Mercurial > repos > iuc > mothur_get_oturep
changeset 3:899ef1660676 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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--- a/get.oturep.xml Tue Sep 05 16:46:21 2017 -0400 +++ b/get.oturep.xml Wed Feb 14 09:44:01 2018 -0500 @@ -7,77 +7,79 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ + +## create symlinks to input datasets +ln -s '$otu' otu.dat && +#if $method_condition.method_switch == "distance": + ln -s '$method_condition.matrix_condition.dist' dist.dat && + ln -s '$method_condition.matrix_condition.nameOrCount' nameOrCount.dat && + ln -s '$method_condition.fasta' fasta.dat && + #if $method_condition.pick.type == "yes": + ln -s '$method_condition.pick.group' group.dat && + #end if +#elif $method_condition.method_switch == "abundance": + ln -s '$method_condition.nameOrCount' nameOrCount.dat && +#end if - ## create symlinks to input datasets - ln -s "$otu" otu.dat && - #if $method_condition.method_switch == "distance": - ln -s "$method_condition.matrix_condition.dist" dist.dat && - ln -s "$method_condition.matrix_condition.nameOrCount" nameOrCount.dat && - ln -s "$method_condition.fasta" fasta.dat && - #if $method_condition.pick.type == "yes": - ln -s "$method_condition.pick.group" group.dat && - #end if - #elif $method_condition.method_switch == "abundance": - ln -s "$method_condition.nameOrCount" nameOrCount.dat && - #end if - - echo 'get.oturep( - list=otu.dat, - #if $sorted: - sorted=$sorted, - #end if - #if $label: - label=${ str($label).replace(",","-") }, +echo 'get.oturep( + list=otu.dat, + #if $sorted: + sorted=$sorted, + #end if + #if $label: + label=${ str($label).replace(",","-") }, + #end if + #if $method_condition.method_switch == "distance": + method=distance, + #if $method_condition.matrix_condition.matrix_format == "column": + column=dist.dat, + #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"): + name=nameOrCount.dat, + #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"): + count=nameOrCount.dat, #end if - #if $method_condition.method_switch == "distance": - method=distance, - #if $method_condition.matrix_condition.matrix_format == "column": - column=dist.dat, - #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"): - name=nameOrCount.dat, - #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"): - count=nameOrCount.dat, - #end if - #elif $method_condition.matrix_condition.matrix_format == "phylip": - phylip=dist.dat, - #if $method_condition.matrix_condition.nameOrCount: - #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"): - name=nameOrCount.dat, - #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"): - count=nameOrCount.dat, - #end if - #end if - #end if - #if $method_condition.fasta: - fasta=fasta.dat, - #end if - #if $method_condition.pick.type == "yes": - #if $method_condition.pick.group: - group=group.dat, - #end if - #if $method_condition.pick.groups: - groups=${ str($method_condition.pick.groups).replace(",","-") }, - #end if - #end if - large=$method_condition.large - #elif $method_condition.method_switch == "abundance": - method=abundance, - #if $method_condition.nameOrCount.is_of_type("mothur.names"): - name=nameOrCount.dat - #elif $method_condition.nameOrCount.is_of_type("mothur.count_table"): - count=nameOrCount.dat + #elif $method_condition.matrix_condition.matrix_format == "phylip": + phylip=dist.dat, + #if $method_condition.matrix_condition.nameOrCount: + #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"): + name=nameOrCount.dat, + #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"): + count=nameOrCount.dat, #end if #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log + #end if + #if $method_condition.fasta: + fasta=fasta.dat, + #end if + #if $method_condition.pick.type == "yes": + #if $method_condition.pick.group: + group=group.dat, + #end if + #if $method_condition.pick.groups: + groups=${ str($method_condition.pick.groups).replace(",","-") }, + #end if + #end if + large=$method_condition.large + #elif $method_condition.method_switch == "abundance": + method=abundance, + #if $method_condition.nameOrCount.is_of_type("mothur.names"): + name=nameOrCount.dat + #elif $method_condition.nameOrCount.is_of_type("mothur.count_table"): + count=nameOrCount.dat + #end if + #end if +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> <conditional name="method_condition"> - <param name="method_switch" type="select" label="Method to use for the selection of the representative sequences" help="The distance method finds the sequence with the smallest maximum distance to other sequences. The abundance method chooses the most abundant sequence in the OTU as the representative."> + <param name="method_switch" type="select" label="Method to use for the selection of the representative sequences" + help="The distance method finds the sequence with the smallest maximum distance to other sequences. The abundance + method chooses the most abundant sequence in the OTU as the representative."> <option value="distance" selected="true">distance</option> <option value="abundance">abundance</option> </param> @@ -112,7 +114,8 @@ </param> </when> </conditional> - <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Distance Matrix is very Large" help="Set this parameter to Yes if your distance matric might not fit in RAM"/> + <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Distance Matrix is very Large" + help="Set this parameter to Yes if your distance matric might not fit in RAM"/> </when> <when value="abundance"> <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/> @@ -237,8 +240,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -250,7 +252,7 @@ .. _get.oturep: https://www.mothur.org/wiki/Get.oturep v1.23.0: Updated to Mothur 1.33, added count and method parameter -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>
--- a/macros.xml Tue Sep 05 16:46:21 2017 -0400 +++ b/macros.xml Wed Feb 14 09:44:01 2018 -0500 @@ -1,11 +1,13 @@ <macros> + <token name="@WRAPPER_VERSION@">1.39.5</token> <xml name="requirements"> <requirements> - <requirement type="package" version="1.36.1">mothur</requirement> + <requirement type="package" version="@WRAPPER_VERSION@">mothur</requirement> + <yield/> </requirements> </xml> <xml name="version_command"> - <version_command>mothur "#help()" | sed '7q;d' | cut -d" " -f2 </version_command> + <version_command><![CDATA[ mothur "#help()" | sed '7q;d' | cut -d" " -f2 ]]></version_command> </xml> <xml name="stdio"> <stdio> @@ -13,20 +15,10 @@ <exit_code range="1:" level="fatal"/> </stdio> </xml> - <token name="@WRAPPER_VERSION@">1.36.1</token> <token name="@SHELL_OPTIONS@">set -o pipefail;</token> - <token name="@MOTHUR_OVERVIEW@"> -<![CDATA[ - -**Mothur Overview** -Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team -in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_. -.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page - -]]> - </token> + <!-- Input parameters --> <xml name="labeloptions"> <options> <filter type="data_meta" ref="otu" key="labels"/> @@ -78,9 +70,65 @@ <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option> <yield/> </xml> + + <!-- CLUSTERING --> + <xml name="param-clustermethods"> + <param argument="method" type="select" label="Clustering Method"> + <option value="opti" selected="true">Opticlust method</option> + <option value="furthest">Furthest neighbor</option> + <option value="nearest">Nearest neighbor</option> + <option value="average">Average neighbor</option> + <yield/> + </param> + </xml> + <xml name="option-vsearch-clustermethods"> + <option value="agc">Abundance-based greedy clustering (agc)(VSEARCH)</option> + <option value="dgc">Distance-based greedy clustering (dgc)(VSEARCH)</option> + </xml> + <xml name="params-opticlust"> + <param argument="metric" type="select" label="metric - select the metric in the opticluster method" + help="Options are Matthews correlation coefficient (mcc), sensitivity (sens), specificity (spec), true positives + true negatives (tptn), + false positives + false negatives (fpfn), true positives (tp), true negative (tn), false positive (fp), false negative (fn), f1score (f1score), + accuracy (accuracy), positive predictive value (ppv), negative predictive value (npv), false discovery rate (fdr). Default=mcc."