{"action":"created","issue":{"url":"https://api.github.com/repos/biocore/biom-format/issues/763","repository_url":"https://api.github.com/repos/biocore/biom-format","labels_url":"https://api.github.com/repos/biocore/biom-format/issues/763/labels{/name}","comments_url":"https://api.github.com/repos/biocore/biom-format/issues/763/comments","events_url":"https://api.github.com/repos/biocore/biom-format/issues/763/events","html_url":"https://github.com/biocore/biom-format/issues/763","id":268110756,"number":763,"title":"convert txt. into biom file ","user":{"login":"Acetylcholine88","id":25853599,"avatar_url":"https://avatars3.githubusercontent.com/u/25853599?v=4","gravatar_id":"","url":"https://api.github.com/users/Acetylcholine88","html_url":"https://github.com/Acetylcholine88","followers_url":"https://api.github.com/users/Acetylcholine88/followers","following_url":"https://api.github.com/users/Acetylcholine88/following{/other_user}","gists_url":"https://api.github.com/users/Acetylcholine88/gists{/gist_id}","starred_url":"https://api.github.com/users/Acetylcholine88/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Acetylcholine88/subscriptions","organizations_url":"https://api.github.com/users/Acetylcholine88/orgs","repos_url":"https://api.github.com/users/Acetylcholine88/repos","events_url":"https://api.github.com/users/Acetylcholine88/events{/privacy}","received_events_url":"https://api.github.com/users/Acetylcholine88/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2017-10-24T17:00:06Z","updated_at":"2018-02-13T05:34:26Z","closed_at":null,"author_association":"NONE","body":"Can someone help?\r\n\r\nTried the following command:\r\n\r\nbiom convert -i OTU_original.txt -o OTU_original.biom --table-type \"OTU table\" --to-hdf5 --process-obs-metadata taxonomy\r\n\r\nthis is what I got:\r\n\r\nbiom convert: error: option -i: file does not exist: 'OTU.txt'\r\n\r\n-bash-4.2$ biom convert -i OTU_original.txt -o OTU_original.biom --table-type \"OTU table\" --process-obs-metadata taxonomy\r\n\r\nTraceback (most recent call last):\r\n\r\nFile \"/ycga-gpfs/apps/hpc/software/Python/2.7.13-foss-2016b/bin/pyqi\", line 4, in\r\n\r\n__import__('pkg_resources').run_script('pyqi==0.3.2', 'pyqi')\r\nFile \"build/bdist.linux-x86_64/egg/pkg_resources/init.py\", line 738, in run_script\r\n\r\nFile \"build/bdist.linux-x86_64/egg/pkg_resources/init.py\", line 1499, in run_script\r\n\r\nFile \"/ycga-gpfs/apps/hpc/software/Python/2.7.13-foss-2016b/lib/python2.7/site-packages/pyqi-0.3.2-py2.7.egg/EGG-INFO/scripts/pyqi\", line 184, in\r\n\r\noptparse_main(cmd_obj, argv[1:])\r\nFile \"/ycga-gpfs/apps/hpc/software/Python/2.7.13-foss-2016b/lib/python2.7/site-packages/pyqi-0.3.2-py2.7.egg/pyqi/core/interfaces/optparse/init.py\", line 275, in optparse_main\r\n\r\nresult = optparse_cmd(local_argv[1:])\r\nFile \"/ycga-gpfs/apps/hpc/software/Python/2.7.13-foss-2016b/lib/python2.7/site-packages/pyqi-0.3.2-py2.7.egg/pyqi/core/interface.py\", line 39, in call\r\n\r\ncmd_result = self.CmdInstance(**cmd_input)\r\nFile \"/ycga-gpfs/apps/hpc/software/Python/2.7.13-foss-2016b/lib/python2.7/site-packages/pyqi-0.3.2-py2.7.egg/pyqi/core/command.py\", line 137, in call\r\n\r\nresult = self.run(**kwargs)\r\nFile \"/ycga-gpfs/apps/hpc/software/Python/2.7.13-foss-2016b/lib/python2.7/site-packages/biom/commands/table_converter.py\", line 217, in run\r\n\r\nraise CommandError(convert_error_msg)\r\npyqi.core.exception.CommandError: Input does not look like a classic table. Did you forget to specify that a classic table file should be created from a BIOM table file?\r\n\r\nHelp would be very much appreciated - I am super lost!\r\n\r\n\r\n[OTU_original_MF_samples_v1v3_sorted_test.txt](https://github.com/biocore/biom-format/files/1411705/OTU_original_MF_samples_v1v3_sorted_test.txt)\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/biocore/biom-format/issues/comments/365156234","html_url":"https://github.com/biocore/biom-format/issues/763#issuecomment-365156234","issue_url":"https://api.github.com/repos/biocore/biom-format/issues/763","id":365156234,"user":{"login":"smajor1","id":16820455,"avatar_url":"https://avatars2.githubusercontent.com/u/16820455?v=4","gravatar_id":"","url":"https://api.github.com/users/smajor1","html_url":"https://github.com/smajor1","followers_url":"https://api.github.com/users/smajor1/followers","following_url":"https://api.github.com/users/smajor1/following{/other_user}","gists_url":"https://api.github.com/users/smajor1/gists{/gist_id}","starred_url":"https://api.github.com/users/smajor1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/smajor1/subscriptions","organizations_url":"https://api.github.com/users/smajor1/orgs","repos_url":"https://api.github.com/users/smajor1/repos","events_url":"https://api.github.com/users/smajor1/events{/privacy}","received_events_url":"https://api.github.com/users/smajor1/received_events","type":"User","site_admin":false},"created_at":"2018-02-13T05:34:26Z","updated_at":"2018-02-13T05:34:26Z","author_association":"NONE","body":"I don't want to open a new issue for a similar command issue so I'll piggy back here a bit. \r\nI'm trying to convert a tab-delimited table to biom in the qiime environment.\r\n```\r\nbiom convert -i filt-otu-tab.txt -o filt.biom --table-type=\"OTU table\" --to-json\r\nValueError: column index exceeds matrix dimensions\r\n```\r\nI can't imagine anything is wrong with my table as I've not manipulated it directly."}}
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