{"action":"created","issue":{"url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/32","labels_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/32/labels{/name}","comments_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/32/comments","events_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/32/events","html_url":"https://github.com/Ecogenomics/CheckM/issues/32","id":91209415,"number":32,"title":"Prodigal output parsing problem","user":{"login":"dturaev","id":8933948,"avatar_url":"https://avatars.githubusercontent.com/u/8933948?v=3","gravatar_id":"","url":"https://api.github.com/users/dturaev","html_url":"https://github.com/dturaev","followers_url":"https://api.github.com/users/dturaev/followers","following_url":"https://api.github.com/users/dturaev/following{/other_user}","gists_url":"https://api.github.com/users/dturaev/gists{/gist_id}","starred_url":"https://api.github.com/users/dturaev/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dturaev/subscriptions","organizations_url":"https://api.github.com/users/dturaev/orgs","repos_url":"https://api.github.com/users/dturaev/repos","events_url":"https://api.github.com/users/dturaev/events{/privacy}","received_events_url":"https://api.github.com/users/dturaev/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-06-26T09:54:49Z","updated_at":"2015-06-29T03:23:29Z","closed_at":"2015-06-29T03:23:29Z","body":"Hi, the prodigal output format seems to have changed between versions 2.60 and 2.61/2.62. The new output can't be parsed.\r\n\r\nExample of old output line:\r\n```\r\n# Model Data: version=Prodigal.v2.60;run_type=Single;model=\"Ab initio\";gc_cont=35.88;transl_table=11;uses_sd=1\r\n```\r\nNew output line:\r\n```\r\n# Model Data: gc_cont=35.88;transl_table=4;uses_sd=1\r\n```\r\n\r\nThe error is:\r\n```\r\n  File \"/apps/python/lib/python2.7/site-packages/checkm/prodigal.py\", line 178, in __parseGFF\r\n    self.translationTable = line.split(';')[4]\r\nIndexError: list index out of range\r\n```\r\n\r\n\r\nAlso, another small request: In the file \"checkm\", please change the line\r\n```\r\nversionFile = open(os.path.join(binDir, '..', 'checkm', 'VERSION'))\r\n```\r\nto\r\n```\r\nimport checkm; versionFile = open(os.path.join(checkm.__path__[0], 'VERSION'))\r\n```\r\nor something similar, this would be more stable."},"comment":{"url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/comments/116411495","html_url":"https://github.com/Ecogenomics/CheckM/issues/32#issuecomment-116411495","issue_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/32","id":116411495,"user":{"login":"dparks1134","id":3688336,"avatar_url":"https://avatars.githubusercontent.com/u/3688336?v=3","gravatar_id":"","url":"https://api.github.com/users/dparks1134","html_url":"https://github.com/dparks1134","followers_url":"https://api.github.com/users/dparks1134/followers","following_url":"https://api.github.com/users/dparks1134/following{/other_user}","gists_url":"https://api.github.com/users/dparks1134/gists{/gist_id}","starred_url":"https://api.github.com/users/dparks1134/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dparks1134/subscriptions","organizations_url":"https://api.github.com/users/dparks1134/orgs","repos_url":"https://api.github.com/users/dparks1134/repos","events_url":"https://api.github.com/users/dparks1134/events{/privacy}","received_events_url":"https://api.github.com/users/dparks1134/received_events","type":"User","site_admin":false},"created_at":"2015-06-29T03:23:29Z","updated_at":"2015-06-29T03:23:29Z","body":"Hello dturaev,\r\n\r\nThank you for bringing this to my attention. This issue has been resolved in CheckM v1.0.3.\r\n\r\nCheers,\r\nDonovan"}}