> + <option value="mcc" selected="true">Matthews correlation coefficient (mcc)</option> + <option value="sens">Sensitivity</option> + <option value="spec">specificity</option> + <option value="tptn">true positives + true negatives</option> + <option value="fpfn">false positives + false negatives</option> + <option value="tp">true positives</option> + <option value="tn">true negative</option> + <option value="fp">false positive</option> + <option value="fn">false negative</option> + <option value="f1score">f1score</option> + <option value="accuracy">accuracy</option> + <option value="ppv">positive predictive value</option> + <option value="npv">negative predictive value</option> + <option value="fdr">false discovery rate</option> + </param> + <param argument="initialize" type="select" label="Initial randomization" + help="singleton: each sequence is randomly assigned to its own OTU; oneotu: all sequences are assigned to one otu"> + <option value="singleton" selected="true">Singleton</option> + <option value="oneotu">Oneotu</option> + </param> + <param argument="delta" type="float" value="0.0001" label="set the stable value for the metric in the opticluster method" + help="The delta parameter allows to set the stable value for the metric in the opticluster method. To reach a full convergence, set delta=0."/> + <param argument="iters" type="integer" value="100" label="Maximum number of iterations"/> + </xml> + <xml name="param-output"> + <param argument="output" type="select" label="Tax summary output type" + help="The detail format outputs the totals at each level, where as the simple format outputs the highest level"> + <option value="simple" selected="true">simple</option> + <option value="detail">detail</option> + </param> + </xml> + <xml name="param-printlevel"> + <param argument="printlevel" type="integer" value="-1" min="-1" label="Print level" help="specify taxlevel of your *tax.summary file to print to. Options are 1 to the maz level in the file. The default is -1, meaning max level" /> + </xml> <xml name="logfile-output"> <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"/> </xml> + + <!-- Output file tests --> <xml name="logfile-test"> <output name="logfile" ftype="txt"> <assert_contents> @@ -89,6 +137,101 @@ </assert_contents> </output> </xml> + + <xml name="test-accnos-format"> + <!-- one or two columns --> + <has_line_matching expression="^[\w\d\-]+(\t[^\t]+)?$"/> + </xml> + <xml name="test-align-format"> + <has_line_matching expression="^>.+$"/> + <has_line_matching expression="^[ACTG\-\.]+$"/> + </xml> + <xml name="test-aligncheck-format"> + <has_n_columns n="9"/> + <has_line_matching expression="^name\tpound\tdash\tplus\tequal\tloop\ttilde\ttotal\tnumseqs$"/> + </xml> + <xml name="test-alignreport-format"> + <has_line_matching expression="^QueryName\tQueryLength\tTemplateName\tTemplateLength\tSearchMethod\tSearchScore\tAlignmentMethod\tQueryStart\tQueryEnd\tTemplateStart\tTemplateEnd\tPairwiseAlignmentLength\tGapsInQuery\tGapsInTemplate\tLongestInsert\tSimBtwnQuery&Template$"/> + </xml> + <xml name="test-axes-format"> + <has_line_matching expression="^group(\taxis\d+)+$"/> + </xml> + <xml name="test-chimera-format"> + <has_line_matching expression="Score\tQuery\tParentA\tParentB\tIdQM\tIdQA\tIdQB\tIdAB\tIdQT\tLY\tLN\tLA\tRY\tRN\tRA\tDiv\tYN"/> + </xml> + <xml name="test-column-format"> + <has_n_columns n="3"/> + <has_line_matching expression="^[\w\d\-]+\t[\w\d\-]+\t[\d\.]+$"/> + </xml> + <xml name="test-contigsreport-format"> + <has_n_columns n="7"/> + <has_line_matching expression="^Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns$"/> + </xml> + <xml name="test-count-format"> + <has_line_matching expression="^Representative_Sequence\ttotal(\t\w+)*$"/> + <has_line_matching expression="^\w+(\t\d+)+(\s)*$"/> + </xml> + <xml name="test-dist-format"> + <has_line_matching expression="^[ \t]*\d+$"/> + <has_line_matching expression="^[\w\d\-]+(\t[\d\.]+)+\s?$"/> + </xml> + <xml name="test-fasta-format"> + <has_line_matching expression="^>.+$"/> + <has_line_matching expression="^[ACTGN-]+$"/> + </xml> + <xml name="test-fastq-format"> + <has_line_matching expression="^@.+$"/> + <has_line_matching expression="^[ACTGN]+$"/> + <has_line_matching expression="^\+$"/> + </xml> + <xml name="test-group-format"> + <has_line_matching expression="^Representative_Sequence\ttotal(\t[\w\d\-]+)+$"/> + <has_line_matching expression="^[\w\d\-]+(\t\d+)+$"/> + </xml> + <xml name="test-list-format"> + <has_line_matching expression="^label\tnumOtus(\tOtu\d+)+$"/> + <has_line_matching expression="^(unique|0\.\d+)\t\d+(\t[\w\d\-,]+)+$"/> + </xml> + <xml name="test-names-format"> + <has_line_matching expression="^[a-zA-Z0-9]+\t[a-zA-Z0-9]+$"/> + </xml> + <xml name="test-qfile-format"> + <has_line_matching expression="^(\d+ )+$"/> + <has_line_matching expression="^>.+$"/> + </xml> + <xml name="test-rabund-format"> + <has_line_matching expression="^(unique|0\.\d+)(\t\d+\.?\d*)+$"/> + </xml> + <xml name="test-sabund-format"> + <has_line_matching expression="^(unique|0\.\d+)(\t\d+)+$"/> + </xml> + <xml name="test-sensspec-format"> + <has_n_columns n="14"/> + <has_line_matching expression="^label\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\t\w+\tf1score$"/> + </xml> + <xml name="test-shared-format"> + <has_line_matching expression="^label\tGroup\tnumOtus(\t(Otu|rareOTUs|.*OTU.*)\d+)+$"/> + </xml> + <xml name="test-taxonomy-format"> + <has_n_columns n="3"/> + <has_line_matching expression="^OTU\tSize\tTaxonomy$"/> + </xml> + <xml name="test-taxsummary-format"> + <has_line_matching expression="^((taxlevel\trankID\ttaxon\tdaughterlevels\ttotal(\t[\w\d\-]+)*)|(taxonomy\ttotal(\t[\w\d]+)*))$"/> + </xml> + <!-- backmatter --> + <token name="@MOTHUR_OVERVIEW@"> +<![CDATA[ + +**Mothur Overview** + +Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team +in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_. + +.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page + +]]> + </token> <xml name="citations"> <citations> <citation type="doi">10.1128/AEM.01541-09</citation>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.accnos Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,1 @@ +00967_43_000000000-A3JHG_1_1101_19936_3208
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.groups Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,25 @@ +M00967_43_000000000-A3JHG_1_1101_19936_3208 groupA +M00967_43_000000000-A3JHG_1_1101_15923_3823 groupA +M00967_43_000000000-A3JHG_1_1101_14010_4122 groupA +M00967_43_000000000-A3JHG_1_1101_10776_4204 groupA +M00967_43_000000000-A3JHG_1_1101_22487_4260 groupA +M00967_43_000000000-A3JHG_1_1101_13293_4703 groupA +M00967_43_000000000-A3JHG_1_1101_24357_4866 groupA +M00967_43_000000000-A3JHG_1_1101_23552_5194 groupA +M00967_43_000000000-A3JHG_1_1101_7326_5417 groupA +M00967_43_000000000-A3JHG_1_1101_11148_6457 groupA +M00967_43_000000000-A3JHG_1_1101_7079_6722 groupA +M00967_43_000000000-A3JHG_1_1101_8607_6805 groupA +M00967_43_000000000-A3JHG_1_1101_15208_7185 groupA +M00967_43_000000000-A3JHG_1_1101_4525_7317 groupA +M00967_43_000000000-A3JHG_1_1101_9121_7358 groupA +M00967_43_000000000-A3JHG_1_1101_8480_7498 groupA +M00967_43_000000000-A3JHG_1_1101_11790_7581 groupA +M00967_43_000000000-A3JHG_1_1101_20566_7622 groupA +M00967_43_000000000-A3JHG_1_1101_10073_7632 groupA +M00967_43_000000000-A3JHG_1_1101_5170_7771 groupA +M00967_43_000000000-A3JHG_1_1101_18966_7778 groupA +M00967_43_000000000-A3JHG_1_1101_5494_7973 groupA +M00967_43_000000000-A3JHG_1_1101_10246_8076 groupA +M00967_43_000000000-A3JHG_1_1101_23931_8157 groupA +M00967_43_000000000-A3JHG_1_1101_18269_8162 groupA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.names Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,19 @@ +M00967_43_000000000-A3JHG_1_1101_19936_3208 M00967_43_000000000-A3JHG_1_1101_19936_3208 +M00967_43_000000000-A3JHG_1_1101_15923_3823 M00967_43_000000000-A3JHG_1_1101_15923_3823,M00967_43_000000000-A3JHG_1_1101_15208_7185 +M00967_43_000000000-A3JHG_1_1101_14010_4122 M00967_43_000000000-A3JHG_1_1101_14010_4122 +M00967_43_000000000-A3JHG_1_1101_10776_4204 M00967_43_000000000-A3JHG_1_1101_10776_4204 +M00967_43_000000000-A3JHG_1_1101_22487_4260 M00967_43_000000000-A3JHG_1_1101_22487_4260 +M00967_43_000000000-A3JHG_1_1101_13293_4703 M00967_43_000000000-A3JHG_1_1101_13293_4703,M00967_43_000000000-A3JHG_1_1101_11148_6457,M00967_43_000000000-A3JHG_1_1101_5170_7771 +M00967_43_000000000-A3JHG_1_1101_24357_4866 M00967_43_000000000-A3JHG_1_1101_24357_4866,M00967_43_000000000-A3JHG_1_1101_11790_7581 +M00967_43_000000000-A3JHG_1_1101_23552_5194 M00967_43_000000000-A3JHG_1_1101_23552_5194 +M00967_43_000000000-A3JHG_1_1101_7326_5417 M00967_43_000000000-A3JHG_1_1101_7326_5417 +M00967_43_000000000-A3JHG_1_1101_7079_6722 M00967_43_000000000-A3JHG_1_1101_7079_6722 +M00967_43_000000000-A3JHG_1_1101_8607_6805 M00967_43_000000000-A3JHG_1_1101_8607_6805,M00967_43_000000000-A3JHG_1_1101_4525_7317 +M00967_43_000000000-A3JHG_1_1101_9121_7358 M00967_43_000000000-A3JHG_1_1101_9121_7358,M00967_43_000000000-A3JHG_1_1101_5494_7973 +M00967_43_000000000-A3JHG_1_1101_8480_7498 M00967_43_000000000-A3JHG_1_1101_8480_7498 +M00967_43_000000000-A3JHG_1_1101_20566_7622 M00967_43_000000000-A3JHG_1_1101_20566_7622 +M00967_43_000000000-A3JHG_1_1101_10073_7632 M00967_43_000000000-A3JHG_1_1101_10073_7632 +M00967_43_000000000-A3JHG_1_1101_18966_7778 M00967_43_000000000-A3JHG_1_1101_18966_7778 +M00967_43_000000000-A3JHG_1_1101_10246_8076 M00967_43_000000000-A3JHG_1_1101_10246_8076 +M00967_43_000000000-A3JHG_1_1101_23931_8157 M00967_43_000000000-A3JHG_1_1101_23931_8157 +M00967_43_000000000-A3JHG_1_1101_18269_8162 M00967_43_000000000-A3JHG_1_1101_18269_8162
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.unique.fasta Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,38 @@ +>M00967_43_000000000-A3JHG_1_1101_19936_3208 +TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_15923_3823 +TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCGG +>M00967_43_000000000-A3JHG_1_1101_14010_4122 +TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGTCTGTAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_10776_4204 +TACGGAGGATNCGAGGTTATCCGGATTTATTGGGTTTAAAGGGNGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGNGGTGTAGCGGTGAAATGCTTAGATATCACGGGGAANTCCGATTGCGAAGGCAGCCNGCTAAGCNGCAACTGACATTGAGGCTNGAAAGTGTGGGTATCAANCAGG +>M00967_43_000000000-A3JHG_1_1101_22487_4260 +TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAANGCGTGGGGAGCGAACAGG +>M00967_43_000000000-A3JHG_1_1101_13293_4703 +TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_24357_4866 +TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGG +>M00967_43_000000000-A3JHG_1_1101_23552_5194 +TACAGAGGGTGCGAGCGTTAATCGGATTTACTGGGCGTAAAGCGTGCGTAGGCGGCTTATTAAGTCGGATGTGAAATCCCCGAGCTTAACTTGGGAATTGCATTCGATACTGGTGAGCTAGAGTATGGGAGAGGATGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGATGGCGAAGGCAGCCATCTGGCCTAATACTGACGCTGAGGTACGAAAGCATGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_7326_5417 +TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCTG +>M00967_43_000000000-A3JHG_1_1101_7079_6722 +TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_8607_6805 +TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_9121_7358 +TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_8480_7498 +TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTACGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_20566_7622 +TACGGAGGGTGCAAGCGTTACTCGGAATCACTGGGCGTAAAGAGCGCGTAGGCGGGATAGTCAGTCAGGTGTGAAATCCTATGGCTTAACCATAGAACTGCATTTGAAACTACTATTCTAGAGTGTGGGAGAGGTAGGTGGAATTCTTGGTGTAGGGGTAAAATCCGTAGAGATCAAGAGGAATACTCATTGCGAAGGCGACCTGCTGGAACATTACTGACGCTGATTGCGCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_10073_7632 +TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTACGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACCGG +>M00967_43_000000000-A3JHG_1_1101_18966_7778 +TACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGGGCGCAGACGGTTACTTAAGCAGGATGTGAAATCCCCGGGCTCAACCCGGGAACTGCGTTCTGAACTGGGTGACTCGAGTGTGTCAGAGGGAGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGACAACACTGACGTTCATGCCCGAAAGCGTGGGTAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_10246_8076 +TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAGGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_23931_8157 +TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGTGGATATTTAAGTGGGATGTGAAATACTCGGGCTTAACCTGGGTGCTGCATTCCAAACTGGANATCTAGAGTGCAGGAGAGGAAAGTAGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAATACCAGTGGCGAAGGCGACTTTCTGGACTGTAACTGACACTGAGGCTCGAAAGCGTGGGGAGCAAACAGG +>M00967_43_000000000-A3JHG_1_1101_18269_8162 +TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTCACTGACGCTGAGGCTCGAAAGCGTGGGTAGCGAACAGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.unique.groups Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,19 @@ +M00967_43_000000000-A3JHG_1_1101_19936_3208 groupA +M00967_43_000000000-A3JHG_1_1101_15923_3823 groupA +M00967_43_000000000-A3JHG_1_1101_14010_4122 groupA +M00967_43_000000000-A3JHG_1_1101_10776_4204 groupA +M00967_43_000000000-A3JHG_1_1101_22487_4260 groupA +M00967_43_000000000-A3JHG_1_1101_13293_4703 groupA +M00967_43_000000000-A3JHG_1_1101_24357_4866 groupA +M00967_43_000000000-A3JHG_1_1101_23552_5194 groupA +M00967_43_000000000-A3JHG_1_1101_7326_5417 groupA +M00967_43_000000000-A3JHG_1_1101_7079_6722 groupA +M00967_43_000000000-A3JHG_1_1101_8607_6805 groupA +M00967_43_000000000-A3JHG_1_1101_9121_7358 groupA +M00967_43_000000000-A3JHG_1_1101_8480_7498 groupA +M00967_43_000000000-A3JHG_1_1101_20566_7622 groupA +M00967_43_000000000-A3JHG_1_1101_10073_7632 groupA +M00967_43_000000000-A3JHG_1_1101_18966_7778 groupA +M00967_43_000000000-A3JHG_1_1101_10246_8076 groupA +M00967_43_000000000-A3JHG_1_1101_23931_8157 groupA +M00967_43_000000000-A3JHG_1_1101_18269_8162 groupA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.an.0.03.pearson.otu.corr Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,3829 @@ +OTUA OTUB pearsonCoef Significance +Otu02 Otu01 -1.000000 0.000000 +Otu03 Otu01 1.000000 0.000000 +Otu03 Otu02 -1.000000 0.000000 +Otu04 Otu01 -1.000000 0.000000 +Otu04 Otu02 1.000000 0.000000 +Otu04 Otu03 -1.000000 0.000000 +Otu05 Otu01 -nan 0.000000 +Otu05 Otu02 -nan 0.000000 +Otu05 Otu03 -nan 0.000000 +Otu05 Otu04 -nan 0.000000 +Otu06 Otu01 1.000000 0.000000 +Otu06 Otu02 -1.000000 0.000000 +Otu06 Otu03 1.000000 0.000000 +Otu06 Otu04 -1.000000 0.000000 +Otu06 Otu05 -nan 0.000000 +Otu07 Otu01 1.000000 0.000000 +Otu07 Otu02 -1.000000 0.000000 +Otu07 Otu03 1.000000 0.000000 +Otu07 Otu04 -1.000000 0.000000 +Otu07 Otu05 -nan 0.000000 +Otu07 Otu06 1.000000 0.000000 +Otu08 Otu01 1.000000 0.000000 +Otu08 Otu02 -1.000000 0.000000 +Otu08 Otu03 1.000000 0.000000 +Otu08 Otu04 -1.000000 0.000000 +Otu08 Otu05 -nan 0.000000 +Otu08 Otu06 1.000000 0.000000 +Otu08 Otu07 1.000000 0.000000 +Otu09 Otu01 1.000000 0.000000 +Otu09 Otu02 -1.000000 0.000000 +Otu09 Otu03 1.000000 0.000000 +Otu09 Otu04 -1.000000 0.000000 +Otu09 Otu05 -nan 0.000000 +Otu09 Otu06 1.000000 0.000000 +Otu09 Otu07 1.000000 0.000000 +Otu09 Otu08 1.000000 0.000000 +Otu10 Otu01 1.000000 0.000000 +Otu10 Otu02 -1.000000 0.000000 +Otu10 Otu03 1.000000 0.000000 +Otu10 Otu04 -1.000000 0.000000 +Otu10 Otu05 -nan 0.000000 +Otu10 Otu06 1.000000 0.000000 +Otu10 Otu07 1.000000 0.000000 +Otu10 Otu08 1.000000 0.000000 +Otu10 Otu09 1.000000 0.000000 +Otu11 Otu01 1.000000 0.000000 +Otu11 Otu02 -1.000000 0.000000 +Otu11 Otu03 1.000000 0.000000 +Otu11 Otu04 -1.000000 0.000000 +Otu11 Otu05 -nan 0.000000 +Otu11 Otu06 1.000000 0.000000 +Otu11 Otu07 1.000000 0.000000 +Otu11 Otu08 1.000000 0.000000 +Otu11 Otu09 1.000000 0.000000 +Otu11 Otu10 1.000000 0.000000 +Otu12 Otu01 1.000000 0.000000 +Otu12 Otu02 -1.000000 0.000000 +Otu12 Otu03 1.000000 0.000000 +Otu12 Otu04 -1.000000 0.000000 +Otu12 Otu05 -nan 0.000000 +Otu12 Otu06 1.000000 0.000000 +Otu12 Otu07 1.000000 