hda", "id": "3a27c90fe001e6a6", "uuid": "002b5114-c0be-4d27-bf98-f2dd5c64f619"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unifrac.weighted(tree=tree.dat,group=group.dat,groups=A-B-C,iters=1000, \rrandom=false,distance=lt,root=false,processors=1)\n\nUsing 1 processors.\nTree#\tGroups\tWScore\t\n1\tA-B\t0.420804\n1\tA-C\t0.561036\n1\tB-C\t0.614747\nIt took 0 secs to run unifrac.weighted.\n\nOutput File Names: \ntree.datwsummary\ntree.dat1.weighted.phylip.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3778.dat' tree.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3779.dat' group.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && echo 'unifrac.weighted( tree=tree.dat, group=group.dat, groups=A-B-C, iters=1000, random=false, distance=lt, root=false, processors='${GALAXY_SLOTS:-1}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:50:41.538022", "params": {"count": "null", "distance": "\"lt\"", "name": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "random": "\"false\"", "dbkey": "\"hg17\"", "groups": "[\"A\", \"B\", \"C\"]", "subsampling": "{\"use\": \"no\", \"__current_case__\": 1}", "root": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8452", "id": "79a8c1c389391c2e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unifrac_weighted.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"group": {"src": "hda", "id": "518ff5e2cb49d7bb"}, "random": true, "tree": {"src": "hda", "id": "fd6333f7835dfe44"}, "groups": ["A", "B", "C"]}, "job": {"inputs": {"group": {"src": "hda", "id": "518ff5e2cb49d7bb", "uuid": "c1210880-04ea-42f6-894f-4590ed23d2a4"}, "tree": {"src": "hda", "id": "fd6333f7835dfe44", "uuid": "7adf2d3b-f9f0-496f-a251-f63bb1005228"}}, "update_time": "2018-02-08T18:51:16.087597", "tool_id": "mothur_unifrac_weighted", "outputs": {"logfile": {"src": "hda", "id": "6c3534f8df79d924", "uuid": "dc7c40ce-158b-4448-b303-fe3039aedc6c"}, "dist": {"src": "hda", "id": "63d28ef2435a4446", "uuid": "d696ec13-f4b0-49be-bae0-ae193f12965d"}, "summary": {"src": "hda", "id": "160ab7f4e3f4c4c1", "uuid": "7723ec4a-7e76-4135-9a4e-bad716710dba"}, "weighted": {"src": "hda", "id": "bd78fbbdf8dac536", "uuid": "269c6665-e3c2-45b2-88a9-b6bc101436af"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unifrac.weighted(tree=tree.dat,group=group.dat,groups=A-B-C,iters=1000, \rrandom=true,distance=lt,root=false,processors=1)\n\nUsing 1 processors.\nTree#\tGroups\tWScore\tWSig\n1\tA-B\t0.420804\t<0.001\n1\tA-C\t0.561036\t<0.001\n1\tB-C\t0.614747\t<0.001\nIt took 3 secs to run unifrac.weighted.\n\nOutput File Names: \ntree.datwsummary\ntree.dat1.weighted\ntree.dat1.weighted.phylip.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3783.dat' tree.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3784.dat' group.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && echo 'unifrac.weighted( tree=tree.dat, group=group.dat, groups=A-B-C, iters=1000, random=true, distance=lt, root=false, processors='${GALAXY_SLOTS:-1}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:51:10.189404", "params": {"count": "null", "distance": "\"lt\"", "name": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "random": "\"true\"", "dbkey": "\"hg17\"", "groups": "[\"A\", \"B\", \"C\"]", "subsampling": "{\"use\": \"no\", \"__current_case__\": 1}", "root": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8562", "id": "9140d1ef204facd8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unifrac_weighted.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"group": {"src": "hda", "id": "22fc2c025e64e76f"}, "tree": {"src": "hda", "id": "31e4d008821c6455"}, "groups": ["A", "B"], "distance": "square"}, "job": {"inputs": {"group": {"src": "hda", "id": "22fc2c025e64e76f", "uuid": "0b953332-ddcc-4b42-9fbd-df180e3a79af"}, "tree": {"src": "hda", "id": "31e4d008821c6455", "uuid": "ccae7e6c-1d7d-42b7-bb86-10ab235256ce"}}, "update_time": "2018-02-08T18:51:47.265203", "tool_id": "mothur_unifrac_weighted", "outputs": {"logfile": {"src": "hda", "id": "584bfbb334e631ee", "uuid": "b8815e25-4a19-41b2-b938-6d6b82239ec8"}, "dist": {"src": "hda", "id": "48f366354bcadc71", "uuid": "5d7c5c74-5472-4d42-b883-1e89e9f05a3a"}, "summary": {"src": "hda", "id": "d6c62cf9da0ecb9f", "uuid": "a001986d-fbef-433c-af54-230fd2fde10e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unifrac.weighted(tree=tree.dat,group=group.dat,groups=A-B,iters=1000,ra \rndom=false,distance=square,root=false,processors=1)\n\nUsing 1 processors.