| Previous changeset 2:53b704cc17ad (2017-09-05) Next changeset 4:0897308ec0e5 (2018-02-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4 |
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modified:
chimera.pintail.xml macros.xml |
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added:
test-data/Fasting_Example1.scrap.sff test-data/Mock_S280_L001_R1_001_small.trim.contigs.accnos test-data/Mock_S280_L001_R1_001_small.trim.contigs.groups test-data/Mock_S280_L001_R1_001_small.trim.contigs.names test-data/Mock_S280_L001_R1_001_small.trim.contigs.unique.fasta test-data/Mock_S280_L001_R1_001_small.trim.contigs.unique.groups test-data/amazon.an.0.03.pearson.otu.corr test-data/amazon.otus.accnos test-data/esophagus.design test-data/esophagus.fn.shared test-data/mothur.1518613794.logfile test-data/mothur.1518613825.logfile test-data/mothur.1518613872.logfile test-data/mothur.1518613887.logfile test-data/mothur.1518613903.logfile test-data/mothur.1518613913.logfile test-data/mothur.1518613936.logfile test-data/mothur.1518613968.logfile test-data/mothur.1518614517.logfile test-data/samplebiom.biom1 test-data/stool.design test-data/stool.final.opti_mcc.shared test-data/stool_small.count_table test-data/stool_small.denovo.vsearch.accnos test-data/stool_small.names test-data/stool_small.unique.fasta test-data/stool_small.vsearch.chimeras test-data/test.design tool_test_output_all.html |
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| diff -r 53b704cc17ad -r 66310f4979aa chimera.pintail.xml --- a/chimera.pintail.xml Tue Sep 05 16:10:47 2017 -0400 +++ b/chimera.pintail.xml Wed Feb 14 09:43:03 2018 -0500 |
| [ |
| b'@@ -7,83 +7,89 @@\n <expand macro="stdio"/>\n <expand macro="version_command"/>\n <command><![CDATA[\n- @SHELL_OPTIONS@\n+@SHELL_OPTIONS@\n \n- ## create symlinks to input datasets\n- ln -s "$fasta" fasta.dat &&\n- ln -s "$alignment.template" alignment.template.dat &&\n- ln -s "$conservation" conservation.dat &&\n- ln -s "$quantile" quantile.dat &&\n- #if $mask.source2 == "history":\n- ln -s "$mask.input" mask.input.dat &&\n- #end if\n+## create symlinks to input datasets\n+ln -s \'$fasta\' fasta.dat &&\n+ln -s \'$alignment.reference\' alignment.reference.dat &&\n+ln -s \'$conservation\' conservation.dat &&\n+ln -s \'$quantile\' quantile.dat &&\n+#if $mask_cond.source2 == "history":\n+ ln -s \'$mask_cond.mask\' mask.dat &&\n+#end if\n \n- echo \'chimera.pintail(\n- fasta=fasta.dat,\n- reference=alignment.template.dat,\n- filter=$filter,\n- #if $mask.source2 == "default":\n- mask=default,\n- #elif $mask.source2 == "history":\n- mask=mask.input.dat,\n- #end if\n- #if $conservation:\n- conservation=conservation.dat,\n- #end if\n- #if $quantile:\n- quantile=quantile.dat,\n- #end if\n- #if int($window) > 0:\n- window=$window,\n- #end if\n- #if int($increment) > 0:\n- increment=$increment,\n- #end if\n- processors=\'\\${GALAXY_SLOTS:-8}\'\n- )\'\n- | sed \'s/ //g\' ## mothur trips over whitespace\n- | mothur\n- | tee mothur.out.log\n+echo \'chimera.pintail(\n+ fasta=fasta.dat,\n+ reference=alignment.reference.dat,\n+ filter=$filter,\n+ #if $mask_cond.source2 == "default":\n+ mask=default,\n+ #elif $mask_cond.source2 == "history":\n+ mask=mask.dat,\n+ #end if\n+ #if $conservation:\n+ conservation=conservation.dat,\n+ #end if\n+ #if $quantile:\n+ quantile=quantile.dat,\n+ #end if\n+ #if int($window) > 0:\n+ window=$window,\n+ #end if\n+ #if int($increment) > 0:\n+ increment=$increment,\n+ #end if\n+ processors=\'\\${GALAXY_SLOTS:-8}\'\n+)\'\n+| sed \'s/ //g\' ## mothur trips over whitespace\n+| mothur\n+| tee mothur.out.log\n ]]></command>\n <inputs>\n- <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>\n+ <param argument="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>\n <conditional name="alignment">\n- <param name="source" type="select" label="Select Reference Template from" help="">\n+ <param name="source" type="select" label="Select Reference Template from">\n <option value="hist">History</option>\n <option value="ref">Cached Reference</option>\n </param>\n <when value="ref">\n- <param name="template" type="select" label="reference - Select an alignment database" help="">\n+ <param argument="reference" type="select" label="reference - Select an alignment database">\n <options from_data_table="mothur_aligndb"/>\n </param>\n </when>\n <when value="hist">\n- <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>\n+ <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/>\n </when>\n </conditional>\n- <param name="filter" type="boolean" falsevalue="false" truevalue="true" checked="false" label="filter - Apply a 50% soft vertical filter"/>\n- <conditional name="mask">\n+ <param argument="filter" type="boolean" falsevalue="false" truevalue="true" checked="false" label="filter - Apply a 50% soft vertical filter"/>\n+ <conditional name="mask_cond">\n <param name="source2" type="'..b'r parameter makes the quantile file\n+ generated specific to the query set you are analyzing."/>\n+ <param argument="window" type="integer" value="300" label="window - Length of sequence you want in each window analyzed (uses default if < 1)"\n+ help="Default is set to 300. Note, changing the window size will require new quantile files to be made."/>\n+ <param argument="increment" type="integer" value="25" label="increment - Increment for window slide on each iteration (uses default if < 1)"\n+ help="Default is 25. Note, changing the increment will require new quantile files to be made."/>\n </inputs>\n <outputs>\n <expand macro="logfile-output"/>\n- <data name="out_file" format="txt" from_work_dir="fasta.*pintail.chimeras" label="${tool.name} on ${on_string}: pintail.chimeras"/>\n+ <data name="pintail.chimeras" format="txt" from_work_dir="fasta.