0.000000 +Otu12 Otu08 1.000000 0.000000 +Otu12 Otu09 1.000000 0.000000 +Otu12 Otu10 1.000000 0.000000 +Otu12 Otu11 1.000000 0.000000 +Otu13 Otu01 1.000000 0.000000 +Otu13 Otu02 -1.000000 0.000000 +Otu13 Otu03 1.000000 0.000000 +Otu13 Otu04 -1.000000 0.000000 +Otu13 Otu05 -nan 0.000000 +Otu13 Otu06 1.000000 0.000000 +Otu13 Otu07 1.000000 0.000000 +Otu13 Otu08 1.000000 0.000000 +Otu13 Otu09 1.000000 0.000000 +Otu13 Otu10 1.000000 0.000000 +Otu13 Otu11 1.000000 0.000000 +Otu13 Otu12 1.000000 0.000000 +Otu14 Otu01 1.000000 0.000000 +Otu14 Otu02 -1.000000 0.000000 +Otu14 Otu03 1.000000 0.000000 +Otu14 Otu04 -1.000000 0.000000 +Otu14 Otu05 -nan 0.000000 +Otu14 Otu06 1.000000 0.000000 +Otu14 Otu07 1.000000 0.000000 +Otu14 Otu08 1.000000 0.000000 +Otu14 Otu09 1.000000 0.000000 +Otu14 Otu10 1.000000 0.000000 +Otu14 Otu11 1.000000 0.000000 +Otu14 Otu12 1.000000 0.000000 +Otu14 Otu13 1.000000 0.000000 +Otu15 Otu01 1.000000 0.000000 +Otu15 Otu02 -1.000000 0.000000 +Otu15 Otu03 1.000000 0.000000 +Otu15 Otu04 -1.000000 0.000000 +Otu15 Otu05 -nan 0.000000 +Otu15 Otu06 1.000000 0.000000 +Otu15 Otu07 1.000000 0.000000 +Otu15 Otu08 1.000000 0.000000 +Otu15 Otu09 1.000000 0.000000 +Otu15 Otu10 1.000000 0.000000 +Otu15 Otu11 1.000000 0.000000 +Otu15 Otu12 1.000000 0.000000 +Otu15 Otu13 1.000000 0.000000 +Otu15 Otu14 1.000000 0.000000 +Otu16 Otu01 1.000000 0.000000 +Otu16 Otu02 -1.000000 0.000000 +Otu16 Otu03 1.000000 0.000000 +Otu16 Otu04 -1.000000 0.000000 +Otu16 Otu05 -nan 0.000000 +Otu16 Otu06 1.000000 0.000000 +Otu16 Otu07 1.000000 0.000000 +Otu16 Otu08 1.000000 0.000000 +Otu16 Otu09 1.000000 0.000000 +Otu16 Otu10 1.000000 0.000000 +Otu16 Otu11 1.000000 0.000000 +Otu16 Otu12 1.000000 0.000000 +Otu16 Otu13 1.000000 0.000000 +Otu16 Otu14 1.000000 0.000000 +Otu16 Otu15 1.000000 0.000000 +Otu17 Otu01 1.000000 0.000000 +Otu17 Otu02 -1.000000 0.000000 +Otu17 Otu03 1.000000 0.000000 +Otu17 Otu04 -1.000000 0.000000 +Otu17 Otu05 -nan 0.000000 +Otu17 Otu06 1.000000 0.000000 +Otu17 Otu07 1.000000 0.000000 +Otu17 Otu08 1.000000 0.000000 +Otu17 Otu09 1.000000 0.000000 +Otu17 Otu10 1.000000 0.000000 +Otu17 Otu11 1.000000 0.000000 +Otu17 Otu12 1.000000 0.000000 +Otu17 Otu13 1.000000 0.000000 +Otu17 Otu14 1.000000 0.000000 +Otu17 Otu15 1.000000 0.000000 +Otu17 Otu16 1.000000 0.000000 +Otu18 Otu01 1.000000 0.000000 +Otu18 Otu02 -1.000000 0.000000 +Otu18 Otu03 1.000000 0.000000 +Otu18 Otu04 -1.000000 0.000000 +Otu18 Otu05 -nan 0.000000 +Otu18 Otu06 1.000000 0.000000 +Otu18 Otu07 1.000000 0.000000 +Otu18 Otu08 1.000000 0.000000 +Otu18 Otu09 1.000000 0.000000 +Otu18 Otu10 1.000000 0.000000 +Otu18 Otu11 1.000000 0.000000 +Otu18 Otu12 1.000000 0.000000 +Otu18 Otu13 1.000000 0.000000 +Otu18 Otu14 1.000000 0.000000 +Otu18 Otu15 1.000000 0.000000 +Otu18 Otu16 1.000000 0.000000 +Otu18 Otu17 1.000000 0.000000 +Otu19 Otu01 1.000000 0.000000 +Otu19 Otu02 -1.000000 0.000000 +Otu19 Otu03 1.000000 0.000000 +Otu19 Otu04 -1.000000 0.000000 +Otu19 Otu05 -nan 0.000000 +Otu19 Otu06 1.000000 0.000000 +Otu19 Otu07 1.000000 0.000000 +Otu19 Otu08 1.000000 0.000000 +Otu19 Otu09 1.000000 0.000000 +Otu19 Otu10 1.000000 0.000000 +Otu19 Otu11 1.000000 0.000000 +Otu19 Otu12 1.000000 0.000000 +Otu19 Otu13 1.000000 0.000000 +Otu19 Otu14 1.000000 0.000000 +Otu19 Otu15 1.000000 0.000000 +Otu19 Otu16 1.000000 0.000000 +Otu19 Otu17 1.000000 0.000000 +Otu19 Otu18 1.000000 0.000000 +Otu20 Otu01 1.000000 0.000000 +Otu20 Otu02 -1.000000 0.000000 +Otu20 Otu03 1.000000 0.000000 +Otu20 Otu04 -1.000000 0.000000 +Otu20 Otu05 -nan 0.000000 +Otu20 Otu06 1.000000 0.000000 +Otu20 Otu07 1.000000 0.000000 +Otu20 Otu08 1.000000 0.000000 +Otu20 Otu09 1.000000 0.000000 +Otu20 Otu10 1.000000 0.000000 +Otu20 Otu11 1.000000 0.000000 +Otu20 Otu12 1.000000 0.000000 +Otu20 Otu13 1.000000 0.000000 +Otu20 Otu14 1.000000 0.000000 +Otu20 Otu15 1.000000 0.000000 +Otu20 Otu16 1.000000 0.000000 +Otu20 Otu17 1.000000 0.000000 +Otu20 Otu18 1.000000 0.000000 +Otu20 Otu19 1.000000 0.000000 +Otu21 Otu01 1.000000 0.000000 +Otu21 Otu02 -1.000000 0.000000 +Otu21 Otu03 1.000000 0.000000 +Otu21 Otu04 -1.000000 0.000000 +Otu21 Otu05 -nan 0.000000 +Otu21 Otu06 1.000000 0.000000 +Otu21 Otu07 1.000000 0.000000 +Otu21 Otu08 1.000000 0.000000 +Otu21 Otu09 1.000000 0.000000 +Otu21 Otu10 1.000000 0.000000 +Otu21 Otu11 1.000000 0.000000 +Otu21 Otu12 1.000000 0.000000 +Otu21 Otu13 1.000000 0.000000 +Otu21 Otu14 1.000000 0.000000 +Otu21 Otu15 1.000000 0.000000 +Otu21 Otu16 1.000000 0.000000 +Otu21 Otu17 1.000000 0.000000 +Otu21 Otu18 1.000000 0.000000 +Otu21 Otu19 1.000000 0.000000 +Otu21 Otu20 1.000000 0.000000 +Otu22 Otu01 1.000000 0.000000 +Otu22 Otu02 -1.000000 0.000000 +Otu22 Otu03 1.000000 0.000000 +Otu22 Otu04 -1.000000 0.000000 +Otu22 Otu05 -nan 0.000000 +Otu22 Otu06 1.000000 0.000000 +Otu22 Otu07 1.000000 0.000000 +Otu22 Otu08 1.000000 0.000000 +Otu22 Otu09 1.000000 0.000000 +Otu22 Otu10 1.000000 0.000000 +Otu22 Otu11 1.000000 0.000000 +Otu22 Otu12 1.000000 0.000000 +Otu22 Otu13 1.000000 0.000000 +Otu22 Otu14 1.000000 0.000000 +Otu22 Otu15 1.000000 0.000000 +Otu22 Otu16 1.000000 0.000000 +Otu22 Otu17 1.000000 0.000000 +Otu22 Otu18 1.000000 0.000000 +Otu22 Otu19 1.000000 0.000000 +Otu22 Otu20 1.000000 0.000000 +Otu22 Otu21 1.000000 0.000000 +Otu23 Otu01 1.000000 0.000000 +Otu23 Otu02 -1.000000 0.000000 +Otu23 Otu03 1.000000 0.000000 +Otu23 Otu04 -1.000000 0.000000 +Otu23 Otu05 -nan 0.000000 +Otu23 Otu06 1.000000 0.000000 +Otu23 Otu07 1.000000 0.000000 +Otu23 Otu08 1.000000 0.000000 +Otu23 Otu09 1.000000 0.000000 +Otu23 Otu10 1.000000 0.000000 +Otu23 Otu11 1.000000 0.000000 +Otu23 Otu12 1.000000 0.000000 +Otu23 Otu13 1.000000 0.000000 +Otu23 Otu14 1.000000 0.000000 +Otu23 Otu15 1.000000 0.000000 +Otu23 Otu16 1.000000 0.000000 +Otu23 Otu17 1.000000 0.000000 +Otu23 Otu18 1.000000 0.000000 +Otu23 Otu19 1.000000 0.000000 +Otu23 Otu20 1.000000 0.000000 +Otu23 Otu21 1.000000 0.000000 +Otu23 Otu22 1.000000 0.000000 +Otu24 Otu01 -1.000000 0.000000 +Otu24 Otu02 1.000000 0.000000 +Otu24 Otu03 -1.000000 0.000000 +Otu24 Otu04 1.000000 0.000000 +Otu24 Otu05 -nan 0.000000 +Otu24 Otu06 -1.000000 0.000000 +Otu24 Otu07 -1.000000 0.000000 +Otu24 Otu08 -1.000000 0.000000 +Otu24 Otu09 -1.000000 0.000000 +Otu24 Otu10 -1.000000 0.000000 +Otu24 Otu11 -1.000000 0.000000 +Otu24 Otu12 -1.000000 0.000000 +Otu24 Otu13 -1.000000 0.000000 +Otu24 Otu14 -1.000000 0.000000 +Otu24 Otu15 -1.000000 0.000000 +Otu24 Otu16 -1.000000 0.000000 +Otu24 Otu17 -1.000000 0.000000 +Otu24 Otu18 -1.000000 0.000000 +Otu24 Otu19 -1.000000 0.000000 +Otu24 Otu20 -1.000000 0.000000 +Otu24 Otu21 -1.000000 0.000000 +Otu24 Otu22 -1.000000 0.000000 +Otu24 Otu23 -1.000000 0.000000 +Otu25 Otu01 1.000000 0.000000 +Otu25 Otu02 -1.000000 0.000000 +Otu25 Otu03 1.000000 0.000000 +Otu25 Otu04 -1.000000 0.000000 +Otu25 Otu05 -nan 0.000000 +Otu25 Otu06 1.000000 0.000000 +Otu25 Otu07 1.000000 0.000000 +Otu25 Otu08 1.000000 0.000000 +Otu25 Otu09 1.000000 0.000000 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.otus.accnos Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,3 @@ +Otu01 +Otu17 +Otu42
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/esophagus.design Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,4 @@ +A group1 +B group2 +C group2 +D group3