\nTree#\tGroups\tWScore\t\n1\tA-B\t0.420804\nIt took 0 secs to run unifrac.weighted.\n\nOutput File Names: \ntree.datwsummary\ntree.dat1.weighted.phylip.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3789.dat' tree.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3790.dat' group.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && echo 'unifrac.weighted( tree=tree.dat, group=group.dat, groups=A-B, iters=1000, random=false, distance=square, root=false, processors='${GALAXY_SLOTS:-1}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:51:44.075183", "params": {"count": "null", "distance": "\"square\"", "name": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "random": "\"false\"", "dbkey": "\"hg17\"", "groups": "[\"A\", \"B\"]", "subsampling": "{\"use\": \"no\", \"__current_case__\": 1}", "root": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8690", "id": "fa032b562e153122", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unifrac_weighted.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"distance": "column", "group": {"src": "hda", "id": "794af97c9033590e"}, "tree": {"src": "hda", "id": "a21fe8ee9e63080c"}, "subsampling\|subsample": "10", "groups": ["A", "B", "C"], "subsampling\|consensus": true, "subsampling\|use": "yes"}, "job": {"inputs": {"group": {"src": "hda", "id": "794af97c9033590e", "uuid": "e20175cd-14b3-49b4-bfce-0142810ff7f3"}, "tree": {"src": "hda", "id": "a21fe8ee9e63080c", "uuid": "fc7d7c2f-d877-492e-83b3-f66d55da81e0"}}, "update_time": "2018-02-08T18:52:14.538020", "tool_id": "mothur_unifrac_weighted", "outputs": {"logfile": {"src": "hda", "id": "5ba55d6a72b87324", "uuid": "f365a4ac-3eab-4c3f-8f34-05411cea8df0"}, "dist": {"src": "hda", "id": "60b877016be95026", "uuid": "f7db84a3-f1f3-4995-a595-b9b554cb6987"}, "cons_tree": {"src": "hda", "id": "c2e52dbcfe49c36d", "uuid": "9f1ef3be-aaff-4eb4-aa98-a5a58105c962"}, "all_tree": {"src": "hda", "id": "707ccea25fc9dd71", "uuid": "f59c4ad1-d5b9-4170-a839-eeb5cbf1e7bf"}, "ave_dist": {"src": "hda", "id": "24b1957315221820", "uuid": "384c63b7-3e46-4cfb-9d54-32a87a8cc979"}, "std_dist": {"src": "hda", "id": "e1f6007d0d1998af", "uuid": "55fe1249-c6a4-4367-b8b8-d0c128cb6473"}, "summary": {"src": "hda", "id": "f478481875067414", "uuid": "f03af451-dab2-4f4d-b556-0339cc0cce02"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unifrac.weighted(tree=tree.dat,group=group.dat,groups=A-B-C,iters=1000, \rsubsample=10,consensus=true,distance=column,root=false,processors=1)\n\nUsing 1 processors.\n100\n200\n300\n400\n500\n600\n700\n800\n900\n1000\nTree#\tGroups\tWScore\t\n1\tA-B\t0.420804\n1\tA-C\t0.561036\n1\tB-C\t0.614747\nIt took 1 secs to run unifrac.weighted.\n\nOutput File Names: \ntree.datwsummary\ntree.dat1.weighted.ave.dist\ntree.dat1.weighted.std.dist\ntree.1.weighted.all.tre\ntree.1.weighted.cons.tre\ntree.dat1.weighted.column.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3794.dat' tree.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3795.dat' group.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && echo 'unifrac.weighted( tree=tree.dat, group=group.dat, groups=A-B-C, iters=1000, subsample=10, consensus=true, distance=column, root=false, processors='${GALAXY_SLOTS:-1}' )' \| sed 's/ //g' \| mothur \| tee mothur.out.log && mv tree..ave.dist tree.ave && mv tree.*.std.dist tree.std", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:52:09.934321", "params": {"count": "null", "distance": "\"column\"", "name": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "random": "\"false\"", "dbkey": "\"hg17\"", "groups": "[\"A\", \"B\", \"C\"]", "subsampling": "{\"consensus\": \"true\", \"subsample\": \"10\", \"use\": \"yes\", \"__current_case__\": 0}", "root": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8802", "id": "b1d26ebda0776d51", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unifrac_weighted.