*pintail.chimeras" label="${tool.name} on ${on_string}: pintail.chimeras"/>\n <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*pintail.accnos" label="${tool.name} on ${on_string}: pintail.accnos"/>\n- <data name="out_freq" format="mothur.freq" from_work_dir="alignment.template.freq" label="${tool.name} on ${on_string}: pintail.freq">\n+ <data name="out_freq" format="mothur.freq" from_work_dir="alignment.reference.freq" label="${tool.name} on ${on_string}: pintail.freq">\n <filter>conservation == None</filter>\n </data>\n <data name="out_quantile" format="mothur.quan" from_work_dir="*.quan" label="${tool.name} on ${on_string}: pintail.quan">\n@@ -94,32 +100,31 @@\n <test>\n <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>\n <param name="source" value="hist"/>\n- <param name="template" value="HMP_MOCK.v35.align"/>\n+ <param name="reference" value="HMP_MOCK.v35.align"/>\n <param name="quantile" value="HMP_MOCK.v35.pintail.quan"/>\n <param name="window" value="200"/>\n- <output name="out_file" md5="644fe23ee459a76de7b225e530361865" ftype="txt"/>\n+ <output name="pintail.chimeras" md5="644fe23ee459a76de7b225e530361865" ftype="txt"/>\n <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.pintail.accnos" ftype="mothur.accnos"/>\n <expand macro="logfile-test"/>\n </test>\n <test>\n <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>\n <param name="source" value="hist"/>\n- <param name="template" value="HMP_MOCK.v35.align"/>\n+ <param name="reference" value="HMP_MOCK.v35.align"/>\n <param name="source2" value="default"/>\n <param name="window" value="200"/>\n- <output name="out_file" ftype="txt">\n+ <output name="pintail.chimeras" ftype="txt">\n <assert_contents>\n <has_text text="Observed"/>\n <has_text text="Expected"/>\n </assert_contents>\n </output>\n- <output name="out_quantile" md5="23a665c9bace6b73efaae1ecf6d88c59" ftype="mothur.quan"/>\n- <output name="out_freq" md5="0381c5adade485cc4341a0ef5674f4d8" ftype="mothur.freq"/>\n+ <output name="out_quantile" md5="74372024214704010aed4f9c8258f77b" ftype="mothur.quan"/>\n+ <output name="out_freq" md5="2d2c4066c5de06c8d1d78ee3784daa3d" ftype="mothur.freq"/>\n <expand macro="logfile-test"/>\n </test>\n </tests>\n- <help>\n-<![CDATA[\n+ <help><![CDATA[\n \n @MOTHUR_OVERVIEW@\n \n@@ -143,8 +148,7 @@\n .. _paper: http://www.ncbi.nlm.nih.gov/pubmed/16332745\n .. _chimera.pintail: https://www.mothur.org/wiki/Chimera.pintail\n \n-]]>\n- </help>\n+ ]]></help>\n <expand macro="citations">\n <citation type="doi">10.1128/AEM.71.12.7724-7736.2005</citation>\n </expand>\n' |
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| diff -r 53b704cc17ad -r 66310f4979aa macros.xml --- a/macros.xml Tue Sep 05 16:10:47 2017 -0400 +++ b/macros.xml Wed Feb 14 09:43:03 2018 -0500 |
| [ |
| b'@@ -1,11 +1,13 @@\n <macros>\n+ <token name="@WRAPPER_VERSION@">1.39.5</token>\n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="1.36.1">mothur</requirement>\n+ <requirement type="package" version="@WRAPPER_VERSION@">mothur</requirement>\n+ <yield/>\n </requirements>\n </xml>\n <xml name="version_command">\n- <version_command>mothur "#help()" | sed \'7q;d\' | cut -d" " -f2 </version_command>\n+ <version_command><![CDATA[ mothur "#help()" | sed \'7q;d\' | cut -d" " -f2 ]]></version_command>\n </xml>\n <xml name="stdio">\n <stdio>\n@@ -13,20 +15,10 @@\n <exit_code range="1:" level="fatal"/>\n </stdio>\n </xml>\n- <token name="@WRAPPER_VERSION@">1.36.1</token>\n <token name="@SHELL_OPTIONS@">set -o pipefail;</token>\n- <token name="@MOTHUR_OVERVIEW@">\n-<![CDATA[\n-\n-**Mothur Overview**\n \n-Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team\n-in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.\n \n-.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page\n-\n-]]>\n- </token>\n+ <!-- Input parameters -->\n <xml name="labeloptions">\n <options>\n <filter type="data_meta" ref="otu" key="labels"/>\n@@ -78,9 +70,65 @@\n <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>\n <yield/>\n </xml>\n+\n+ <!-- CLUSTERING -->\n+ <xml name="param-clustermethods">\n+ <param argument="method" type="select" label="Clustering Method">\n+ <option value="opti" selected="true">Opticlust method</option>\n+ <option value="furthest">Furthest neighbor</option>\n+ <option value="nearest">Nearest neighbor</option>\n+ <option value="average">Average neighbor</option>\n+ <yield/>\n+ </param>\n+ </xml>\n+ <xml name="option-vsearch-clustermethods">\n+ <option value="agc">Abundance-based greedy clustering (agc)(VSEARCH)</option>\n+ <option value="dgc">Distance-based greedy clustering (dgc)(VSEARCH)</option>\n+ </xml>\n+ <xml name="params-opticlust">\n+ <param argument="metric" type="select" label="metric - select the metric in the opticluster method"\n+ help="Options are Matthews correlation coefficient (mcc), sensitivity (sens), specificity (spec), true positives + true negatives (tptn),\n+ false positives + false negatives (fpfn), true positives (tp), true negative (tn), false positive (fp), false negative (fn), f1score (f1score),\n+ accuracy (accuracy), positive predictive value (ppv), negative predictive value (npv), false discovery rate (fdr). Default=mcc.">\n+ <option value="mcc" selected="true">Matthews correlation coefficient (mcc)</option>\n+ <option value="sens">Sensitivity</option>\n+ <option value="spec">specificity</option>\n+ <option value="tptn">true positives + true negatives</option>\n+ <option value="fpfn">false positives + false negatives</option>\n+ <option value="tp">true positives</option>\n+ <option value="tn">true negative</option>\n+ <option value="fp">false positive</option>\n+ <option value="fn">false negative</option>\n+ <option value="f1score">f1score</option>\n+ <option value="accuracy">accuracy</option>\n+ <option value="ppv">positive predictive value</option>\n+ <option value="npv">negative predictive value</option>\n+ <option value="fdr">false discovery rate</option>\n+ </param>\n+ <param argument="initialize" type="select" label="Initial randomization"\n+ help="singleton: each sequence is randomly assigned to its own OTU; oneotu: all sequences are assigned to one'..b'ng expression="^name\\tpound\\tdash\\tplus\\tequal\\tloop\\ttilde\\ttotal\\tnumseqs$"/>\n+ </xml>\n+ <xml name="test-alignreport-format">\n+ <has_line_matching expression="^QueryName\\tQueryLength\\tTemplateName\\tTemplateLength\\tSearchMethod\\tSearchScore\\tAlignmentMethod\\tQueryStart\\tQueryEnd\\tTemplateStart\\tTemplateEnd\\tPairwiseAlignmentLength\\tGapsInQuery\\tGapsInTemplate\\tLongestInsert\\tSimBtwnQuery&Template$"/>\n+ </xml>\n+ <xml name="test-axes-format">\n+ <has_line_matching expression="^group(\\taxis\\d+)+$"/>\n+ </xml>\n+ <xml name="test-chimera-format">\n+ <has_line_matching expression="Score\\tQuery\\tParentA\\tParentB\\tIdQM\\tIdQA\\tIdQB\\tIdAB\\tIdQT\\tLY\\tLN\\tLA\\tRY\\tRN\\tRA\\tDiv\\tYN"/>\n+ </xml>\n+ <xml name="test-column-format">\n+ <has_n_columns n="3"/>\n+ <has_line_matching expression="^[\\w\\d\\-]+\\t[\\w\\d\\-]+\\t[\\d\\.]