{"action":"opened","issue":{"url":"https://api.github.com/repos/ENCODE-DCC/kentUtils/issues/8","repository_url":"https://api.github.com/repos/ENCODE-DCC/kentUtils","labels_url":"https://api.github.com/repos/ENCODE-DCC/kentUtils/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/ENCODE-DCC/kentUtils/issues/8/comments","events_url":"https://api.github.com/repos/ENCODE-DCC/kentUtils/issues/8/events","html_url":"https://github.com/ENCODE-DCC/kentUtils/issues/8","id":153687348,"number":8,"title":"gtfToGenePred: \"doesn't appear to be a GTF file (GFF not supported by this program)\"","user":{"login":"remimarenco","id":2152858,"avatar_url":"https://avatars.githubusercontent.com/u/2152858?v=3","gravatar_id":"","url":"https://api.github.com/users/remimarenco","html_url":"https://github.com/remimarenco","followers_url":"https://api.github.com/users/remimarenco/followers","following_url":"https://api.github.com/users/remimarenco/following{/other_user}","gists_url":"https://api.github.com/users/remimarenco/gists{/gist_id}","starred_url":"https://api.github.com/users/remimarenco/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/remimarenco/subscriptions","organizations_url":"https://api.github.com/users/remimarenco/orgs","repos_url":"https://api.github.com/users/remimarenco/repos","events_url":"https://api.github.com/users/remimarenco/events{/privacy}","received_events_url":"https://api.github.com/users/remimarenco/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-05-09T00:59:23Z","updated_at":"2016-05-09T00:59:23Z","closed_at":null,"body":"Hi!\r\n\r\nFirst, thanks for your awesome tool suite, it is really helpful everyday in my job.\r\n\r\nSecond, the less nice part...I have an issue with gtfToGenePred :/.\r\n\r\nWhen I am running the tool against a (supposed) GTF file, gtfToGenePred outputs me that it `doesn't appear to be a GTF file (GFF not supported by this program)`.\r\n\r\n[myGtf_original.gtf.txt](https://github.com/ENCODE-DCC/kentUtils/files/254200/myGtf_original.gtf.txt)\r\n\r\nI have tried to look into the GTF specification format, in case the tool I am using (Augustus) does not output a real GTF, and maybe it appears the second column with the name of the tool, is not in the specification.\r\n\r\nSo I removed it (as attached), and so the tool outputs me `col 3 or 4 not a number  Bad line 3 of myGtf.gtf`.\r\n\r\n[myGtf_without_2nd_column.tabular.txt](https://github.com/ENCODE-DCC/kentUtils/files/254201/myGtf_without_2nd_column.tabular.txt)\r\n\r\nSo I thought maybe it was because of the comments, so I cleaned everything (as attached), and I got back the message that it is not a GTF File :(.\r\n\r\n[myGtf_without_comments.gtf.txt](https://github.com/ENCODE-DCC/kentUtils/files/254202/myGtf_without_comments.gtf.txt)\r\n\r\nDo you have any idea about what is going on?\r\n\r\nThanks a lot!"}}