{"action":"created","issue":{"url":"https://api.github.com/repos/dieterich-lab/DCC/issues/5","labels_url":"https://api.github.com/repos/dieterich-lab/DCC/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/dieterich-lab/DCC/issues/5/comments","events_url":"https://api.github.com/repos/dieterich-lab/DCC/issues/5/events","html_url":"https://github.com/dieterich-lab/DCC/issues/5","id":118100760,"number":5,"title":"issue with pybedtools groupby","user":{"login":"e-hutchins","id":13385262,"avatar_url":"https://avatars.githubusercontent.com/u/13385262?v=3","gravatar_id":"","url":"https://api.github.com/users/e-hutchins","html_url":"https://github.com/e-hutchins","followers_url":"https://api.github.com/users/e-hutchins/followers","following_url":"https://api.github.com/users/e-hutchins/following{/other_user}","gists_url":"https://api.github.com/users/e-hutchins/gists{/gist_id}","starred_url":"https://api.github.com/users/e-hutchins/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/e-hutchins/subscriptions","organizations_url":"https://api.github.com/users/e-hutchins/orgs","repos_url":"https://api.github.com/users/e-hutchins/repos","events_url":"https://api.github.com/users/e-hutchins/events{/privacy}","received_events_url":"https://api.github.com/users/e-hutchins/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-11-20T18:43:28Z","updated_at":"2015-11-22T21:26:51Z","closed_at":null,"body":"When I run DCC, I get an error with pybedtools groupby:\r\n\r\n<code>\r\npython2.7 /home/ehutchins/tools/DCC/DCC/main.py @chimeric_junctions -mt1 @chimeric_junctions_mate1 -mt2 @chimeric_junctions_mate2 -D -N -temp -an ensembl_genome/Homo_sapiens.GRCh37.75.gtf -Pi -F -M -R hg19_combined_repeats.gtf -Nr 2 1 -fg -G -A ensembl_genome/Homo_sapiens.GRCh37.75.dna.toplevel.fa\r\n</code>\r\n\r\nWARNING: nonstrand data, the strand of circRNAs guessed from the strandness of host genes.\r\n===== Please make sure that you mapped both the paired mates togethor and seperately!!! =====\r\nCollect chimera from mates-seperate mapping.\r\nstarted detect circRNA from Sample_S_001_PC02_ACTTGAChimeric.out.junction.fixed\r\nstarted detect circRNA from Sample_S_002_PC02_TTAGGCChimeric.out.junction.fixed\r\nstarted detect circRNA from Sample_S_007_PC02_GATCAGChimeric.out.junction.fixed\r\nstarted detect circRNA from Sample_S_023_PC02_CTTGTAChimeric.out.junction.fixed\r\nstarted detect circRNA from Sample_S_024_PC02_ACAGTGChimeric.out.junction.fixed\r\nstarted detect circRNA from Sample_S_170_PC02_CGATGTChimeric.out.junction.fixed\r\n\r\nStart to combine individual circRNA read counts.\r\n\r\nTraceback (most recent call last):\r\n  File \"/home/ehutchins/tools/DCC/DCC/main.py\", line 507, in <module>\r\n    main()\r\n  File \"/home/ehutchins/tools/DCC/DCC/main.py\", line 244, in main\r\n    circAnn.annotate('_tmp_DCC/tmp_coordinates','_tmp_DCC/tmp_'+getfilename(options.annotate)+'.gene','_tmp_DCC/tmp_coordinatesannotated')\r\n  File \"/home/ehutchins/tools/DCC/DCC/circAnnotate.py\", line 54, in annotate\r\n    tmpresult = tmpintersect.groupby(g=(1,2,3,5),c=(ncol+7,ncol+9),o=('first','distinct'))\r\n  File \"/home/ehutchins/.local/lib/python2.7/site-packages/pybedtools-0.7.1-py2.7-linux-x86_64.egg/pybedtools/bedtool.py\", line 775, in decorated\r\n    result = method(self, *args, **kwargs)\r\n  File \"/home/ehutchins/.local/lib/python2.7/site-packages/pybedtools-0.7.1-py2.7-linux-x86_64.egg/pybedtools/bedtool.py\", line 336, in wrapped\r\n    decode_output=decode_output,\r\n  File \"/home/ehutchins/.local/lib/python2.7/site-packages/pybedtools-0.7.1-py2.7-linux-x86_64.egg/pybedtools/helpers.py\", line 378, in call_bedtools\r\n    raise BEDToolsError(subprocess.list2cmdline(cmds), stderr)\r\npybedtools.helpers.BEDToolsError:\r\nCommand was:\r\n\r\n\tbedtools groupby -o first,distinct -i /tmp/pybedtools.kYcZIv.tmp -g 1,2,3,5 -c 13,15\r\n\r\nError message was:\r\n\r\n*****\r\n***** ERROR: Requested column 13, but database file /tmp/pybedtools.kYcZIv.tmp only has fields 1 - 0.\r\n\r\nTool:    bedtools groupby\r\nVersion: v2.24.0-34-ge542de7\r\nSummary: Summarizes a dataset column based upon\r\n\t common column groupings. Akin to the SQL \"group by\" command.\r\n\r\nUsage:\t bedtools groupby -g [group_column(s)] -c [op_column(s)] -o [ops]\r\n\t cat [FILE] | bedtools groupby -g [group_column(s)] -c [op_column(s)] -o [ops]"},"comment":{"url":"https://api.github.com/repos/dieterich-lab/DCC/issues/comments/158800949","html_url":"https://github.com/dieterich-lab/DCC/issues/5#issuecomment-158800949","issue_url":"https://api.github.com/repos/dieterich-lab/DCC/issues/5","id":158800949,"user":{"login":"CDieterich","id":7941393,"avatar_url":"https://avatars.githubusercontent.com/u/7941393?v=3","gravatar_id":"","url":"https://api.github.com/users/CDieterich","html_url":"https://github.com/CDieterich","followers_url":"https://api.github.com/users/CDieterich/followers","following_url":"https://api.github.com/users/CDieterich/following{/other_user}","gists_url":"https://api.github.com/users/CDieterich/gists{/gist_id}","starred_url":"https://api.github.com/users/CDieterich/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/CDieterich/subscriptions","organizations_url":"https://api.github.com/users/CDieterich/orgs","repos_url":"https://api.github.com/users/CDieterich/repos","events_url":"https://api.github.com/users/CDieterich/events{/privacy}","received_events_url":"https://api.github.com/users/CDieterich/received_events","type":"User","site_admin":false},"created_at":"2015-11-22T21:26:51Z","updated_at":"2015-11-22T21:26:51Z","body":"Hi,\n\nthanks for interested in DCC and report the issue.\n\ncould you please show me the following things:\n1. A few lines of Sample_S_001_PC02_ACTTGAChimeric.out.junction.fixed in\nyour sample directory.\n2. A few lines of any *.circRNA file in _tmp_DCC directory?\n3. A ll command result of  _tmp_DCC directory, I'm interested in the file\nsizes.\n\nThanks again.\n\nBest,\nJun\n"}}