Mercurial > repos > iuc > mothur_get_oturep
changeset 4:f45e7f3675e2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 12:03:33 -0500 |
| parents | 899ef1660676 |
| children | 2ac0e471b97a |
| files | 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/esophagus.design 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/stool.design test-data/stool.final.opti_mcc.shared test-data/test.design |
| diffstat | 18 files changed, 0 insertions(+), 26281 deletions(-) [+] |
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--- a/test-data/Mock_S280_L001_R1_001_small.trim.contigs.accnos Wed Feb 14 09:44:01 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -00967_43_000000000-A3JHG_1_1101_19936_3208
--- a/test-data/Mock_S280_L001_R1_001_small.trim.contigs.groups Wed Feb 14 09:44:01 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ -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
--- a/test-data/Mock_S280_L001_R1_001_small.trim.contigs.names Wed Feb 14 09:44:01 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -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
--- a/test-data/Mock_S280_L001_R1_001_small.trim.contigs.unique.fasta Wed Feb 14 09:44:01 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ ->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
--- a/test-data/Mock_S280_L001_R1_001_small.trim.contigs.unique.groups Wed Feb 14 09:44:01 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -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
--- a/test-data/esophagus.design Wed Feb 14 09:44:01 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -A group1 -B group2 -C group2 -D group3
--- a/test-data/mothur.1518613794.logfile Wed Feb 14 09:44:01 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5963 +0,0 @@ -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) -1 -transforming data to have zero mean and unit variance -SVM-RFE round 1: -44 unranked features - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -failed to train SVM on labels A and B -[ERROR]: std::exceptionRAM used: 0.0056572Gigabytes . 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.
--- a/test-data/mothur.1518613825.logfile Wed Feb 14 09:44:01 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ -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
--- a/test-data/mothur.1518613872.logfile Wed Feb 14 09:44:01 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6051 +0,0 @@ -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, stdthreshold=0.1) -1 -feature index 43 -feature 43 has std 1.13039 -feature index 42 -feature 42 has std 0.333333 -feature index 41 -feature 41 has std 1.13039 -feature index 40 -feature 40 has std 0.666667 -feature index 39 -feature 39 has std 0.707107 -feature index 38 -feature 38 has std 0.726483 -feature index 37 -feature 37 has std 1.41421 -feature index 36 -feature 36 has std 0.440959 -feature index 35 -feature 35 has std 1.05409 -feature index 34 -feature 34 has std 1.11803 -feature index 33 -feature 33 has std 2.59808 -feature index 32 -feature 32 has std 1.5899 -feature index 31 -feature 31 has std 0.440959 -feature index 30 -feature 30 has std 1.11803 -feature index 29 -feature 29 has std 1.30171 -feature index 28 -feature 28 has std 0.666667 -feature index 27 -feature 27 has std 0.333333 -feature index 26 -feature 26 has std 0.833333 -feature index 25 -feature 25 has std 0.726483 -feature index 24 -feature 24 has std 0.666667 -feature index 23 -feature 23 has std 0.333333 -feature index 22 -feature 22 has std 1.50923 -feature index 21 -feature 21 has std 1.53659 -feature index 20 -feature 20 has std 1.16667 -feature index 19 -feature 19 has std 1.41421 -feature index 18 -feature 18 has std 14.8577 -feature index 17 -feature 17 has std 1.66667 -feature index 16 -feature 16 has std 3.32081 -feature index 15 -feature 15 has std 7.93375 -feature index 14 -feature 14 has std 18.2422 -feature index 13 -feature 13 has std 42.354 -feature index 12 -feature 12 has std 10.7471 -feature index 11 -feature 11 has std 261.303 -feature index 10 -feature 10 has std 36.524 -feature index 9 -feature 9 has std 78.4301 -feature index 8 -feature 8 has std 58.3919 -feature index 7 -feature 7 has std 33.6022 -feature index 6 -feature 6 has std 107.001 -feature index 5 -feature 5 has std 15.6 -feature index 4 -feature 4 has std 184.297 -feature index 3 -feature 3 has std 278.832 -feature index 2 -feature 2 has std 182.178 -feature index 1 -feature 1 has std 111.537 -feature index 0 -feature 0 has std 398.811 -transforming data to have zero mean and unit variance -SVM-RFE round 1: -44 unranked features - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -failed to train SVM on labels A and B -[ERROR]: std::exceptionRAM used: 0.00559998Gigabytes . Total Ram: 62.8475Gigabytes. - - has occurred in the ClassifySvmSharedCommand class function processSharedAndDesignData. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.
--- a/test-data/mothur.1518613903.logfile Wed Feb 14 09:44:01 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ -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.
--- a/test-data/mothur.1518613913.logfile Wed Feb 14 09:44:01 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ -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.
--- a/test-data/mothur.1518613936.logfile Wed Feb 14 09:44:01 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ -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.
--- a/test-data/mothur.1518613968.logfile Wed Feb 14 09:44:01 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7954 +0,0 @@ -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,transform=zeroone) -1 -transforming data to lie within range [0,1] -SVM-RFE round 1: -44 unranked features - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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Total Ram: 62.8475Gigabytes. - - has occurred in the ClassifySvmSharedCommand class function processSharedAndDesignData. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.
--- a/test-data/mothur.1518614517.logfile Wed Feb 14 09:44:01 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -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 -
--- a/test-data/stool.design Wed Feb 14 09:44:01 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -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
--- a/test-data/stool.final.opti_mcc.shared Wed Feb 14 09:44:01 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ -label Group numOtus Otu0001 Otu0002 Otu0003 Otu0004 Otu0005 Otu0006 Otu0007 Otu0008 Otu0009 Otu0010 Otu0011 Otu0012 Otu0013 Otu0014 Otu0015 Otu0016 Otu0017 Otu0018 Otu0019 Otu0020 Otu0021 Otu0022 Otu0023 Otu0024 Otu0025 Otu0026 Otu0027 Otu0028 Otu0029 Otu0030 Otu0031 Otu0032 Otu0033 Otu0034 Otu0035 Otu0036 Otu0037 Otu0038 Otu0039 Otu0040 Otu0041 Otu0042 Otu0043 Otu0044 Otu0045 Otu0046 Otu0047 Otu0048 Otu0049 Otu0050 Otu0051 Otu0052 Otu0053 Otu0054 Otu0055 Otu0056 Otu0057 Otu0058 Otu0059 Otu0060 Otu0061 Otu0062 Otu0063 Otu0064 Otu0065 Otu0066 Otu0067 Otu0068 Otu0069 Otu0070 Otu0071 Otu0072 Otu0073 Otu0074 Otu0075 Otu0076 Otu0077 Otu0078 Otu0079 Otu0080 Otu0081 Otu0082 Otu0083 Otu0084 Otu0085 Otu0086 Otu0087 Otu0088 Otu0089 Otu0090 Otu0091 Otu0092 Otu0093 Otu0094 Otu0095 Otu0096 Otu0097 Otu0098 Otu0099 Otu0100 Otu0101 Otu0102 Otu0103 Otu0104 Otu0105 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