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mothur.1518613887.logfile Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,5966 @@ +Linux version + +Using ReadLine + +Running 64Bit Version + +mothur v.1.39.5 +Last updated: 3/20/2017 + +by +Patrick D. Schloss + +Department of Microbiology & Immunology +University of Michigan +http://www.mothur.org + +When using, please cite: +Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +failed to train SVM on labels A and B +[ERROR]: std::exceptionRAM used: 0.00559998Gigabytes . Total Ram: 62.8475Gigabytes. + + has occurred in the ClassifySvmSharedCommand class function processSharedAndDesignData. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mothur.1518613903.logfile Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,41 @@ +Linux version + +Using ReadLine + +Running 64Bit Version + +mothur v.1.39.5 +Last updated: 3/20/2017 + +by +Patrick D. Schloss + +Department of Microbiology & Immunology +University of Michigan +http://www.mothur.org + +When using, please cite: +Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41. + +Distributed under the GNU General Public License + +Type 'help()' for information on the commands that are available + +For questions and analysis support, please visit our forum at https://www.mothur.org/forum + +Type 'quit()' to exit program +Interactive Mode + + +mothur > classify.svm(shared=final.tx.1.subsample.1.pick.shared,design=test.design, kernel=sigmoid) +removing kernel linear +removing kernel polynomial +removing kernel rbf +1 +transforming data to have zero mean and unit variance +SVM-RFE round 1: +44 unranked features +failed to train SVM on labels A and B +[ERROR]: std::exceptionRAM used: 0.00562668Gigabytes . Total Ram: 62.8475Gigabytes. + + has occurred in the ClassifySvmSharedCommand class function processSharedAndDesignData. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mothur.1518613913.logfile Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,41 @@ +Linux version + +Using ReadLine + +Running 64Bit Version + +mothur v.1.39.5 +Last updated: 3/20/2017 + +by +Patrick D. Schloss + +Department of Microbiology & Immunology +University of Michigan +http://www.mothur.org + +When using, please cite: +Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41. + +Distributed under the GNU General Public License + +Type 'help()' for information on the commands that are available + +For questions and analysis support, please visit our forum at https://www.mothur.org/forum + +Type 'quit()' to exit program +Interactive Mode + + +mothur > classify.svm(shared=final.tx.1.subsample.1.pick.shared,design=test.design, kernel=rbf) +removing kernel linear +removing kernel polynomial +removing kernel sigmoid +1 +transforming data to have zero mean and unit variance +SVM-RFE round 1: +44 unranked features +failed to train SVM on labels A and B +[ERROR]: std::exceptionRAM used: 0.00563049Gigabytes . Total Ram: 62.8475Gigabytes. + + has occurred in the ClassifySvmSharedCommand class function processSharedAndDesignData. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mothur.1518613936.logfile Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,41 @@ +Linux version + +Using ReadLine + +Running 64Bit Version + +mothur v.1.39.5 +Last updated: 3/20/2017 + +by +Patrick D. Schloss + +Department of Microbiology & Immunology +University of Michigan +http://www.mothur.org + +When using, please cite: +Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41. + +Distributed under the GNU General Public License + +Type 'help()' for information on the commands that are available + +For questions and analysis support, please visit our forum at https://www.mothur.org/forum + +Type 'quit()' to exit program +Interactive Mode + + +mothur > classify.svm(shared=final.tx.1.subsample.1.pick.shared,design=test.design, kernel=polynomial) +removing kernel linear +removing kernel rbf +removing kernel sigmoid +1 +transforming data to have zero mean and unit variance +SVM-RFE round 1: +44 unranked features +failed to train SVM on labels A and B +[ERROR]: std::exceptionRAM used: 0.00564575Gigabytes . Total Ram: 62.8475Gigabytes. + + has occurred in the ClassifySvmSharedCommand class function processSharedAndDesignData. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mothur.1518613968.logfile Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,7954 @@ +Linux version + +Using ReadLine + +Running 64Bit Version + +mothur v.1.39.5 +Last updated: 3/20/2017 + +by +Patrick D. Schloss + +Department of Microbiology & Immunology +University of Michigan +http://www.mothur.org + +When using, please cite: +Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. 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Total Ram: 62.8475Gigabytes. + + has occurred in the ClassifySvmSharedCommand class function processSharedAndDesignData. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mothur.1518614517.logfile Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,28 @@ +Linux version + +Using ReadLine + +Running 64Bit Version + +mothur v.1.39.5 +Last updated: 3/20/2017 + +by +Patrick D. Schloss + +Department of Microbiology & Immunology +University of Michigan +http://www.mothur.org + +When using, please cite: +Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41. + +Distributed under the GNU General Public License + +Type 'help()' for information on the commands that are available + +For questions and analysis support, please visit our forum at https://www.mothur.org/forum + +Type 'quit()' to exit program +Interactive Mode +
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool.design Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,24 @@ +F11Fcsw F +F12Fcsw F +F13Fcsw F +F14Fcsw F +F21Fcsw F +F22Fcsw F +F23Fcsw F +F24Fcsw F +F31Fcsw F +F32Fcsw F +F33Fcsw F +F34Fcsw F +M11Fcsw M +M12Fcsw M +M13Fcsw M +M14Fcsw M +M21Fcsw M +M22Fcsw M +M23Fcsw M +M24Fcsw M +M41Fcsw M +M42Fcsw M +M43Fcsw M +M44Fcsw M
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool.final.opti_mcc.shared Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,25 @@ +label Group numOtus Otu0001 Otu0002 Otu0003 Otu0004 Otu0005 Otu0006 Otu0007 Otu0008 Otu0009 Otu0010 Otu0011 Otu0012 Otu0013 Otu0014 Otu0015 Otu0016 Otu0017 Otu0018 Otu0019 Otu0020 Otu0021 Otu0022 Otu0023 Otu0024 Otu0025 Otu0026 Otu0027 Otu0028 Otu0029 Otu0030 Otu0031 Otu0032 Otu0033 Otu0034 Otu0035 Otu0036 Otu0037 Otu0038 Otu0039 Otu0040 Otu0041 Otu0042 Otu0043 Otu0044 Otu0045 Otu0046 Otu0047 Otu0048 Otu0049 Otu0050 Otu0051 Otu0052 Otu0053 Otu0054 Otu0055 Otu0056 Otu0057 Otu0058 Otu0059 Otu0060 Otu0061 Otu0062 Otu0063 Otu0064 Otu0065 Otu0066 Otu0067 Otu0068 Otu0069 Otu0070 Otu0071 Otu0072 Otu0073 Otu0074 Otu0075 Otu0076 Otu0077 Otu0078 Otu0079 Otu0080 Otu0081 Otu0082 Otu0083 Otu0084 Otu0085 Otu0086 Otu0087 Otu0088 Otu0089 Otu0090 Otu0091 Otu0092 Otu0093 Otu0094 Otu0095 Otu0096 Otu0097 Otu0098 Otu0099 Otu0100 Otu0101 Otu0102 Otu0103 Otu0104 Otu0105 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.count_table Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,47 @@ +Representative_Sequence total +F11Fcsw_12747 1 +F11Fcsw_13125 1 +F11Fcsw_13572 2 +F11Fcsw_13584 1 +F11Fcsw_13612 2 +F11Fcsw_13784 2 +F11Fcsw_14513 1 +F11Fcsw_14920 1 +F11Fcsw_14954 1 +F11Fcsw_14980 1 +F11Fcsw_15042 1 +F11Fcsw_15664 1 +F11Fcsw_17394 1 +F11Fcsw_17898 1 +F11Fcsw_18564 1 +F11Fcsw_19115 1 +F11Fcsw_19402 1 +F11Fcsw_19500 1 +F11Fcsw_20028 1 +F11Fcsw_20361 1 +F11Fcsw_20429 1 +F11Fcsw_20462 1 +F11Fcsw_20686 1 +F11Fcsw_21035 1 +F11Fcsw_21196 1 +F11Fcsw_21505 1 +F11Fcsw_21636 1 +F11Fcsw_21645 1 +F11Fcsw_21954 1 +F11Fcsw_22687 1 +F11Fcsw_22831 1 +F11Fcsw_22880 1 +F11Fcsw_22900 1 +F11Fcsw_23043 1 +F11Fcsw_23322 1 +F11Fcsw_23608 1 +F11Fcsw_23684 1 +F11Fcsw_24087 1 +F11Fcsw_24273 1 +F11Fcsw_24701 2 +F11Fcsw_24967 1 +F11Fcsw_25501 1 +F11Fcsw_25574 1 +F11Fcsw_26078 1 +F11Fcsw_26175 1 +F11Fcsw_26418 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.denovo.vsearch.accnos Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,2 @@ +F11Fcsw_21505 +F11Fcsw_23322
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.names Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,46 @@ +F11Fcsw_12747 F11Fcsw_12747 +F11Fcsw_13125 F11Fcsw_13125 +F11Fcsw_13572 F11Fcsw_13572,F11Fcsw_14202 +F11Fcsw_13584 F11Fcsw_13584 +F11Fcsw_13612 F11Fcsw_13612,F11Fcsw_23132 +F11Fcsw_13784 F11Fcsw_13784,F11Fcsw_21715 +F11Fcsw_14513 F11Fcsw_14513 +F11Fcsw_14920 F11Fcsw_14920 +F11Fcsw_14954 F11Fcsw_14954 +F11Fcsw_14980 F11Fcsw_14980 +F11Fcsw_15042 F11Fcsw_15042 +F11Fcsw_15664 F11Fcsw_15664 +F11Fcsw_17394 F11Fcsw_17394 +F11Fcsw_17898 F11Fcsw_17898 +F11Fcsw_18564 F11Fcsw_18564 +F11Fcsw_19115 F11Fcsw_19115 +F11Fcsw_19402 F11Fcsw_19402 +F11Fcsw_19500 F11Fcsw_19500 +F11Fcsw_20028 F11Fcsw_20028 +F11Fcsw_20361 F11Fcsw_20361 +F11Fcsw_20429 F11Fcsw_20429 +F11Fcsw_20462 F11Fcsw_20462 +F11Fcsw_20686 F11Fcsw_20686 +F11Fcsw_21035 F11Fcsw_21035 +F11Fcsw_21196 F11Fcsw_21196 +F11Fcsw_21505 F11Fcsw_21505 +F11Fcsw_21636 F11Fcsw_21636 +F11Fcsw_21645 F11Fcsw_21645 +F11Fcsw_21954 F11Fcsw_21954 +F11Fcsw_22687 F11Fcsw_22687 +F11Fcsw_22831 F11Fcsw_22831 +F11Fcsw_22880 F11Fcsw_22880 +F11Fcsw_22900 F11Fcsw_22900 +F11Fcsw_23043 F11Fcsw_23043 +F11Fcsw_23322 F11Fcsw_23322 +F11Fcsw_23608 F11Fcsw_23608 +F11Fcsw_23684 F11Fcsw_23684 +F11Fcsw_24087 F11Fcsw_24087 +F11Fcsw_24273 F11Fcsw_24273 +F11Fcsw_24701 F11Fcsw_24701,F11Fcsw_24794 +F11Fcsw_24967 F11Fcsw_24967 +F11Fcsw_25501 F11Fcsw_25501 +F11Fcsw_25574 F11Fcsw_25574 +F11Fcsw_26078 F11Fcsw_26078 +F11Fcsw_26175 F11Fcsw_26175 +F11Fcsw_26418 F11Fcsw_26418