+$"/>\n+ </xml>\n+ <xml name="test-contigsreport-format">\n+ <has_n_columns n="7"/>\n+ <has_line_matching expression="^Name\\tLength\\tOverlap_Length\\tOverlap_Start\\tOverlap_End\\tMisMatches\\tNum_Ns$"/>\n+ </xml>\n+ <xml name="test-count-format">\n+ <has_line_matching expression="^Representative_Sequence\\ttotal(\\t\\w+)*$"/>\n+ <has_line_matching expression="^\\w+(\\t\\d+)+(\\s)*$"/>\n+ </xml>\n+ <xml name="test-dist-format">\n+ <has_line_matching expression="^[ \\t]*\\d+$"/>\n+ <has_line_matching expression="^[\\w\\d\\-]+(\\t[\\d\\.]+)+\\s?$"/>\n+ </xml>\n+ <xml name="test-fasta-format">\n+ <has_line_matching expression="^>.+$"/>\n+ <has_line_matching expression="^[ACTGN-]+$"/>\n+ </xml>\n+ <xml name="test-fastq-format">\n+ <has_line_matching expression="^@.+$"/>\n+ <has_line_matching expression="^[ACTGN]+$"/>\n+ <has_line_matching expression="^\\+$"/>\n+ </xml>\n+ <xml name="test-group-format">\n+ <has_line_matching expression="^Representative_Sequence\\ttotal(\\t[\\w\\d\\-]+)+$"/>\n+ <has_line_matching expression="^[\\w\\d\\-]+(\\t\\d+)+$"/>\n+ </xml>\n+ <xml name="test-list-format">\n+ <has_line_matching expression="^label\\tnumOtus(\\tOtu\\d+)+$"/>\n+ <has_line_matching expression="^(unique|0\\.\\d+)\\t\\d+(\\t[\\w\\d\\-,]+)+$"/>\n+ </xml>\n+ <xml name="test-names-format">\n+ <has_line_matching expression="^[a-zA-Z0-9]+\\t[a-zA-Z0-9]+$"/>\n+ </xml>\n+ <xml name="test-qfile-format">\n+ <has_line_matching expression="^(\\d+ )+$"/>\n+ <has_line_matching expression="^>.+$"/>\n+ </xml>\n+ <xml name="test-rabund-format">\n+ <has_line_matching expression="^(unique|0\\.\\d+)(\\t\\d+\\.?\\d*)+$"/>\n+ </xml>\n+ <xml name="test-sabund-format">\n+ <has_line_matching expression="^(unique|0\\.\\d+)(\\t\\d+)+$"/>\n+ </xml>\n+ <xml name="test-sensspec-format">\n+ <has_n_columns n="14"/>\n+ <has_line_matching expression="^label\\tcutoff\\ttp\\ttn\\tfp\\tfn\\tsensitivity\\tspecificity\\tppv\\tnpv\\tfdr\\taccuracy\\t\\w+\\tf1score$"/>\n+ </xml>\n+ <xml name="test-shared-format">\n+ <has_line_matching expression="^label\\tGroup\\tnumOtus(\\t(Otu|rareOTUs|.*OTU.*)\\d+)+$"/>\n+ </xml>\n+ <xml name="test-taxonomy-format">\n+ <has_n_columns n="3"/>\n+ <has_line_matching expression="^OTU\\tSize\\tTaxonomy$"/>\n+ </xml>\n+ <xml name="test-taxsummary-format">\n+ <has_line_matching expression="^((taxlevel\\trankID\\ttaxon\\tdaughterlevels\\ttotal(\\t[\\w\\d\\-]+)*)|(taxonomy\\ttotal(\\t[\\w\\d]+)*))$"/>\n+ </xml>\n+ <!-- backmatter -->\n+ <token name="@MOTHUR_OVERVIEW@">\n+<![CDATA[\n+\n+**Mothur Overview**\n+\n+Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team\n+in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.\n+\n+.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page\n+\n+]]>\n+ </token>\n <xml name="citations">\n <citations>\n <citation type="doi">10.1128/AEM.01541-09</citation>\n' |
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| diff -r 53b704cc17ad -r 66310f4979aa test-data/Fasting_Example1.scrap.sff |
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| Binary file test-data/Fasting_Example1.scrap.sff has changed |
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| diff -r 53b704cc17ad -r 66310f4979aa test-data/Mock_S280_L001_R1_001_small.trim.contigs.accnos --- /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 09:43:03 2018 -0500 |
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| @@ -0,0 +1,1 @@ +00967_43_000000000-A3JHG_1_1101_19936_3208 |
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| diff -r 53b704cc17ad -r 66310f4979aa test-data/Mock_S280_L001_R1_001_small.trim.contigs.groups --- /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 09:43:03 2018 -0500 |
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| @@ -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 |
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| diff -r 53b704cc17ad -r 66310f4979aa test-data/Mock_S280_L001_R1_001_small.trim.contigs.names --- /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 09:43:03 2018 -0500 |
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| @@ -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 |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/Mock_S280_L001_R1_001_small.trim.contigs.unique.fasta --- /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 09:43:03 2018 -0500 |
| b |
| @@ -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 |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/Mock_S280_L001_R1_001_small.trim.contigs.unique.groups --- /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 09:43:03 2018 -0500 |
| b |
| @@ -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 |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/amazon.an.0.03.pearson.otu.corr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.an.0.03.pearson.otu.corr Wed Feb 14 09:43:03 2018 -0500 |
| b |
| b'@@ -0,0 +1,3829 @@\n+OTUA\tOTUB\tpearsonCoef\tSignificance\n+Otu02\tOtu01\t-1.000000\t0.000000\n+Otu03\tOtu01\t1.000000\t0.000000\n+Otu03\tOtu02\t-1.000000\t0.000000\n+Otu04\tOtu01\t-1.000000\t0.000000\n+Otu04\tOtu02\t1.000000\t0.000000\n+Otu04\tOtu03\t-1.000000\t0.000000\n+Otu05\tOtu01\t-nan\t0.000000\n+Otu05\tOtu02\t-nan\t0.000000\n+Otu05\tOtu03\t-nan\t0.000000\n+Otu05\tOtu04\t-nan\t0.000000\n+Otu06\tOtu01\t1.000000\t0.000000\n+Otu06\tOtu02\t-1.000000\t0.000000\n+Otu06\tOtu03\t1.000000\t0.000000\n+Otu06\tOtu04\t-1.000000\t0.000000\n+Otu06\tOtu05\t-nan\t0.000000\n+Otu07\tOtu01\t1.000000\t0.000000\n+Otu07\tOtu02\t-1.000000\t0.000000\n+Otu07\tOtu03\t1.000000\t0.000000\n+Otu07\tOtu04\t-1.000000\t0.000000\n+Otu07\tOtu05\t-nan\t0.000000\n+Otu07\tOtu06\t1.000000\t0.000000\n+Otu08\tOtu01\t1.000000\t0.000000\n+Otu08\tOtu02\t-1.000000\t0.000000\n+Otu08\tOtu03\t1.000000\t0.000000\n+Otu08\tOtu04\t-1.000000\t0.000000\n+Otu08\tOtu05\t-nan\t0.000000\n+Otu08\tOtu06\t1.000000\t0.000000\n+Otu08\tOtu07\t1.000000\t0.000000\n+Otu09\tOtu01\t1.000000\t0.000000\n+Otu09\tOtu02\t-1.000000\t0.000000\n+Otu09\tOtu03\t1.000000\t0.000000\n+Otu09\tOtu04\t-1.000000\t0.000000\n+Otu09\tOtu05\t-nan\t0.000000\n+Otu09\tOtu06\t1.000000\t0.000000\n+Otu09\tOtu07\t1.000000\t0.000000\n+Otu09\tOtu08\t1.000000\t0.000000\n+Otu10\tOtu01\t1.000000\t0.000000\n+Otu10\tOtu02\t-1.000000\t0.000000\n+Otu10\tOtu03\t1.000000\t0.000000\n+Otu10\tOtu04\t-1.000000\t0.000000\n+Otu10\tOtu05\t-nan\t0.000000\n+Otu10\tOtu06\t1.000000\t0.000000\n+Otu10\tOtu07\t1.000000\t0.000000\n+Otu10\tOtu08\t1.000000\t0.000000\n+Otu10\tOtu09\t1.000000\t0.000000\n+Otu11\tOtu01\t1.000000\t0.000000\n+Otu11\tOtu02\t-1.000000\t0.000000\n+Otu11\tOtu03\t1.000000