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "f8823dc7d466d97b"}, "names": {"src": "hda", "id": "8187faee9c922310"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "f8823dc7d466d97b", "uuid": "eb69bb90-2c63-414e-9416-14bac878965b"}, "names": {"src": "hda", "id": "8187faee9c922310", "uuid": "bc005bee-5b71-43d0-9208-591b7c0ccd59"}}, "update_time": "2018-02-08T18:53:02.690147", "tool_id": "mothur_unique_seqs", "outputs": {"out_names": {"src": "hda", "id": "8b0f9f257ede5df4", "uuid": "41b0e472-5881-44be-8df3-b79fe480143f"}, "logfile": {"src": "hda", "id": "f3df144761c5b956", "uuid": "5dc05b2e-6f8a-48b7-82ed-e1ff821dba29"}, "out_fasta": {"src": "hda", "id": "66d3fd607ddc158a", "uuid": "53038c6e-0d47-4faa-aa0d-e1db2f95bfc9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unique.seqs(name=names.dat,fasta=fasta.dat)\n98\t96\n\nOutput File Names: \nfasta.names\nfasta.unique.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3804.dat' names.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3803.dat' fasta.dat && echo 'unique.seqs( name=names.dat, fasta=fasta.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:52:59.577595", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8930", "id": "c239c296c8b002ba", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unique_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "8aaa031deda3761e"}, "names": {"src": "hda", "id": "864bc422cb6c6663"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "8aaa031deda3761e", "uuid": "cbb5a981-dd46-4e6d-a26b-0f7397e76300"}, "names": {"src": "hda", "id": "864bc422cb6c6663", "uuid": "ca478712-7077-485d-bbf7-d6349244011d"}}, "update_time": "2018-02-08T18:53:28.461742", "tool_id": "mothur_unique_seqs", "outputs": {"out_count": {"src": "hda", "id": "b1b0e3e670e9fef5", "uuid": "b6579f3e-d17c-4ae3-9909-afe68c12e00d"}, "logfile": {"src": "hda", "id": "5cdc51911a37e673", "uuid": "08e8438b-a641-43e4-83f2-47bcb535c92e"}, "out_fasta": {"src": "hda", "id": "5fab573ff4009995", "uuid": "838a2f8a-9284-4d3e-a768-0a69cb33a7d4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unique.seqs(count=names.dat,fasta=fasta.dat)\n96\t96\n\nOutput File Names: \nfasta.count_table\nfasta.unique.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3809.dat' names.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3808.dat' fasta.dat && echo 'unique.seqs( count=names.dat, fasta=fasta.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:53:25.211028", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "9040", "id": "5498b8b462f50992", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unique_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "7b00e7fa90e73a2c"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "7b00e7fa90e73a2c", "uuid": "8dbab685-56c7-4b8f-b547-9f2f9bfb7cf2"}}, "update_time": "2018-02-08T18:53:51.166544", "tool_id": "mothur_unique_seqs", "outputs": {"out_names": {"src": "hda", "id": "ddd777d89c6d8995", "uuid": "eb0f6782-ae6b-4df5-9e88-2eaca0da2a0c"}, "logfile": {"src": "hda", "id": "6e4eaae38f2fd10c", "uuid": "efec61f4-381e-4e05-ba55-0d10262d1963"}, "out_fasta": {"src": "hda", "id": "ea5794814dd23e3d", "uuid": "33dadcf5-75a9-4702-8a3a-745d0bf290a5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unique.seqs(fasta=fasta.dat)\n98\t96\n\nOutput File Names: \nfasta.names\nfasta.unique.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s 'None' names.