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.unique.fasta Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,92 @@ +>F11Fcsw_12747 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGCAGCCTTGGTGAGCCGTTACCTCACCAACTAGCTAATCAGATATGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATCCCAGAGATGCCTCCAAAATACATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGG +>F11Fcsw_13125 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAATGTGGCCGTTCATCCTCTCAGACCGGCTACTGATCGTCGCCTTGGTAGGCCGTTACCCCACCAACTAGCTAATCAGACGCAGACCCATCGTAAAGCGATAGCTTACAAGTAGAGGCCATCTTTAGTCGAGCTTCCATGCGGAAGTTCGACAACATTCGGTATTAGCAGTCCTTTCGAACTGTTGTCCCCATCTTTACGG +>F11Fcsw_13572 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACCCATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATGGGACGCATCCCCATCCTTTACCAATTAATCTTTATTTGTCGCTCCCATGCGGAAAGACAAACACATCCGGTATTAAACTCCCTTTCAGGAGACTATCCCGGAGTAAAGGGCAGGTTGGATACGCGTTACTCACCCGTGCGCCGGTCGCCATCAAAA +>F11Fcsw_13584 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGATGTCTTGGTGGGCCGTTACCCCGCCAACAAACTAATGGAACGCATCCCCATCGGTTATCGAAATTCTTTAATAACAAGAAGATGCCTTCTCGTTATACTATCCGGTATTAATCTTTCTTTCGAAAGGCTATCCCGGAATAACCGGTAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCATCAACCTA +>F11Fcsw_13612 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGTCCGTGTCTCAGTACCAATGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTTGGTGGGCCGTTACCCCCCAACTAGCTAATGCGCCGCATGCCCATCCCTGTCCGGATTACTCCTTTGGCGCTCGCAGGATGCCCCGCAAACGCTTTATGCGATATTAGACCGGATTTCTCCGGATTATCCCTCTGACAGGGGCAGGTTGCATACGTGTTACTCACCCG +>F11Fcsw_13784 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACCGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCGGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGATCACTGTATCATGCGGTACTGTAATCTTATGCGGTATTAGCATCTGTTTCCAAATGTTATCCCCCTCTGAAAGGCAGGTTG +>F11Fcsw_14513 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTATCTCAGTTCCAATGTGGCCGATCACCCTCTCAGGTCGGCTAACCATCGTCGACTTGGTAGTCCGTTACACTACCAACTATCTAATGGTACGCGAGCCCATCCACATCCGATAAATCTTTTACCCCTGAGAGATGCCTCTCTGTGGTCTTATGCGGTATTAGCACACATTTCTATGTGTTATTCCCCAGATGTGGGCAGGTTG +>F11Fcsw_14920 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCATCCTCTCAGACCGGCTACTGATCGTCGCCTTGGTGAGCCATTACCTCTCCAACTAGCTAATCAGACGCGGGCCCATCCTATACCACCTGAGTTTTTCCTACCGTATCATGCGGTACTGTAGGCTTATGCGGTTTTAGCACAGATTTCTCTGTGTTATCCCCTGTATAGGGCAGGTTACCCACGCGTTT +>F11Fcsw_14954 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGGCCAACCTCTCAGTCCGGCTACCGATCGTCGACTTGGTGGGCCGTTACCCCGCCAACTATCTAATCGGACGCGAGGCCATCTTTCAGCGATAAATCTTTGGCATGTCCGGGATGCCCCGGTCATGCGTCATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTCCTCACGCGTTACT +>F11Fcsw_14980 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTTTCTCAGTTCCAATGTGGCCGTTCATCCTCTCAGATCGGCTACCCATCGTCGCCTTGGTGAGCCGTTACCTCTCCAACTAGCTAATGGGCCGCGAGCCCCTCCTATACCGCCTCAGCTTTTACCCCTCTCCGATGCCGGAGTGTGGTCTTATACCGTATTAGCACAAATTTCTCTGTGTTATCCCGTTGTATAGGATAGGTTGCTCACGTGTTACTCACCCG +>F11Fcsw_15042 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCGCCCTCTCAGGCCGGCTACTGATCGTCGGTTTGGTGGGCCGTTACCCCGCCAACTGCCTAATCAGACGCGGGCCCATCCCATACCACCGGAGTTTTTCACACTGAGCCATGCAGCTCTGTGCGCTTATGCGGTATTAGCAGCCGTTTCCAGCTGTTATCCCCCGGTATGGGGCAGGTCACCCACGCGTTACT +>F11Fcsw_15664 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCAGTACAAGGCAGGTTACCCACGCGTTACT +>F11Fcsw_17394 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTTGCCTTGGTAGGCCGTTACCCCGCCAACAAGCTAATCAGACGCGGGTCCATCTCACACCACCGGAGTTTTTCACACTGTACCATGCGGTACTGTGCGCTTATGCGGTATTATCAGCCGTTTCCAACTGCTATCCCCCTGTGTGAGGCAGGTTACCCACGCGTTA +>F11Fcsw_17898 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACTGTATCATGCGATACCGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTATCCCCCTGTATAAGGCAGGTTACCCACGCGTTACTCACCCG +>F11Fcsw_18564 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCGGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGATCACTGTATCATGCGGTACTGTAATCTTATGCGGTATTAGCATCTGTTTCCAAATGTTATCCCCCTCTGAAAGG +>F11Fcsw_19115 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTTGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCTCTTTCAGATGCCTTCTAGAGATATCATTGGGTATTAGTCTTACTTTGCAGGTTATCCCCAACGTGGTGGGCGAGGTTGGATACGCGTTACTCACCCGTCCCG +>F11Fcsw_19402 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCTGTGTCTCAGTCCCAATGTGGCCGATCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCAGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGATTGCCAAACGATGCCGTTCGGCAATGTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCACTGAAAGGTAGGTTG +>F11Fcsw_19500 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGAGGCCATCTTTCAGCGGATTGCTCCTTTGATCACTGTATCATGCGGTACTGTAATCTTATGCGGTATTAGCATCTGTTTCCAAATGTTATCCCCCTCTGAAAGGCAGGTTG +>F11Fcsw_20028 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTATGGGCCGTGTCTCAGTCCCATTGTGGCTGATCATCCTCTCAAACCAGCTACTGATCGTCGCCTTGGTAGTCCATTACACCACCAACAAGCTAATCAGGTGCAGGCTCATCCTAGAGCACCGGAGTTTTCAAGATTGGTATTTCAACCAAGCTCATATGGGGTATTAGCAGAAGTTTCCTTCTGTTGTCCCCCTCTCTAGGGCAGATTT +>F11Fcsw_20361 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGTCCGTGTCTCAGTACCAGTGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTTGCCTTGGTGAGCCGTTACCTCACCAACTAGCTAATACAACGCATGTCCATCTATAACCACCGGAGTTTTCAACCCGGAGAGATGCCTCTCCGAATATTATGGGGAATTAGTACCAATTTCTCAGTGTTATGCCCCTGTTATAGGTAGGTTACATACGCGTTACGCACCCGTGCGCCGG +>F11Fcsw_20429 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGTTGTCTTGGTGGGCCGTTACCCCGCCAACAAACTAATGGAACGCATCCCCATCGATAACCGAAATTCTTTAATAAAAATATCATGCGATATTCGTATGCTATCCGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTTATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCA +>F11Fcsw_20462 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTATGGGCCGTGTCTCAGTCCCATTGTGGCTGATCATCCTCTCAAACCAGCTACTGATCGTCGCCTTGGTAGTCCATTACACCACCAACAAGCTAATCAGGTGCAGGCTCATCCTAGAGCACCGGAGTTTTCAAGATTGGTATTTCAACCAAGCTCATATGGGGTATTAGCAGAAGTTTCCTTCTGTTGTCCCCCTCTCTAGGGCAGATTTT +>F11Fcsw_20686 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACGGAACCATGCGGTTCTGTGCGCTTATGCGGTATTAGCAGCCATTTCTGGCTGTTATCCCCCTCTGAAAGGCAGGTTGCTCACGCG +>F11Fcsw_21035 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTATCTCAGTTCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGGCTTGGTGAGCCGTTACCTCACCAACTACCTAATCAGACGCGAGTCCATCTGCAAGCGGTTTCCCTTTGGCATCATCTCCATGCGGAATCGATGCGTTATGCGGTATTAGCAACAGTTTCCCGTTGTTATCCCCCTCTCGCAGGCAGGTTACT +>F11Fcsw_21196 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACCGATCGTCGGCTTGGTGGGCTGTTATCTCACCAACTACCTAATCGGCCGCGAGCCCATCTCTCAGCGATAAAATCTTTGATAGTCTCCGGATGCCCGGAAACTATGTTATGCGGTATTAGCGTTCGTTTCCAAACGTTATTCCACTCTGAAAGGCAGGTTACTCACGTGTTACT +>F11Fcsw_21505 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACCCATCGTTGGCTTGGTGGGCCGTTACCCCTCCAACTACCTAATGGGACGCGAACCCCTCTCAAAGCGATAAATCTTTGACCCCTTCATCATGCGGTGTTGTGGTCTCATGCGGTATTAGCAACAGTTTCCCGTTGTTATCCCCCTCTTTGAGTCAGGTTATCCACGCGTTACTCACCCGTCCGCCACTCAGT +>F11Fcsw_21636 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCATCCTCTCAGACCGGCTACTGATCATCGCCTTGGTAGGCCGTTACCCCACCAACTAGCTAATCAGACGCAGGCCCATCCTCTAGCGATAGCTTATAAATAGAGGCCATCTTTCACAGCATCCTCATGCGAGATTGCTGTCACATTCGGTATTAGCACCCTTCGGA +>F11Fcsw_21645 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACAACCTAATGGAACGCATCCCCATCGATGACCGAAATTCTTTAATAGTTCTACCATGCGGAAGAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCG +>F11Fcsw_21954 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACCCATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATGGGACGCATCCCCATCCTTTACCAATTAATCTTTATTTGTCGCTCCCATGCGGAAAGACAAACACATCCGGTATTAAACTCCCTTTCAGGAGACTATCCCGGAGTAAAGGGCAGGTTGGATACGCGTTACTCACCCGTGCGCCGGTCGCCATCAAA +>F11Fcsw_22687 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTTGCCTTGGTGGGCCATTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCTCTTTCAGATGTCTTCTAGAGATATCATTGGGTATTAGTCTTACTTTGCAGGTTATCCCAACGTGGTGGGCGAGGTTGGATACGCGTTACTCACCCG +>F11Fcsw_22831 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGGCCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACT +>F11Fcsw_22880 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTATGGATCGTCGCCTTGGTGGGCCGTTACCCCACCAACTAGCTAATCCAACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACTGAGCCATGCAGCTCTGTGCGCTTATGCGGTATTAGCAGTCATTTCTGACTGTTATCCCCCTGTATAAGGCAGGTTACCCACGCG +>F11Fcsw_22900 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTTGGCTTGGTGGGCCGTTACCCCTCCAACTACCTAATGGGACGCGAACCCCTCTCAAAGCGATAAATCTTTGACCCCTTCATCATGCGGTGTTGTGGTCTCATGCGGTATTAGCAACAGTTTCCCGTTGTTATCCCCCTCTTTGAGTCAGGTTATTCACGCGTTACTCACCCG +>F11Fcsw_23043 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGGTCAACCTCTCAGTCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCAGTACAAGGCAGGTTACCCACGCGTTA +>F11Fcsw_23322 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCCGTTACCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCACCCGTGCGCCAA +>F11Fcsw_23608 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTAGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCTCTTTCAGATGTCTTCTAGAGATATCATTGGGTATTAGTCTTACTTTGCAAGGTTATCCCAAGTGATGGGCAGGTTGGATACGCGTTACTCACCCG +>F11Fcsw_23684 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCCCTTTCAGATGTCTTCTAGAGACGTCATTGGGTATTAGTCTTACTTTCGCAAGGTTATCCCAAGTGATGGGCAGGTTGGATACGCGTTACTCACCCGTGCG +>F11Fcsw_24087 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTATGGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACAAGCTAATCCAACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACTGAGCCATGCAGCTCTGTGCGCTTATGCGGTATTAGCAGCCATTTCTGACTGTTATCCCCCTGTATAAGGCAGGTTACCCACG +>F11Fcsw_24273 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTAGGCCGTTACCCCACCAACTATCTAATCAGACGCGAGCCCATCTATCAGCGGATTACTCCTTTCCCACTTTCATCATGTGATATTTATTGGCATATGCGGTATTAGCAATGATTTCTCACTGTTATTCCCCTCCTGATAGGCG +>F11Fcsw_24701 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCTGTTACCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCACCCGTGCG +>F11Fcsw_24967 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACT +>F11Fcsw_25501 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGGGCCGTTACCCCGCCAACTATCTAATCAGACGCGAGGCCATCTTTCAGCGATAAATCTTTGGCATTTCGACCATGCGATCAAAATGCGTCATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTCCTCACG +>F11Fcsw_25574 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAAATCTTTTACCTCAGAACCATGTGATCCCGTGGTCTTATGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCCTGTCTGGAAAAGGTTGCTCACGCGTTACTCACCCGTCCGCCGCTAAAACAG +>F11Fcsw_26078 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCTGTTATCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCA +>F11Fcsw_26175 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAAATCTTTTACCCCAGAACCATGTGATCCCGTGGTCTTATGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCCTGTCTGGGAAAGGTTGCTCACGCGTTACTCACCCGTCCGCCGCTAAAACAG +>F11Fcsw_26418 +AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACCAGCTAATCAGACGCGGGTCCATCCTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTGTACAGGGCAGGTTACCCACGCGTTACT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.vsearch.chimeras Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,47 @@ +Score Query ParentA ParentB IdQM IdQA IdQB IdAB IdQT LY LN LA RY RN RA Div YN +0.0000 F11Fcsw_13572;size=2; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_13612;size=2; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_13784;size=2; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_24701;size=2; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_12747;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0514 F11Fcsw_13125;size=1; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; F11Fcsw_13784;size=2; 80.5 77.1 80.1 72.7 80.1 21 20 19 8 0 6 0.4 N +0.1560 F11Fcsw_13584;size=1; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; 82.5 80.4 72.9 73.3 80.4 23 0 8 15 10 24 2.1 N +0.0259 F11Fcsw_14513;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 82.7 79.3 81.4 81.9 81.4 11 8 11 11 3 19 1.3 N +0.0550 F11Fcsw_14920;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_13784;size=2; 84.7 83.5 76.3 80.9 83.5 23 3 21 5 2 10 1.3 N +0.0000 F11Fcsw_14954;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0216 F11Fcsw_14980;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 82.0 79.1 80.8 82.4 80.8 7 4 6 12 5 28 1.3 N +0.0400 F11Fcsw_15042;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_13784;size=2; 84.6 82.9 79.1 79.9 82.9 21 8 18 5 1 9 1.7 N +0.0524 F11Fcsw_15664;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 84.6 83.8 71.7 72.9 83.8 41 10 25 3 1 1 0.8 N +0.0000 F11Fcsw_17394;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0428 F11Fcsw_17898;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 86.7 86.2 71.7 72.5 86.2 45 9 21 2 1 1 0.4 N +0.0000 F11Fcsw_18564;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_19115;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_19402;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_19500;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0158 F11Fcsw_20028;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 77.8 77.4 70.4 73.0 77.4 32 15 35 1 0 1 0.4 N +0.0161 F11Fcsw_20361;size=1; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; F11Fcsw_13784;size=2; 77.5 71.4 77.1 73.1 77.1 2 1 3 28 14 33 0.4 N +0.1919 F11Fcsw_20429;size=1; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; 84.6 82.1 75.4 73.3 82.1 22 0 5 16 10 22 2.5 N +0.0158 F11Fcsw_20462;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 77.8 77.4 70.4 73.0 77.4 32 15 35 1 0 1 0.4 N +0.0000 F11Fcsw_20686;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0422 F11Fcsw_21035;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_13784;size=2; 86.3 84.6 81.3 82.2 84.6 16 4 4 8 4 21 1.7 N +0.0000 F11Fcsw_21196;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.5878 F11Fcsw_21505;size=1; F11Fcsw_13572;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 92.4 76.7 88.2 72.1 88.2 11 0 0 48 7 13 4.2 Y +0.0000 F11Fcsw_21636;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_21645;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_21954;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_22687;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_22831;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0322 F11Fcsw_22880;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 83.3 82.9 70.8 72.5 82.9 41 11 27 2 1 1 0.4 N +0.0000 F11Fcsw_22900;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_23043;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.5123 F11Fcsw_23322;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 99.2 83.0 97.9 81.7 97.9 3 0 1 40 1 0 1.2 Y +0.0000 F11Fcsw_23608;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_23684;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0324 F11Fcsw_24087;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 83.8 83.3 71.2 72.5 83.3 41 11 26 2 1 1 0.4 N +0.0000 F11Fcsw_24273;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_24967;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_25501;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0461 F11Fcsw_25574;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 84.9 80.8 82.0 82.4 82.0 12 5 3 14 4 24 2.9 N +0.0000 F11Fcsw_26078;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0509 F11Fcsw_26175;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 85.8 81.2 82.8 82.4 82.8 12 5 3 15 4 22 2.9 N +0.0696 F11Fcsw_26418;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 83.3 82.1 72.5 72.9 82.1 38 12 27 3 0 1 1.2 N
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.design Wed Feb 14 09:44:01 2018 -0500 @@ -0,0 +1,9 @@ +F003D000 A +F003D002 B +F003D006 B +F003D008 A +F003D142 A +F003D144 A +F003D146 B +F003D148 B +F003D150 A