\t0.000000\n+Otu11\tOtu04\t-1.000000\t0.000000\n+Otu11\tOtu05\t-nan\t0.000000\n+Otu11\tOtu06\t1.000000\t0.000000\n+Otu11\tOtu07\t1.000000\t0.000000\n+Otu11\tOtu08\t1.000000\t0.000000\n+Otu11\tOtu09\t1.000000\t0.000000\n+Otu11\tOtu10\t1.000000\t0.000000\n+Otu12\tOtu01\t1.000000\t0.000000\n+Otu12\tOtu02\t-1.000000\t0.000000\n+Otu12\tOtu03\t1.000000\t0.000000\n+Otu12\tOtu04\t-1.000000\t0.000000\n+Otu12\tOtu05\t-nan\t0.000000\n+Otu12\tOtu06\t1.000000\t0.000000\n+Otu12\tOtu07\t1.000000\t0.000000\n+Otu12\tOtu08\t1.000000\t0.000000\n+Otu12\tOtu09\t1.000000\t0.000000\n+Otu12\tOtu10\t1.000000\t0.000000\n+Otu12\tOtu11\t1.000000\t0.000000\n+Otu13\tOtu01\t1.000000\t0.000000\n+Otu13\tOtu02\t-1.000000\t0.000000\n+Otu13\tOtu03\t1.000000\t0.000000\n+Otu13\tOtu04\t-1.000000\t0.000000\n+Otu13\tOtu05\t-nan\t0.000000\n+Otu13\tOtu06\t1.000000\t0.000000\n+Otu13\tOtu07\t1.000000\t0.000000\n+Otu13\tOtu08\t1.000000\t0.000000\n+Otu13\tOtu09\t1.000000\t0.000000\n+Otu13\tOtu10\t1.000000\t0.000000\n+Otu13\tOtu11\t1.000000\t0.000000\n+Otu13\tOtu12\t1.000000\t0.000000\n+Otu14\tOtu01\t1.000000\t0.000000\n+Otu14\tOtu02\t-1.000000\t0.000000\n+Otu14\tOtu03\t1.000000\t0.000000\n+Otu14\tOtu04\t-1.000000\t0.000000\n+Otu14\tOtu05\t-nan\t0.000000\n+Otu14\tOtu06\t1.000000\t0.000000\n+Otu14\tOtu07\t1.000000\t0.000000\n+Otu14\tOtu08\t1.000000\t0.000000\n+Otu14\tOtu09\t1.000000\t0.000000\n+Otu14\tOtu10\t1.000000\t0.000000\n+Otu14\tOtu11\t1.000000\t0.000000\n+Otu14\tOtu12\t1.000000\t0.000000\n+Otu14\tOtu13\t1.000000\t0.000000\n+Otu15\tOtu01\t1.000000\t0.000000\n+Otu15\tOtu02\t-1.000000\t0.000000\n+Otu15\tOtu03\t1.000000\t0.000000\n+Otu15\tOtu04\t-1.000000\t0.000000\n+Otu15\tOtu05\t-nan\t0.000000\n+Otu15\tOtu06\t1.000000\t0.000000\n+Otu15\tOtu07\t1.000000\t0.000000\n+Otu15\tOtu08\t1.000000\t0.000000\n+Otu15\tOtu09\t1.000000\t0.000000\n+Otu15\tOtu10\t1.000000\t0.000000\n+Otu15\tOtu11\t1.000000\t0.000000\n+Otu15\tOtu12\t1.000000\t0.000000\n+Otu15\tOtu13\t1.000000\t0.000000\n+Otu15\tOtu14\t1.000000\t0.000000\n+Otu16\tOtu01\t1.000000\t0.000000\n+Otu16\tOtu02\t-1.000000\t0.000000\n+Otu16\tOtu03\t1.000000\t0.000000\n+Otu16\tOtu04\t-1.000000\t0.000000\n+Otu16\tOtu05\t-nan\t0.000000\n+Otu16\tOtu06\t1.000000\t0.000000\n+Otu16\tOtu07\t1.000000\t0.000000\n+Otu16\tOtu08\t1.000000\t0.000000\n+Otu16\tOtu09\t1.000000\t0.000000\n+Otu16\tOtu10\t1.000000\t0.000000\n+Otu16\tOtu11\t1.000000\t0.000000\n+Otu16\tOtu12\t1.000000\t0.000000\n+Otu16\tOtu13\t1.000000\t0.000000\n+Otu16\tOtu14\t1.000000\t0.000000\n+Otu16\tOtu15\t1.000000\t0.000000\n+Otu17\tOtu01\t1.000000\t0.000000\n+Otu17\tOtu02\t-1.000000\t0.000000\n+Otu17\tOtu03\t1.000000\t0.000000\n+Otu17\tOtu04\t-1.000000\t0.000000\n+Otu17\tOtu05\t-nan\t0.000000\n+Otu17\tOtu06\t1.000000\t0.000000\n+Otu17\tOtu07\t1.000000\t0.000000\n+Otu17\tOtu08\t1.000000\t0.000000\n+Otu17\tOtu09'..b'tu46\t-1.000000\t0.000000\n+Otu87\tOtu47\t1.000000\t0.000000\n+Otu87\tOtu48\t1.000000\t0.000000\n+Otu87\tOtu49\t1.000000\t0.000000\n+Otu87\tOtu50\t1.000000\t0.000000\n+Otu87\tOtu51\t1.000000\t0.000000\n+Otu87\tOtu52\t1.000000\t0.000000\n+Otu87\tOtu53\t1.000000\t0.000000\n+Otu87\tOtu54\t1.000000\t0.000000\n+Otu87\tOtu55\t1.000000\t0.000000\n+Otu87\tOtu56\t1.000000\t0.000000\n+Otu87\tOtu57\t1.000000\t0.000000\n+Otu87\tOtu58\t1.000000\t0.000000\n+Otu87\tOtu59\t1.000000\t0.000000\n+Otu87\tOtu60\t1.000000\t0.000000\n+Otu87\tOtu61\t1.000000\t0.000000\n+Otu87\tOtu62\t1.000000\t0.000000\n+Otu87\tOtu63\t1.000000\t0.000000\n+Otu87\tOtu64\t1.000000\t0.000000\n+Otu87\tOtu65\t1.000000\t0.000000\n+Otu87\tOtu66\t1.000000\t0.000000\n+Otu87\tOtu67\t1.000000\t0.000000\n+Otu87\tOtu68\t1.000000\t0.000000\n+Otu87\tOtu69\t1.000000\t0.000000\n+Otu87\tOtu70\t1.000000\t0.000000\n+Otu87\tOtu71\t1.000000\t0.000000\n+Otu87\tOtu72\t1.000000\t0.000000\n+Otu87\tOtu73\t1.000000\t0.000000\n+Otu87\tOtu74\t1.000000\t0.000000\n+Otu87\tOtu75\t1.000000\t0.000000\n+Otu87\tOtu76\t1.000000\t0.000000\n+Otu87\tOtu77\t1.000000\t0.000000\n+Otu87\tOtu78\t1.000000\t0.000000\n+Otu87\tOtu79\t1.000000\t0.000000\n+Otu87\tOtu80\t1.000000\t0.000000\n+Otu87\tOtu81\t1.000000\t0.000000\n+Otu87\tOtu82\t1.000000\t0.000000\n+Otu87\tOtu83\t1.000000\t0.000000\n+Otu87\tOtu84\t1.000000\t0.000000\n+Otu87\tOtu85\t1.000000\t0.000000\n+Otu87\tOtu86\t1.000000\t0.000000\n+Otu88\tOtu01\t-1.000000\t0.000000\n+Otu88\tOtu02\t1.000000\t0.000000\n+Otu88\tOtu03\t-1.000000\t0.000000\n+Otu88\tOtu04\t1.000000\t0.000000\n+Otu88\tOtu05\t-nan\t0.000000\n+Otu88\tOtu06\t-1.000000\t0.000000\n+Otu88\tOtu07\t-1.000000\t0.000000\n+Otu88\tOtu08\t-1.000000\t0.000000\n+Otu88\tOtu09\t-1.000000\t0.000000\n+Otu88\tOtu10\t-1.000000\t0.000000\n+Otu88\tOtu11\t-1.000000\t0.000000\n+Otu88\tOtu12\t-1.000000\t0.000000\n+Otu88\tOtu13\t-1.000000\t0.000000\n+Otu88\tOtu14\t-1.000000\t0.000000\n+Otu88\tOtu15\t-1.000000\t0.000000\n+Otu88\tOtu16\t-1.000000\t0.000000\n+Otu88\tOtu17\t-1.000000\t0.000000\n+Otu88\tOtu18\t-1.000000\t0.000000\n+Otu88\tOtu19\t-1.000000\t0.000000\n+Otu88\tOtu20\t-1.000000\t0.000000\n+Otu88\tOtu21\t-1.000000\t0.000000\n+Otu88\tOtu22\t-1.000000\t0.000000\n+Otu88\tOtu23\t-1.000000\t0.000000\n+Otu88\tOtu24\t1.000000\t0.000000\n+Otu88\tOtu25\t-1.000000\t0.000000\n+Otu88\tOtu26\t-1.000000\t0.000000\n+Otu88\tOtu27\t-1.000000\t0.000000\n+Otu88\tOtu28\t-1.000000\t0.000000\n+Otu88\tOtu29\t-1.000000\t0.000000\n+Otu88\tOtu30\t-1.000000\t0.000000\n+Otu88\tOtu31\t-1.000000\t0.000000\n+Otu88\tOtu32\t-1.000000\t0.000000\n+Otu88\tOtu33\t-1.000000\t0.000000\n+Otu88\tOtu34\t-1.000000\t0.000000\n+Otu88\tOtu35\t-1.000000\t0.000000\n+Otu88\tOtu36\t-1.000000\t0.000000\n+Otu88\tOtu37\t-1.000000\t0.000000\n+Otu88\tOtu38\t-1.000000\t0.000000\n+Otu88\tOtu39\t-1.000000\t0.000000\n+Otu88\tOtu40\t-1.000000\t0.000000\n+Otu88\tOtu41\t-1.000000\t0.000000\n+Otu88\tOtu42\t-1.000000\t0.000000\n+Otu88\tOtu43\t-1.000000\t0.000000\n+Otu88\tOtu44\t-1.000000\t0.000000\n+Otu88\tOtu45\t-1.000000\t0.000000\n+Otu88\tOtu46\t-1.000000\t0.000000\n+Otu88\tOtu47\t1.000000\t0.000000\n+Otu88\tOtu48\t1.000000\t0.000000\n+Otu88\tOtu49\t1.000000\t0.000000\n+Otu88\tOtu50\t1.000000\t0.000000\n+Otu88\tOtu51\t1.000000\t0.000000\n+Otu88\tOtu52\t1.000000\t0.000000\n+Otu88\tOtu53\t1.000000\t0.000000\n+Otu88\tOtu54\t1.000000\t0.000000\n+Otu88\tOtu55\t1.000000\t0.000000\n+Otu88\tOtu56\t1.000000\t0.000000\n+Otu88\tOtu57\t1.000000\t0.000000\n+Otu88\tOtu58\t1.000000\t0.000000\n+Otu88\tOtu59\t1.000000\t0.000000\n+Otu88\tOtu60\t1.000000\t0.000000\n+Otu88\tOtu61\t1.000000\t0.000000\n+Otu88\tOtu62\t1.000