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3813.dat' fasta.dat && echo 'unique.seqs( fasta=fasta.dat )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:53:47.926817", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "names": "null", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "9135", "id": "af3fae2a84d45574", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unique_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"input\|source": "shared", "input\|groups": ["forest", "pasture"], "input\|calc": ["sharedsobs", "sharedchao"], "input\|otu": {"src": "hda", "id": "55d76a6980ecb718"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "55d76a6980ecb718", "uuid": "33113dd2-1063-4523-a1f2-cfc9ba04cf55"}}, "update_time": "2018-02-08T18:54:19.954686", "tool_id": "mothur_venn", "outputs": {"__new_primary_file_unique.sharedsobs.forest-pasture\|0.07.sharedchao.forest-pasture__": {"src": "hda", "id": "c306e715ccd40732", "uuid": "fa6ba2aa-af1b-4dfc-8926-db0f300de15b"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.07.sharedsobs.forest-pasture__": {"src": "hda", "id": "08f916effa074623", "uuid": "b8665eb1-b958-41c7-87d0-50597ecb2727"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.23.sharedchao.forest-pasture__": {"src": "hda", "id": "77cfdc5505f4d0df", "uuid": "357d9ce7-8bc6-4070-aafb-261fe7aabb06"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.10.sharedsobs.forest-pasture__": {"src": "hda", "id": "01b91c84f878a8a3", "uuid": "dd129a22-8873-4724-a260-c2aedce68903"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.26.sharedsobs.forest-pasture__": {"src": "hda", "id": "d35b70885c06631c", "uuid": "3f444a73-c012-42e1-b6fa-af1fe54c4277"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.06.sharedsobs.forest-pasture__": {"src": "hda", "id": "c690dd6a085605ea", "uuid": "96f6496f-9f8c-4dd3-89ee-2b7e22571162"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.13.sharedsobs.forest-pasture__": {"src": "hda", "id": "1fe0a7c632f57060", "uuid": "679228e1-25c0-4fa1-a1d7-d952b4e22669"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.20.sharedsobs.forest-pasture__": {"src": "hda", "id": "1523f6ea5a5d73b3", "uuid": "8dda66dd-d4ee-4d4f-a3d2-7a49863e6138"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.22.sharedsobs.forest-pasture__": {"src": "hda", "id": "2def870856cfe4c6", "uuid": "dc241149-1824-49bd-86e6-39bb7bf7e87d"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.24.sharedchao.forest-pasture__": {"src": "hda", "id": "18952bd2de03ae52", "uuid": "fd336735-6fb2-4817-9ced-d495295b6db0"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.13.sharedsobs.forest-pasture__": {"src": "hda", "id": "c15f789a5ecae62b", "uuid": "3d29aaf9-2223-4d5a-9628-d58ea3127f32"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.10.sharedsobs.forest-pasture__": {"src": "hda", "id": 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"__new_primary_file_unique.sharedsobs.forest-pasture\|0.02.sharedsobs.forest-pasture__": {"src": "hda", "id": "5865039f88f5eda6", "uuid": "e1fca256-1d40-417c-b731-c42e6f7d5427"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.25.sharedsobs.forest-pasture__": {"src": "hda", "id": "c2612d032c4568a1", "uuid": "c6df8086-e262-4fbf-b09b-d4d086db7aec"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.27.sharedsobs.forest-pasture__": {"src": "hda", "id": "161c583a884ffe70", "uuid": "5544a40f-2159-4166-be0b-bc589cde1c39"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.55.sharedchao.forest-pasture__": {"src": "hda", "id": "7ad21bd20a86fbf6", "uuid": "55dc1aca-bad5-4749-b0a3-f013c6c351af"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.45.sharedsobs.forest-pasture__": {"src": "hda", "id": "ed13f92e503181c1", "uuid": "28e90ac8-14b6-4ce8-9c23-9edff1e0d81f"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.29.sharedsobs.forest-pasture__": {"src": "hda", "id": "ff2b605985e5b37e", "uuid": "b0f5b97f-b3d3-4519-93de-91f189d0562d"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.33.sharedsobs.forest-pasture__": {"src": "hda", "id": "a8099d2409335c38", "uuid": "70407edc-f1e2-4892-a83b-4c3d6d52dcd9"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.02.sharedchao.forest-pasture__": {"src": "hda", "id": "99a1f27df53815fe", "uuid": "435d5f82-22de-40ae-9555-c6768884c47f"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.41.sharedsobs.forest-pasture__": {"src": "hda", "id": "5d31cbfd86ba9238", "uuid": "28267b93-9e64-4099-ab3d-9700057dace6"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.14.sharedsobs.forest-pasture__": {"src": "hda", "id": "3c13c8d3678bff11", "uuid": "71fa1471-af01-4a45-9cde-448c4f0ff9ae"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