{"action":"closed","issue":{"url":"https://api.github.com/repos/biocore/qiime/issues/2013","labels_url":"https://api.github.com/repos/biocore/qiime/issues/2013/labels{/name}","comments_url":"https://api.github.com/repos/biocore/qiime/issues/2013/comments","events_url":"https://api.github.com/repos/biocore/qiime/issues/2013/events","html_url":"https://github.com/biocore/qiime/issues/2013","id":77768929,"number":2013,"title":"Problem parsing mapping file in supervised_learning.py","user":{"login":"mortonjt","id":4184797,"avatar_url":"https://avatars.githubusercontent.com/u/4184797?v=3","gravatar_id":"","url":"https://api.github.com/users/mortonjt","html_url":"https://github.com/mortonjt","followers_url":"https://api.github.com/users/mortonjt/followers","following_url":"https://api.github.com/users/mortonjt/following{/other_user}","gists_url":"https://api.github.com/users/mortonjt/gists{/gist_id}","starred_url":"https://api.github.com/users/mortonjt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mortonjt/subscriptions","organizations_url":"https://api.github.com/users/mortonjt/orgs","repos_url":"https://api.github.com/users/mortonjt/repos","events_url":"https://api.github.com/users/mortonjt/events{/privacy}","received_events_url":"https://api.github.com/users/mortonjt/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-05-18T19:07:33Z","updated_at":"2015-05-19T22:10:37Z","closed_at":"2015-05-19T22:10:37Z","body":"I'm having a bit of a problem running `supervised_learning.py` - it seems that R is having a hard time parsing the mapping file.\r\n\r\nHere's the error message below.\r\n```\r\nsupervised_learning.py -i data/otu_table.json -m data/combined_mapping.txt -c BODY_SITE -o results -f\r\nTraceback (most recent call last):\r\n  File \"/Users/mortonyt/.virtualenvs/qiime/bin/supervised_learning.py\", line 5, in <module>\r\n    pkg_resources.run_script('qiime==1.8.0-dev', 'supervised_learning.py')\r\n  File \"/Users/mortonjt/.virtualenvs/qiime/lib/python2.7/site-packages/pkg_resources.py\", line 534, in run_script\r\n    self.require(requires)[0].run_script(script_name, ns)\r\n  File \"/Users/mortonjt/.virtualenvs/qiime/lib/python2.7/site-packages/pkg_resources.py\", line 1434, in run_script\r\n    execfile(script_filename, namespace, namespace)\r\n  File \"/Users/mortonjt/.virtualenvs/qiime/lib/python2.7/site-packages/qiime-1.8.0_dev-py2.7.egg/EGG-INFO/scripts/supervised_learning.py\", line 255, in <module>\r\n    main()\r\n  File \"/Users/mortonjt/.virtualenvs/qiime/lib/python2.7/site-packages/qiime-1.8.0_dev-py2.7.egg/EGG-INFO/scripts/supervised_learning.py\", line 196, in main\r\n    ntree, errortype, output_dir, verbose)\r\n  File \"/Users/mortonjt/.virtualenvs/qiime/lib/python2.7/site-packages/qiime-1.8.0_dev-py2.7.egg/qiime/supervised_learning.py\", line 64, in run_supervised_learning\r\n    app_result = rsl(predictor_fp)\r\n  File \"/Users/mortonjt/.virtualenvs/qiime/lib/python2.7/site-packages/cogent/app/util.py\", line 251, in __call__\r\n    open(errfile).read())\r\ncogent.app.util.ApplicationError: Unacceptable application exit status: 1\r\nCommand:\r\ncd \"/Users/mortonjt/Documents/CUBio/AmericanGut/workspace/mislabel/\"; R --slave --no-restore --args --source_dir /Users/mortonjt/.virtualenvs/qiime/lib/python2.7/site-packages/qiime-1.8.0_dev-py2.7.egg/qiime/support_files/R -e oob -c BODY_SITE -m \"data/combined_mapping.txt\" -o \"results\" -n 500 -i \"results/otu_table.txt\" < /Users/mortonjt/.virtualenvs/qiime/lib/python2.7/site-packages/qiime-1.8.0_dev-py2.7.egg/qiime/support_files/R/randomforests.r > \"/tmp/tmpbiz0pziv9BnQcFbHzfef.txt\" 2> \"/tmp/tmpwBYW93EXGoTTXNWxNp6w.txt\"\r\nStdOut:\r\n\r\nStdErr:\r\nWarning message:\r\npackage ‘optparse’ was built under R version 3.1.2 \r\nError in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : \r\n  line 204 did not have 298 elements\r\nCalls: load.qiime.mapping.file -> read.qiime.table -> read.table -> scan\r\nExecution halted\r\n```\r\n\r\nI have no problems parsing this file using pandas at all."}}