000\t0.000000\n+Otu88\tOtu63\t1.000000\t0.000000\n+Otu88\tOtu64\t1.000000\t0.000000\n+Otu88\tOtu65\t1.000000\t0.000000\n+Otu88\tOtu66\t1.000000\t0.000000\n+Otu88\tOtu67\t1.000000\t0.000000\n+Otu88\tOtu68\t1.000000\t0.000000\n+Otu88\tOtu69\t1.000000\t0.000000\n+Otu88\tOtu70\t1.000000\t0.000000\n+Otu88\tOtu71\t1.000000\t0.000000\n+Otu88\tOtu72\t1.000000\t0.000000\n+Otu88\tOtu73\t1.000000\t0.000000\n+Otu88\tOtu74\t1.000000\t0.000000\n+Otu88\tOtu75\t1.000000\t0.000000\n+Otu88\tOtu76\t1.000000\t0.000000\n+Otu88\tOtu77\t1.000000\t0.000000\n+Otu88\tOtu78\t1.000000\t0.000000\n+Otu88\tOtu79\t1.000000\t0.000000\n+Otu88\tOtu80\t1.000000\t0.000000\n+Otu88\tOtu81\t1.000000\t0.000000\n+Otu88\tOtu82\t1.000000\t0.000000\n+Otu88\tOtu83\t1.000000\t0.000000\n+Otu88\tOtu84\t1.000000\t0.000000\n+Otu88\tOtu85\t1.000000\t0.000000\n+Otu88\tOtu86\t1.000000\t0.000000\n+Otu88\tOtu87\t1.000000\t0.000000\n' |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/amazon.otus.accnos --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.otus.accnos Wed Feb 14 09:43:03 2018 -0500 |
| b |
| @@ -0,0 +1,3 @@ +Otu01 +Otu17 +Otu42 |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/esophagus.design --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/esophagus.design Wed Feb 14 09:43:03 2018 -0500 |
| b |
| @@ -0,0 +1,4 @@ +A group1 +B group2 +C group2 +D group3 |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/esophagus.fn.shared --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/esophagus.fn.shared Wed Feb 14 09:43:03 2018 -0500 |
| b |
| @@ -0,0 +1,12 @@ +unique B 593 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 5 1 1 1 3 1 1 1 1 1 1 4 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 4 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +unique C 593 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 5 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +unique D 593 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 30 1 1 8 3 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 5 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +0.03 B 87 12 17 16 14 1 2 39 1 1 18 8 6 1 1 2 5 1 7 3 1 12 3 6 2 1 1 1 3 1 2 1 1 1 2 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0.03 C 87 0 0 19 42 0 0 6 2 10 19 7 1 0 0 2 0 5 0 3 2 0 4 2 0 0 0 1 0 0 0 2 0 2 14 0 0 0 7 0 0 0 0 0 29 14 4 2 2 3 2 11 1 3 3 1 8 6 4 1 1 1 1 4 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0.03 D 87 0 2 3 10 0 2 103 2 0 15 1 0 0 1 5 2 1 5 0 0 1 0 0 0 0 3 6 7 1 1 1 0 1 3 0 0 0 1 0 0 1 0 3 0 0 0 1 0 0 0 0 0 1 0 1 0 4 0 0 0 0 0 0 0 0 2 1 3 2 2 1 3 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1 +0.05 B 74 12 23 34 14 3 47 1 1 8 6 1 1 2 5 1 3 2 12 3 2 1 1 4 1 2 1 1 1 2 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0.05 C 74 14 2 38 42 0 12 2 10 7 1 0 0 2 0 5 3 2 3 4 0 0 1 29 0 0 2 0 2 14 0 0 0 7 0 0 0 0 4 2 2 2 11 1 3 3 1 8 4 1 1 1 1 4 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0.05 D 74 0 2 18 10 2 115 2 0 1 3 0 1 5 2 1 0 0 1 0 0 0 6 7 1 1 2 0 1 4 0 0 0 1 0 0 1 3 0 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 2 1 2 2 1 3 1 1 1 1 1 1 1 1 1 1 3 1 1 +0.10 B 58 50 37 14 52 2 1 8 6 1 1 3 5 1 2 3 2 1 1 2 1 1 1 2 1 2 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0.10 C 58 19 41 42 41 2 10 7 1 0 0 2 0 5 13 4 0 0 1 0 6 0 2 14 0 0 7 0 0 4 2 2 2 4 3 1 8 4 1 1 1 1 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0.10 D 58 5 18 10 124 2 0 1 3 0 1 9 2 1 0 0 0 0 6 1 2 0 1 4 0 1 1 0 0 0 1 1 0 1 0 1 0 0 0 0 1 0 0 0 2 1 2 2 3 1 1 1 1 1 1 1 1 3 1 |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/mothur.1518613794.logfile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mothur.1518613794.logfile Wed Feb 14 09:43:03 2018 -0500 |
| [ |
| b"@@ -0,0 +1,5963 @@\n+Linux version\n+\n+Using ReadLine\n+\n+Running 64Bit Version\n+\n+mothur v.1.39.5\n+Last updated: 3/20/2017\n+\n+by\n+Patrick D. Schloss\n+\n+Department of Microbiology & Immunology\n+University of Michigan\n+http://www.mothur.org\n+\n+When using, please cite:\n+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.\n+\n+Distributed under the GNU General Public License\n+\n+Type 'help()' for information on the commands that are available\n+\n+For questions and analysis support, please visit our forum at https://www.mothur.org/forum\n+\n+Type 'quit()' to exit program\n+Interactive Mode\n+\n+\n+mothur > classify.svm(shared=final.tx.1.subsample.1.pick.shared, design=test.design)\n+1\n+transforming data to have zero mean and unit variance\n+SVM-RFE round 1:\n+44 unranked features\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+"..b'+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+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+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+failed to train SVM on labels A and B\n+[ERROR]: std::exceptionRAM used: 0.0056572Gigabytes . Total Ram: 62.8475Gigabytes.\n+\n+ 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.\n' |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/mothur.1518613825.logfile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mothur.1518613825.logfile Wed Feb 14 09:43:03 2018 -0500 |
| b |
| @@ -0,0 +1,32 @@ +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, mode=classify) +1 +transforming data to have zero mean and unit variance |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/mothur.1518613872.logfile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mothur.1518613872.logfile Wed Feb 14 09:43:03 2018 -0500 |
| [ |