.29.sharedchao.forest-pasture__": {"src": "hda", "id": "b0979d3f12e2ca7c", "uuid": "c0cdaf63-9009-4bd1-b8bb-563612d52ead"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.29.sharedsobs.forest-pasture__": {"src": "hda", "id": "95ebc02141d52b2e", "uuid": "4c6c8f67-65f6-4309-9f9b-288fd4472965"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.12.sharedsobs.forest-pasture__": {"src": "hda", "id": "d44076581aae3b2d", "uuid": "8868b0f7-c31c-4d0e-9b62-a60beab07c48"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.26.sharedchao.forest-pasture__": {"src": "hda", "id": "3809f3db44f7f537", "uuid": "00971f04-a834-44c5-be7d-315e0a75b22c"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.27.sharedsobs.forest-pasture__": {"src": "hda", "id": "4726084e39a28c6b", "uuid": "7d8a5eee-c89e-4e14-a228-8c96a6f92e7a"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.41.sharedchao.forest-pasture__": {"src": "hda", "id": "5500dc8db971ab8a", "uuid": "2c1a6f1e-0b8f-47da-974d-383005e13016"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.36.sharedsobs.forest-pasture__": {"src": "hda", "id": "56a988c6136c7433", "uuid": "dd8cc604-6e02-4af2-8c28-06768011fa54"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.36.sharedsobs.forest-pasture__": {"src": "hda", "id": "8b0dcee2afd18683", "uuid": "c382feef-80f9-410d-9dcd-b22af6bd3fab"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.45.sharedchao.forest-pasture__": {"src": "hda", "id": "5c2b4bb7b7fc05df", "uuid": "6c9bd34c-e80b-4dde-bfee-7f97c9eb4bb5"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.12.sharedchao.forest-pasture__": {"src": "hda", "id": "53a005f8d9691e08", "uuid": "7395c9fd-4b1e-4c83-833d-8a0bb5fe3a53"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.36.sharedchao.forest-pasture__": {"src": "hda", "id": "7d5118fbc3106cab", "uuid": "1bc0f87f-f7ed-454d-b0b5-6d588555ece0"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.01.sharedchao.forest-pasture__": {"src": "hda", "id": "7a49ab297bab6207", "uuid": "21adb8e8-7fec-42fa-89f7-a4c809e65103"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.15.sharedchao.forest-pasture__": {"src": "hda", "id": "0bd3ae7c57261b58", "uuid": "44ffe1ec-9f86-4159-8976-38d9c96014a7"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.09.sharedchao.forest-pasture__": {"src": "hda", "id": "67a71e47792722f3", "uuid": "b3bdd0fd-2d4d-4b14-9860-ed10dca6779f"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.01.sharedsobs.forest-pasture__": {"src": "hda", "id": "b24813383c927074", "uuid": "315b8ad7-a808-4419-b27d-227aa4686931"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.02.sharedsobs.forest-pasture__": {"src": "hda", "id": "da17aca212b7e975", "uuid": "8a4464ba-7372-430c-a1d8-9f7e98aa6bc7"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.21.sharedsobs.forest-pasture__": {"src": "hda", "id": "0dd63dbbe68f15eb", "uuid": "002ea9f7-1a3e-44a5-820d-b2119ed98732"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.12.sharedsobs.forest-pasture__": {"src": "hda", "id": "af254de203595b9a", "uuid": "567e57f9-572f-4983-b64f-3074984a1c20"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.23.sharedsobs.forest-pasture__": {"src": "hda", "id": "28bfbd1f682a023c", "uuid": "891629f4-d2fc-481f-827c-39a6498153ed"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.06.sharedsobs.forest-pasture__": {"src": "hda", "id": "037eb00486bbcd0f", "uuid": "e6a36cd8-14e8-4f5e-99ec-97f1da77b706"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.09.sharedsobs.forest-pasture__": {"src": "hda", "id": "605eafdc6b29e694", "uuid": "a989c780-1391-4dfb-b4e2-fb12300181f1"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.25.sharedsobs.forest-pasture__": {"src": "hda", "id": "e2ffe484c9600cc9", "uuid": "a1e7f9f4-6eb2-4883-a3d0-5301f5e884ea"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.32.sharedsobs.forest-pasture__": {"src": "hda", "id": "2a3d51fcdfd2c354", "uuid": "4a3fa689-e8f7-4a62-99e5-0ad75b65dea8"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.33.sharedchao.forest-pasture__": {"src": "hda", "id": "f2fcc124cffbfab3", "uuid": "0ee6