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#fff; + background-color: #428bca; +} + + +/* + * Main content + */ + +.main { + padding: 20px; +} +@media (min-width: 768px) { + .main { + padding-right: 40px; + padding-left: 40px; + } +} +.main .page-header { + margin-top: 0; +} + + +/* + * Placeholder dashboard ideas + */ + +.placeholders { + margin-bottom: 30px; + text-align: center; +} +.placeholders h4 { + margin-bottom: 0; +} +.placeholder { + margin-bottom: 20px; +} +.placeholder img { + display: inline-block; + border-radius: 50%; +} + +.text-success-custom{ + color: rgba(6, 108, 8, 1); +} +.text-danger-custom{ + font-weight: bold; + color: rgba(213, 24, 20, 1); +} +.panel-danger-custom .panel-title{ + font-weight: bold; + color: rgba(213, 24, 20, 1); +}t status + +.panel-success-custom .panel-title{ + color: rgba(6, 108, 8, 1); +}t status +</style> + + <!-- HTML5 shim and Respond.js for IE8 support of HTML5 elements and media queries --> + <!-- WARNING: Respond.js doesn't work if you view the page via file:// --> + <!--[if lt IE 9]> + <script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script> + <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> + <![endif]--> + + </head> + <body> + + <nav class="navbar navbar-inverse navbar-fixed-top" role="navigation"> + <div class="container-fluid"> + <div class="navbar-header"> + + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false" aria-controls="navbar"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="#">Tool Test Results (powered by Planemo)</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav navbar-right"> + <li><a href="https://galaxyproject.org">Galaxy</a></li> + <li><a href="https://planemo.readthedocs.org">Planemo</a></li> + </ul> + <div class="navbar-form 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[ split.slice(0, -maxsplit).join(sep) ].concat(split.slice(-maxsplit)) : split; +} + + +// http://stackoverflow.com/questions/19491336/get-url-parameter-jquery +function getUrlParameter(sParam) +{ + var sPageURL = window.location.search.substring(1); + var sURLVariables = sPageURL.split('&'); + for (var i = 0; i < sURLVariables.length; i++) + { + var sParameterName = sURLVariables[i].split('='); + if (sParameterName[0] == sParam) + { + return sParameterName[1]; + } + } +} +</script> + <script> + var testDataUrl = getUrlParameter("test_data_url"); + if(testDataUrl) { + $.ajax( + {'url': testDataUrl, + 'type': 'GET', + } + ) + .success(function(content) { renderTestResults( $.parseJSON(content) ); }) + .failure(function() { alert("Failed to load test data.")} ); + } else { + 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__": {"src": 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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": 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Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor 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: \notu.jclass.unique.lt.dist\notu.thetayc.unique.lt.dist\notu.jclass.0.01.lt.dist\notu.thetayc.0.01.lt.dist\notu.jclass.0.02.lt.dist\notu.thetayc.0.02.lt.dist\notu.jclass.0.03.lt.dist\notu.thetayc.0.03.lt.dist\notu.jclass.0.04.lt.dist\notu.thetayc.0.04.lt.dist\notu.jclass.0.05.lt.dist\notu.thetayc.0.05.lt.dist\notu.jclass.0.06.lt.dist\notu.thetayc.0.06.lt.dist\notu.jclass.0.07.lt.dist\notu.thetayc.0.07.lt.dist\notu.jclass.0.08.lt.dist\notu.thetayc.0.08.lt.dist\notu.jclass.0.09.lt.dist\notu.thetayc.0.09.lt.dist\notu.jclass.0.10.lt.dist\notu.thetayc.0.10.lt.dist\notu.jclass.0.11.lt.dist\notu.thetayc.0.11.lt.dist\notu.jclass.0.12.lt.dist\notu.thetayc.0.12.lt.dist\notu.jclass.0.13.lt.dist\notu.thetayc.0.13.lt.dist\notu.jclass.0.14.lt.dist\notu.thetayc.0.14.lt.dist\notu.jclass.0.15.lt.dist\notu.thetayc.0.15.lt.dist\notu.jclass.0.16.lt.dist\notu.thetayc.0.16.lt.dist\notu.jclass.0.17.lt.dist\notu.thetayc.0.17.lt.dist\notu.jclass.0.18.lt.dist\notu.thetayc.0.18.lt.dist\notu.jclass.0.19.lt.dist\notu.thetayc.0.19.lt.dist\notu.jclass.0.20.lt.dist\notu.thetayc.0.20.lt.dist\notu.jclass.0.21.lt.dist\notu.thetayc.0.21.lt.dist\notu.jclass.0.22.lt.dist\notu.thetayc.0.22.lt.dist\notu.jclass.0.23.lt.dist\notu.thetayc.0.23.lt.dist\notu.jclass.0.24.lt.dist\notu.thetayc.0.24.lt.dist\notu.jclass.0.25.lt.dist\notu.thetayc.0.25.lt.dist\notu.jclass.0.26.lt.dist\notu.thetayc.0.26.lt.dist\notu.jclass.0.27.lt.dist\notu.thetayc.0.27.lt.dist\notu.jclass.0.29.lt.dist\notu.thetayc.0.29.lt.dist\notu.jclass.0.32.lt.dist\notu.thetayc.0.32.lt.dist\notu.jclass.0.33.lt.dist\notu.thetayc.0.33.lt.dist\notu.jclass.0.36.lt.dist\notu.thetayc.0.36.lt.dist\notu.jclass.0.38.lt.dist\notu.thetayc.0.38.lt.dist\notu.jclass.0.41.lt.dist\notu.thetayc.0.41.lt.dist\notu.jclass.0.45.lt.dist\notu.thetayc.0.45.lt.dist\notu.jclass.0.55.lt.dist\notu.thetayc.0.55.lt.dist\n\n\nmothur > 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", "tool_id": "mothur_dist_shared", "outputs": {"__new_primary_file_whittaker.0.22.lt|structchi2.0.05.lt__": {"src": "hda", "id": "262bf9b3975abb37", "uuid": "fa686ffc-7e74-489c-9ddc-fef0951ef56b"}, "__new_primary_file_whittaker.0.22.lt|hamming.0.22.lt__": {"src": "hda", "id": "86691025752e063e", "uuid": "7ebee5d3-336c-45ac-a066-db1a5d42091f"}, "__new_primary_file_whittaker.0.22.lt|hamming.0.05.lt__": {"src": "hda", "id": "e1d20895c4a97cda", "uuid": "4503ea8a-a9ae-4b19-88e5-19b6b5da79a5"}, "__new_primary_file_whittaker.0.22.lt|anderberg.0.05.lt__": {"src": "hda", "id": "e1e5b8e8ee3824ac", "uuid": "237bf93f-55ac-45ae-98f7-48b93cae2306"}, "__new_primary_file_whittaker.0.22.lt|anderberg.0.22.lt__": {"src": "hda", "id": "e0b8f8f721986493", "uuid": "6f204ed0-aedc-433d-8303-405c4c4e3ff0"}, "__new_primary_file_whittaker.0.22.lt|kulczynski.0.22.lt__": {"src": "hda", "id": "211e907a60c908e9", "uuid": "dd64cb3b-db72-4b37-ac2f-386c6720aa8d"}, "__new_primary_file_whittaker.0.22.lt|ochiai.0.05.lt__": 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"__new_primary_file_whittaker.0.22.lt|kstest.0.22.lt__": {"src": "hda", "id": "25291f5c38a3933e", "uuid": "c4bbdf16-7eb5-423d-9c7e-19adcd5fb7cf"}, "__new_primary_file_whittaker.0.22.lt|ochiai.0.22.lt__": {"src": "hda", "id": "5e88180b10a9ebfa", "uuid": "26004881-94f6-486b-8741-3a6ce83cb184"}, "__new_primary_file_whittaker.0.22.lt|thetan.0.05.lt__": {"src": "hda", "id": "f625822a9112fb52", "uuid": "446db58e-70e6-42fd-a8d5-0e12dabc15ea"}, "__new_primary_file_whittaker.0.22.lt|memchord.0.22.lt__": {"src": "hda", "id": "97b9d06753322a7d", "uuid": "fa38519c-c58e-49ef-ba70-ac3455b20106"}, "__new_primary_file_whittaker.0.22.lt|structchi2.0.22.lt__": {"src": "hda", "id": "8ef1d4aff90ec17a", "uuid": "e604291f-3802-4038-95f1-5df643dbb2d8"}, "__new_primary_file_whittaker.0.22.lt|jclass.0.22.lt__": {"src": "hda", "id": "d4c7c64f8097c7e3", "uuid": "6875af93-528f-4296-b440-eb1cef990173"}, "__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"}, 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"__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__": 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"__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", 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"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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"\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor 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": 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{"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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"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": {"input|subsampling|use": 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"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", "speciesprofile", 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{"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": 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"__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": 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"__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}}; + renderTestResults(test_data); + } + </script> + </body> +</html> \ No newline at end of file