| b"@@ -0,0 +1,6051 @@\n+Linux version\n+\n+Using ReadLine\n+\n+Running 64Bit Version\n+\n+mothur v.1.39.5\n+Last updated: 3/20/2017\n+\n+by\n+Patrick D. Schloss\n+\n+Department of Microbiology & Immunology\n+University of Michigan\n+http://www.mothur.org\n+\n+When using, please cite:\n+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.\n+\n+Distributed under the GNU General Public License\n+\n+Type 'help()' for information on the commands that are available\n+\n+For questions and analysis support, please visit our forum at https://www.mothur.org/forum\n+\n+Type 'quit()' to exit program\n+Interactive Mode\n+\n+\n+mothur > classify.svm(shared=final.tx.1.subsample.1.pick.shared,design=test.design, stdthreshold=0.1)\n+1\n+feature index 43\n+feature 43 has std 1.13039\n+feature index 42\n+feature 42 has std 0.333333\n+feature index 41\n+feature 41 has std 1.13039\n+feature index 40\n+feature 40 has std 0.666667\n+feature index 39\n+feature 39 has std 0.707107\n+feature index 38\n+feature 38 has std 0.726483\n+feature index 37\n+feature 37 has std 1.41421\n+feature index 36\n+feature 36 has std 0.440959\n+feature index 35\n+feature 35 has std 1.05409\n+feature index 34\n+feature 34 has std 1.11803\n+feature index 33\n+feature 33 has std 2.59808\n+feature index 32\n+feature 32 has std 1.5899\n+feature index 31\n+feature 31 has std 0.440959\n+feature index 30\n+feature 30 has std 1.11803\n+feature index 29\n+feature 29 has std 1.30171\n+feature index 28\n+feature 28 has std 0.666667\n+feature index 27\n+feature 27 has std 0.333333\n+feature index 26\n+feature 26 has std 0.833333\n+feature index 25\n+feature 25 has std 0.726483\n+feature index 24\n+feature 24 has std 0.666667\n+feature index 23\n+feature 23 has std 0.333333\n+feature index 22\n+feature 22 has std 1.50923\n+feature index 21\n+feature 21 has std 1.53659\n+feature index 20\n+feature 20 has std 1.16667\n+feature index 19\n+feature 19 has std 1.41421\n+feature index 18\n+feature 18 has std 14.8577\n+feature index 17\n+feature 17 has std 1.66667\n+feature index 16\n+feature 16 has std 3.32081\n+feature index 15\n+feature 15 has std 7.93375\n+feature index 14\n+feature 14 has std 18.2422\n+feature index 13\n+feature 13 has std 42.354\n+feature index 12\n+feature 12 has std 10.7471\n+feature index 11\n+feature 11 has std 261.303\n+feature index 10\n+feature 10 has std 36.524\n+feature index 9\n+feature 9 has std 78.4301\n+feature index 8\n+feature 8 has std 58.3919\n+feature index 7\n+feature 7 has std 33.6022\n+feature index 6\n+feature 6 has std 107.001\n+feature index 5\n+feature 5 has std 15.6\n+feature index 4\n+feature 4 has std 184.297\n+feature index 3\n+feature 3 has std 278.832\n+feature index 2\n+feature 2 has std 182.178\n+feature index 1\n+feature 1 has std 111.537\n+feature index 0\n+feature 0 has std 398.811\n+transforming data to have zero mean and unit variance\n+SVM-RFE round 1:\n+44 unranked features\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n"..b'\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n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to train SVM on labels A and B\n+[ERROR]: std::exceptionRAM used: 0.00563812Gigabytes . Total Ram: 62.8475Gigabytes.\n+\n+ 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.\n' |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/mothur.1518613887.logfile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mothur.1518613887.logfile Wed Feb 14 09:43:03 2018 -0500 |
| [ |
| b"@@ -0,0 +1,5966 @@\n+Linux version\n+\n+Using ReadLine\n+\n+Running 64Bit Version\n+\n+mothur v.1.39.5\n+Last updated: 3/20/2017\n+\n+by\n+Patrick D. Schloss\n+\n+Department of Microbiology & Immunology\n+University of Michigan\n+http://www.mothur.org\n+\n+When using, please cite:\n+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.\n+\n+Distributed under the GNU General Public License\n+\n+Type 'help()' for information on the commands that are available\n+\n+For questions and analysis support, please visit our forum at https://www.mothur.org/forum\n+\n+Type 'quit()' to exit program\n+Interactive Mode\n+\n+\n+mothur > classify.svm(shared=final.tx.1.subsample.1.pick.shared,design=test.design, kernel=linear)\n+removing kernel polynomial\n+removing kernel rbf\n+removing kernel sigmoid\n+1\n+transforming data to have zero mean and unit variance\n+SVM-RFE round 1:\n+44 unranked features\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+"..b'\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\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failed to train SVM on labels A and B\n+[ERROR]: std::exceptionRAM used: 0.00559998Gigabytes . Total Ram: 62.8475Gigabytes.\n+\n+ 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.\n' |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/mothur.1518613903.logfile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mothur.1518613903.logfile Wed Feb 14 09:43:03 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. |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/mothur.1518613913.logfile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mothur.1518613913.logfile Wed Feb 14 09:43:03 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. |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/mothur.1518613936.logfile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mothur.1518613936.logfile Wed Feb 14 09:43:03 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. |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/mothur.1518613968.logfile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mothur.1518613968.logfile Wed Feb 14 09:43:03 2018 -0500 |
| [ |
| b"@@ -0,0 +1,7954 @@\n+Linux version\n+\n+Using ReadLine\n+\n+Running 64Bit Version\n+\n+mothur v.1.39.5\n+Last updated: 3/20/2017\n+\n+by\n+Patrick D. Schloss\n+\n+Department of Microbiology & Immunology\n+University of Michigan\n+http://www.mothur.org\n+\n+When using, please cite:\n+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.\n+\n+Distributed under the GNU General Public License\n+\n+Type 'help()' for information on the commands that are available\n+\n+For questions and analysis support, please visit our forum at https://www.mothur.org/forum\n+\n+Type 'quit()' to exit program\n+Interactive Mode\n+\n+\n+mothur > classify.svm(shared=final.tx.1.subsample.1.pick.shared,design=test.design,transform=zeroone)\n+1\n+transforming data to lie within range [0,1]\n+SVM-RFE round 1:\n+44 unranked features\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n"..b'\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n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n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+failed to train SVM on labels A and B\n+[ERROR]: std::exceptionRAM used: 0.00565338Gigabytes . Total Ram: 62.8475Gigabytes.\n+\n+ 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.\n' |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/mothur.1518614517.logfile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mothur.1518614517.logfile Wed Feb 14 09:43:03 2018 -0500 |
| b |
| @@ -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 + |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/samplebiom.biom1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samplebiom.biom1 Wed Feb 14 09:43:03 2018 -0500 |
| [ |