ba67-680c-424f-9e3b-0565209774b2"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.03.sharedchao.forest-pasture__": {"src": "hda", "id": "1df5bd22b3fa40b7", "uuid": "8c7d429a-c401-4b26-b18d-c829b3166bbf"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.01.sharedsobs.forest-pasture__": {"src": "hda", "id": "eaf5a18433a155d9", "uuid": "254f3491-597c-48b3-829b-83105582f8e5"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.03.sharedsobs.forest-pasture__": {"src": "hda", "id": "ae3e576e3ad064fc", "uuid": "dc1f0494-ef72-4e87-bf10-b6552fdb6e19"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.19.sharedsobs.forest-pasture__": {"src": "hda", "id": "c6fa67e3e6b69811", "uuid": "abc37e39-abf0-4b89-b866-a97bd798c274"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.04.sharedsobs.forest-pasture__": {"src": "hda", "id": "fb2aea7dd0de2197", "uuid": "64a2fc40-6296-4c89-be07-74d8dab70167"}, "__new_primary_file_unique.sharedsobs.forest-pasture\|0.19.sharedsobs.forest-pasture__": {"src": "hda", "id": "16059f9897e605d5", "uuid": "6c898ee3-9fe8-4583-a149-835cef0d9dbe"}, "__new_primary_file_0.55.sharedsobs.forest-pasture\|0.33.sharedsobs.forest-pasture__": {"src": "hda", "id": "74e0351813a079c6", "uuid": "84464478-e368-48a5-9e29-0cd01802d833"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > venn(shared=input_otu.dat,nseqs=false,permute=4,groups=forest-pasture,c \ralc=sharedsobs-sharedchao,fontsize=24,sharedotus=true)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu.unique.sharedsobs.forest-pasture.svg\ninput_otu.unique.sharedchao.forest-pasture.svg\ninput_otu.0.01.sharedsobs.forest-pasture.svg\ninput_otu.0.01.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.01.sharedchao.forest-pasture.svg\ninput_otu.0.02.sharedsobs.forest-pasture.svg\ninput_otu.0.02.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.02.sharedchao.forest-pasture.svg\ninput_otu.0.03.sharedsobs.forest-pasture.svg\ninput_otu.0.03.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.03.sharedchao.forest-pasture.svg\ninput_otu.0.04.sharedsobs.forest-pasture.svg\ninput_otu.0.04.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.04.sharedchao.forest-pasture.svg\ninput_otu.0.05.sharedsobs.forest-pasture.svg\ninput_otu.0.05.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.05.sharedchao.forest-pasture.svg\ninput_otu.0.06.sharedsobs.forest-pasture.svg\ninput_otu.0.06.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.06.sharedchao.forest-pasture.svg\ninput_otu.0.07.sharedsobs.forest-pasture.svg\ninput_otu.0.07.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.07.sharedchao.forest-pasture.svg\ninput_otu.0.08.sharedsobs.forest-pasture.svg\ninput_otu.0.08.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.08.sharedchao.forest-pasture.svg\ninput_otu.0.09.sharedsobs.forest-pasture.svg\ninput_otu.0.09.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.09.sharedchao.forest-pasture.svg\ninput_otu.0.10.sharedsobs.forest-pasture.svg\ninput_otu.0.10.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.10.sharedchao.forest-pasture.svg\ninput_otu.0.11.sharedsobs.forest-pasture.svg\ninput_otu.0.11.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.11.sharedchao.forest-pasture.svg\ninput_otu.0.12.sharedsobs.forest-pasture.svg\ninput_otu.0.12.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.12.sharedchao.forest-pasture.svg\ninput_otu.0.13.sharedsobs.forest-pasture.svg\ninput_otu.0.13.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.13.sharedchao.forest-pasture.svg\ninput_otu.0.14.sharedsobs.forest-pasture.svg\ninput_otu.0.14.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.14.sharedchao.forest-pasture.svg\ninput_otu.0.15.sharedsobs.forest-pasture.svg\ninput_otu.0.15.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.15.sharedchao.forest-pasture.svg\ninput_otu.0.16.sharedsobs.forest-pasture.svg\ninput_otu.0.16.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.16.sharedchao.forest-pasture.svg\ninput_otu.0.17.sharedsobs.forest-pasture.svg\ninput_otu.0.17.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.17.sharedchao.forest-pasture.svg\ninput_otu.0.18.sharedsobs.forest-pasture.svg\ninput_otu.0.18.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.18.sharedchao.forest-pasture.svg\ninput_otu.0.19.sharedsobs.forest-pasture.svg\ninput_otu.0.19.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.19.sharedchao.forest-pasture.svg\ninput_otu.0.20.sharedsobs.forest-pasture.svg\ninput_otu.0.20.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.20.sharedchao.forest-pasture.svg\ninput_otu.0.21.sharedsobs.forest-pasture.svg\ninput_otu.0.21.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.21.sharedchao.forest-pasture.svg\ninput_otu.0.22.sharedsobs.forest-pasture.svg\ninput_otu.0.22.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.22.sharedchao.forest-pasture.svg\ninput_otu.0.23.sharedsobs.forest-pasture.svg\ninput_otu.0.23.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.23.sharedchao.forest-pasture.svg\ninput_otu.0.24.sharedsobs.forest-pasture.svg\ninput_otu.0.24.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.24.sharedchao.forest-pasture.svg\ninput_otu.0.25.sharedsobs.forest-pasture.svg\ninput_otu.0.25.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.25.sharedchao.forest-pasture.svg\ninput_otu.0.26.sharedsobs.forest-pasture.svg\ninput_otu.0.26.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.26.sharedchao.forest-pasture.svg\ninput_otu.0.27.sharedsobs.forest-pasture.svg\ninput_otu.0.27.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.27.sharedchao.forest-pasture.svg\ninput_otu.0.29.sharedsobs.forest-pasture.svg\ninput_otu.0.29.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.29.sharedchao.forest-pasture.svg\ninput_otu.0.32.sharedsobs.forest-pasture.svg\ninput_otu.0.32.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.32.sharedchao.forest-pasture.svg\ninput_otu.0.33.sharedsobs.forest-pasture.svg\ninput_otu.0.33.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.33.sharedchao.forest-pasture.svg\ninput_otu.0.36.sharedsobs.forest-pasture.svg\ninput_otu.0.36.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.36.sharedchao.forest-pasture.svg\ninput_otu.0.38.sharedsobs.forest-pasture.svg\ninput_otu.0.38.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.38.sharedchao.forest-pasture.svg\ninput_otu.0.41.sharedsobs.forest-pasture.svg\ninput_otu.0.41.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.41.sharedchao.forest-pasture.svg\ninput_otu.0.45.sharedsobs.forest-pasture.svg\ninput_otu.0.45.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.45.sharedchao.forest-pasture.svg\ninput_otu.0.55.sharedsobs.forest-pasture.svg\ninput_otu.0.55.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.55.sharedchao.forest-pasture.svg\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3817.dat' input_otu.dat && echo 'venn( shared=input_otu.dat, nseqs=false, permute=4, groups=forest-pasture, calc=sharedsobs-sharedchao, fontsize=24, sharedotus=true )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:54:10.814484", "params": {"sharedotus": "\"true\"", "nseqs": "\"false\"", "dbkey": "\"hg17\"", "fontsize": "\"24\"", "input": "{\"__current_case__\": 0, \"label\": null, \"source\": \"shared\", \"groups\": [\"forest\", \"pasture\"], \"calc\": [\"sharedsobs\", \"sharedchao\"], \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3817}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "permute": "\"4\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by 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"__new_primary_file_.unique.sobs\|.0.36.sobs__": {"src": "hda", "id": "06f863c370e9a218", "uuid": "4e126c04-1424-4e31-9746-dbd4430506c4"}, "__new_primary_file_.unique.sobs\|.0.16.ace__": {"src": "hda", "id": "7a12ab7b858daf17", "uuid": "507438b3-2a42-4d78-8804-cbf96a2e25a3"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > venn(list=input_otu.dat,abund=10,calc=sobs-chao-ace,fontsize=24,sharedo \rtus=true)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu..unique.sobs.svg\ninput_otu..unique.chao.svg\ninput_otu..unique.ace.svg\ninput_otu..0.01.sobs.svg\ninput_otu..0.01.chao.svg\ninput_otu..0.01.ace.svg\ninput_otu..0.02.sobs.svg\ninput_otu..0.02.chao.svg\ninput_otu..0.02.ace.svg\ninput_otu..0.03.sobs.svg\ninput_otu..0.03.chao.svg\ninput_otu..0.03.ace.svg\ninput_otu..0.04.sobs.svg\ninput_otu..0.04.chao.svg\ninput_otu..0.04.ace.svg\ninput_otu..0.05.sobs.svg\ninput_otu..0.05.chao.svg\ninput_otu..0.05.ace.svg\ninput_otu..0.06.sobs.svg\ninput_otu..0.06.chao.svg\ninput_otu..0.06.ace.svg\ninput_otu..0.07.sobs.svg\ninput_otu..0.07.chao.svg\ninput_otu..0.07.ace.svg\ninput_otu..0.08.sobs.svg\ninput_otu..0.08.chao.svg\ninput_otu..0.08.ace.svg\ninput_otu..0.09.sobs.svg\ninput_otu..0.09.chao.svg\ninput_otu..0.09.ace.svg\ninput_otu..0.10.sobs.svg\ninput_otu..0.10.chao.svg\ninput_otu..0.10.ace.svg\ninput_otu..0.11.sobs.svg\ninput_otu..0.11.chao.svg\ninput_otu..0.11.ace.svg\ninput_otu..0.12.sobs.svg\ninput_otu..0.12.chao.svg\ninput_otu..0.12.ace.svg\ninput_otu..0.13.sobs.svg\ninput_otu..0.13.chao.svg\ninput_otu..0.13.ace.svg\ninput_otu..0.14.sobs.svg\ninput_otu..0.14.chao.svg\ninput_otu..0.14.ace.svg\ninput_otu..0.15.sobs.svg\ninput_otu..0.15.chao.svg\ninput_otu..0.15.ace.svg\ninput_otu..0.16.sobs.svg\ninput_otu..0.16.chao.svg\ninput_otu..0.16.ace.svg\ninput_otu..0.17.sobs.svg\ninput_otu..0.17.chao.svg\ninput_otu..0.17.ace.svg\ninput_otu..0.18.sobs.svg\ninput_otu..0.18.chao.svg\ninput_otu..0.18.ace.svg\ninput_otu..0.19.sobs.svg\ninput_otu..0.19.chao.svg\ninput_otu..0.19.ace.svg\ninput_otu..0.20.sobs.svg\ninput_otu..0.20.chao.svg\ninput_otu..0.20.ace.svg\ninput_otu..0.21.sobs.svg\ninput_otu..0.21.chao.svg\ninput_otu..0.21.ace.svg\ninput_otu..0.22.sobs.svg\ninput_otu..0.22.chao.svg\ninput_otu..0.22.ace.svg\ninput_otu..0.23.sobs.svg\ninput_otu..0.23.chao.svg\ninput_otu..0.23.ace.svg\ninput_otu..0.24.sobs.svg\ninput_otu..0.24.chao.svg\ninput_otu..0.24.ace.svg\ninput_otu..0.25.sobs.svg\ninput_otu..0.25.chao.svg\ninput_otu..0.25.ace.svg\ninput_otu..0.26.sobs.svg\ninput_otu..0.26.chao.svg\ninput_otu..0.26.ace.svg\ninput_otu..0.27.sobs.svg\ninput_otu..0.27.chao.svg\ninput_otu..0.27.ace.svg\ninput_otu..0.29.sobs.svg\ninput_otu..0.29.chao.svg\ninput_otu..0.29.ace.svg\ninput_otu..0.32.sobs.svg\ninput_otu..0.32.chao.svg\ninput_otu..0.32.ace.svg\ninput_otu..0.33.sobs.svg\ninput_otu..0.33.chao.svg\ninput_otu..0.33.ace.svg\ninput_otu..0.36.sobs.svg\ninput_otu..0.36.chao.svg\ninput_otu..0.36.ace.svg\ninput_otu..0.38.sobs.svg\ninput_otu..0.38.chao.svg\ninput_otu..0.38.ace.svg\ninput_otu..0.41.sobs.svg\ninput_otu..0.41.chao.svg\ninput_otu..0.41.ace.svg\ninput_otu..0.45.sobs.svg\ninput_otu..0.45.chao.svg\ninput_otu..0.45.ace.svg\ninput_otu..0.55.sobs.svg\ninput_otu..0.55.chao.svg\ninput_otu..0.55.ace.svg\n\n\nmothur > quit\n", "command_line": "set -o pipefail; ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3926.dat' input_otu.dat && echo 'venn( list=input_otu.dat, abund=10, calc=sobs-chao-ace, fontsize=24, sharedotus=true )' \| sed 's/ //g' \| mothur \| tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:54:39.400697", "params": {"sharedotus": "\"true\"", "nseqs": "\"false\"", "dbkey": "\"hg17\"", "fontsize": "\"24\"", "input": "{\"abund\": \"10\", \"label\": null, \"source\": \"similarity\", \"__current_case__\": 1, \"calc\": [\"sobs\", \"chao\", \"ace\"], \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3926}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "permute": "\"4\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "9316", "id": "ec7711f2346cbca2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_venn.test_tool_000001", "has_data": true}], "version": "0.1", "exit_code": 1, "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 1, "num_tests": 305}};
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	379 renderTestResults(test_data);
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	380 }
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	381 </script>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	382 </body>
c4db2a4fdb42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 iuc parents: diff changeset	383 </html>

Mercurial > repos > iuc > mothur_summary_single

annotate tool_test_output_all.html @ 4:c4db2a4fdb42 draft