| b'@@ -0,0 +1,8668 @@\n+{\n+ "id":"otu.dat-0.03",\n+ "format": "Biological Observation Matrix 0.9.1",\n+ "format_url": "http://biom-format.org",\n+ "type": "OTU table",\n+ "generated_by": "mothur1.36.1",\n+ "date": "Mon Jun 26 15:11:52 2017",\n+ "rows":[\n+ {"id":"Otu00001", "metadata":null},\n+ {"id":"Otu00002", "metadata":null},\n+ {"id":"Otu00003", "metadata":null},\n+ {"id":"Otu00004", "metadata":null},\n+ {"id":"Otu00005", "metadata":null},\n+ {"id":"Otu00006", "metadata":null},\n+ {"id":"Otu00007", "metadata":null},\n+ {"id":"Otu00008", "metadata":null},\n+ {"id":"Otu00009", "metadata":null},\n+ {"id":"Otu00010", "metadata":null},\n+ {"id":"Otu00011", "metadata":null},\n+ {"id":"Otu00012", "metadata":null},\n+ {"id":"Otu00013", "metadata":null},\n+ {"id":"Otu00014", "metadata":null},\n+ {"id":"Otu00015", "metadata":null},\n+ {"id":"Otu00016", "metadata":null},\n+ {"id":"Otu00017", "metadata":null},\n+ {"id":"Otu00018", "metadata":null},\n+ {"id":"Otu00019", "metadata":null},\n+ 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[3944,0,1],\n+ [3945,0,1],\n+ [3946,0,1],\n+ [3947,0,1],\n+ [3948,1,1],\n+ [3949,0,1],\n+ [3950,1,1],\n+ [3951,0,1],\n+ [3952,1,1],\n+ [3953,0,1],\n+ [3954,0,1],\n+ [3955,0,1],\n+ [3956,0,1],\n+ [3957,1,1],\n+ [3958,0,1],\n+ [3959,0,1],\n+ [3960,0,1],\n+ [3961,1,1],\n+ [3962,1,1],\n+ [3963,0,1],\n+ [3964,0,1],\n+ [3965,0,1],\n+ [3966,0,1],\n+ [3967,0,1],\n+ [3968,1,1],\n+ [3969,0,1],\n+ [3970,0,1],\n+ [3971,0,1],\n+ [3972,0,1],\n+ [3973,0,1],\n+ [3974,0,1],\n+ [3975,0,1],\n+ [3976,1,1],\n+ [3977,1,1],\n+ [3978,0,1],\n+ [3979,0,1],\n+ [3980,0,1],\n+ [3981,1,1],\n+ [3982,0,1],\n+ [3983,1,1],\n+ [3984,0,1],\n+ [3985,0,1],\n+ [3986,0,1]]\n+}\n' |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/stool.design --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool.design Wed Feb 14 09:43:03 2018 -0500 |
| b |
| @@ -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 |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/stool.final.opti_mcc.shared --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool.final.opti_mcc.shared Wed Feb 14 09:43:03 2018 -0500 |
| b |
| b'@@ -0,0 +1,25 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\t0\t0\t0\t1\t1\t1\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n' |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/stool_small.count_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.count_table Wed Feb 14 09:43:03 2018 -0500 |
| b |
| @@ -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 |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/stool_small.denovo.vsearch.accnos --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.denovo.vsearch.accnos Wed Feb 14 09:43:03 2018 -0500 |
| b |
| @@ -0,0 +1,2 @@ +F11Fcsw_21505 +F11Fcsw_23322 |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/stool_small.names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.names Wed Feb 14 09:43:03 2018 -0500 |
| b |
| @@ -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 |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/stool_small.unique.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.unique.fasta Wed Feb 14 09:43:03 2018 -0500 |
| b |
| b'@@ -0,0 +1,92 @@\n+>F11Fcsw_12747\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGCAGCCTTGGTGAGCCGTTACCTCACCAACTAGCTAATCAGATATGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATCCCAGAGATGCCTCCAAAATACATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGG\n+>F11Fcsw_13125\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAATGTGGCCGTTCATCCTCTCAGACCGGCTACTGATCGTCGCCTTGGTAGGCCGTTACCCCACCAACTAGCTAATCAGACGCAGACCCATCGTAAAGCGATAGCTTACAAGTAGAGGCCATCTTTAGTCGAGCTTCCATGCGGAAGTTCGACAACATTCGGTATTAGCAGTCCTTTCGAACTGTTGTCCCCATCTTTACGG\n+>F11Fcsw_13572\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACCCATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATGGGACGCATCCCCATCCTTTACCAATTAATCTTTATTTGTCGCTCCCATGCGGAAAGACAAACACATCCGGTATTAAACTCCCTTTCAGGAGACTATCCCGGAGTAAAGGGCAGGTTGGATACGCGTTACTCACCCGTGCGCCGGTCGCCATCAAAA\n+>F11Fcsw_13584\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGATGTCTTGGTGGGCCGTTACCCCGCCAACAAACTAATGGAACGCATCCCCATCGGTTATCGAAATTCTTTAATAACAAGAAGATGCCTTCTCGTTATACTATCCGGTATTAATCTTTCTTTCGAAAGGCTATCCCGGAATAACCGGTAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCATCAACCTA\n+>F11Fcsw_13612\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGTCCGTGTCTCAGTACCAATGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTTGGTGGGCCGTTACCCCCCAACTAGCTAATGCGCCGCATGCCCATCCCTGTCCGGATTACTCCTTTGGCGCTCGCAGGATGCCCCGCAAACGCTTTATGCGATATTAGACCGGATTTCTCCGGATTATCCCTCTGACAGGGGCAGGTTGCATACGTGTTACTCACCCG\n+>F11Fcsw_13784\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACCGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCGGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGATCACTGTATCATGCGGTACTGTAATCTTATGCGGTATTAGCATCTGTTTCCAAATGTTATCCCCCTCTGAAAGGCAGGTTG\n+>F11Fcsw_14513\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTATCTCAGTTCCAATGTGGCCGATCACCCTCTCAGGTCGGCTAACCATCGTCGACTTGGTAGTCCGTTACACTACCAACTATCTAATGGTACGCGAGCCCATCCACATCCGATAAATCTTTTACCCCTGAGAGATGCCTCTCTGTGGTCTTATGCGGTATTAGCACACATTTCTATGTGTTATTCCCCAGATGTGGGCAGGTTG\n+>F11Fcsw_14920\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCATCCTCTCAGACCGGCTACTGATCGTCGCCTTGGTGAGCCATTACCTCTCCAACTAGCTAATCAGACGCGGGCCCATCCTATACCACCTGAGTTTTTCCTACCGTATCATGCGGTACTGTAGGCTTATGCGGTTTTAGCACAGATTTCTCTGTGTTATCCCCTGTATAGGGCAGGTTACCCACGCGTTT\n+>F11Fcsw_14954\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGGCCAACCTCTCAGTCCGGCTACCGATCGTCGACTTGGTGGGCCGTTACCCCGCCAACTATCTAATCGGACGCGAGGCCATCTTTCAGCGATAAATCTTTGGCATGTCCGGGATGCCCCGGTCATGCGTCATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTCCTCACGCGTTACT\n+>F11Fcsw_14980\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTTTCTCAGTTCCAATGTGGCCGTTCATCCTCTCAGATCGGCTACCCATCGTCGCCTTGGTGAGCCGTTACCTCTCCAACTAGCTAATGGGCCGCGAGCCCCTCCTATACCGCCTCAGCTTTTACCCCTCTCCGATGCCGGAGTGTGGTCTTATACCGTATTAGCACAAATTTCTCTGTGTTATCCCGTTGTATAGGATAGGTTGCTCACGTGTTACTCACCCG\n+>F11Fcsw_15042\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCGCCCTCTCAGGCCGGCTACTGATCGTCGGTTTGGTGGGCCGTTACCCCGCCAACTGCCTAATCAGACGCGGGCCCATCCCATACCACCGGAGTTTTTCACACTGAGCCATGCAGCTCTGTGCGCTTATGCGGTATTAGCAGCCGTTTCCAGCTGTTATCCCCCGGTATGGGGCAGGTCACCCACGCGTTACT\n+>F11Fcsw_15664\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCAGTACAAGGCAGGTTACCCACGCGTTACT\n+>F11Fcsw_17394\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTTGCCTTGGTAGGCCGTTACCCCGCCAACAAGCTAATCAGACGCGGGTCCATCTCACACCACCGGAGTTTTTCACACTGTACCATGCGGTACTGTGCGCTTATGCGGTATTATCAGCCGTTTCCAACTGCTATCCCCCTGTGTGAGGCAGGTTACCCACGCGTTA\n+>F11Fcsw_17898\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACTGTATCATGCGATACCGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTATCCCCCTGTATAAGGCAGGTTACCCACGCGTTACTCACCCG\n+>F11Fcsw_18564\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAACCTCTCA'..b'GCAGCTCTGTGCGCTTATGCGGTATTAGCAGTCATTTCTGACTGTTATCCCCCTGTATAAGGCAGGTTACCCACGCG\n+>F11Fcsw_22900\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTTGGCTTGGTGGGCCGTTACCCCTCCAACTACCTAATGGGACGCGAACCCCTCTCAAAGCGATAAATCTTTGACCCCTTCATCATGCGGTGTTGTGGTCTCATGCGGTATTAGCAACAGTTTCCCGTTGTTATCCCCCTCTTTGAGTCAGGTTATTCACGCGTTACTCACCCG\n+>F11Fcsw_23043\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGGTCAACCTCTCAGTCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCAGTACAAGGCAGGTTACCCACGCGTTA\n+>F11Fcsw_23322\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCCGTTACCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCACCCGTGCGCCAA\n+>F11Fcsw_23608\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTAGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCTCTTTCAGATGTCTTCTAGAGATATCATTGGGTATTAGTCTTACTTTGCAAGGTTATCCCAAGTGATGGGCAGGTTGGATACGCGTTACTCACCCG\n+>F11Fcsw_23684\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCCCTTTCAGATGTCTTCTAGAGACGTCATTGGGTATTAGTCTTACTTTCGCAAGGTTATCCCAAGTGATGGGCAGGTTGGATACGCGTTACTCACCCGTGCG\n+>F11Fcsw_24087\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTATGGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACAAGCTAATCCAACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACTGAGCCATGCAGCTCTGTGCGCTTATGCGGTATTAGCAGCCATTTCTGACTGTTATCCCCCTGTATAAGGCAGGTTACCCACG\n+>F11Fcsw_24273\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTAGGCCGTTACCCCACCAACTATCTAATCAGACGCGAGCCCATCTATCAGCGGATTACTCCTTTCCCACTTTCATCATGTGATATTTATTGGCATATGCGGTATTAGCAATGATTTCTCACTGTTATTCCCCTCCTGATAGGCG\n+>F11Fcsw_24701\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCTGTTACCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCACCCGTGCG\n+>F11Fcsw_24967\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACT\n+>F11Fcsw_25501\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGGGCCGTTACCCCGCCAACTATCTAATCAGACGCGAGGCCATCTTTCAGCGATAAATCTTTGGCATTTCGACCATGCGATCAAAATGCGTCATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTCCTCACG\n+>F11Fcsw_25574\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAAATCTTTTACCTCAGAACCATGTGATCCCGTGGTCTTATGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCCTGTCTGGAAAAGGTTGCTCACGCGTTACTCACCCGTCCGCCGCTAAAACAG\n+>F11Fcsw_26078\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCTGTTATCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCA\n+>F11Fcsw_26175\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAAATCTTTTACCCCAGAACCATGTGATCCCGTGGTCTTATGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCCTGTCTGGGAAAGGTTGCTCACGCGTTACTCACCCGTCCGCCGCTAAAACAG\n+>F11Fcsw_26418\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACCAGCTAATCAGACGCGGGTCCATCCTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTGTACAGGGCAGGTTACCCACGCGTTACT\n' |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/stool_small.vsearch.chimeras --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.vsearch.chimeras Wed Feb 14 09:43:03 2018 -0500 |
| b |
| @@ -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 |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa test-data/test.design --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.design Wed Feb 14 09:43:03 2018 -0500 |
| b |
| @@ -0,0 +1,9 @@ +F003D000 A +F003D002 B +F003D006 B +F003D008 A +F003D142 A +F003D144 A +F003D146 B +F003D148 B +F003D150 A |
| b |
| diff -r 53b704cc17ad -r 66310f4979aa tool_test_output_all.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_test_output_all.html Wed Feb 14 09:43:03 2018 -0500 |
| [ |
| b'@@ -0,0 +1,383 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <meta http-equiv="X-UA-Compatible" content="IE=edge">\n+ <meta name="viewport" content="width=device-width, initial-scale=1">\n+ <title>Tool Test Results (powered by Planemo)</title>\n+\n+ <!-- Bootstrap -->\n+ <style>/*!\n+ * Bootstrap v3.3.1 (http://getbootstrap.com)\n+ * Copyright 2011-2014 Twitter, Inc.\n+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)\n+ *//*! normalize.css v3.0.2 | MIT License | git.io/normalize */html{font-family:sans-serif;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%}body{margin:0}article,aside,details,figcaption,figure,footer,header,hgroup,main,menu,nav,section,summary{display:block}audio,canvas,progress,video{display:inline-block;vertical-align:baseline}audio:not([controls]){display:none;height:0}[hidden],template{display:none}a{background-color:transparent}a:active,a:hover{outline:0}abbr[title]{border-bottom:1px dotted}b,strong{font-weight:700}dfn{font-style:italic}h1{margin:.67em 0;font-size:2em}mark{color:#000;background:#ff0}small{font-size:80%}sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline}sup{top:-.5em}sub{bottom:-.25em}img{border:0}svg:not(:root){overflow:hidden}figure{margin:1em 40px}hr{height:0;-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box}pre{overflow:auto}code,kbd,pre,samp{font-family:monospace,monospace;font-size:1em}button,input,optgroup,select,textarea{margin:0;font:inherit;color:inherit}button{overflow:visible}button,select{text-transform:none}button,html input[type=button],input[type=reset],input[type=submit]{-webkit-appearance:button;cursor:pointer}button[disabled],html input[disabled]{cursor:default}button::-moz-focus-inner,input::-moz-focus-inner{padding:0;border:0}input{line-height:normal}input[type=checkbox],input[type=radio]{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;padding:0}input[type=number]::-webkit-inner-spin-button,input[type=number]::-webkit-outer-spin-button{height:auto}input[type=search]{-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;-webkit-appearance:textfield}input[type=search]::-webkit-search-cancel-button,input[type=search]::-webkit-search-decoration{-webkit-appearance:none}fieldset{padding:.35em .625em .75em;margin:0 2px;border:1px solid silver}legend{padding:0;border:0}textarea{overflow:auto}optgroup{font-weight:700}table{border-spacing:0;border-collapse:collapse}td,th{padding:0}/*! 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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}};\n+ renderTestResults(test_data);\n+ }\n+ </script>\n+ </body>\n+</html>\n\\ No newline at end of file\n' |