{"action":"created","issue":{"url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/65","repository_url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit","labels_url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/65/labels{/name}","comments_url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/65/comments","events_url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/65/events","html_url":"https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/65","id":253539576,"number":65,"title":"InvalidInputException: Unable to extract coding transcripts from the filtered transMap genePred.","user":{"login":"fbemm","id":8361254,"avatar_url":"https://avatars3.githubusercontent.com/u/8361254?v=4","gravatar_id":"","url":"https://api.github.com/users/fbemm","html_url":"https://github.com/fbemm","followers_url":"https://api.github.com/users/fbemm/followers","following_url":"https://api.github.com/users/fbemm/following{/other_user}","gists_url":"https://api.github.com/users/fbemm/gists{/gist_id}","starred_url":"https://api.github.com/users/fbemm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fbemm/subscriptions","organizations_url":"https://api.github.com/users/fbemm/orgs","repos_url":"https://api.github.com/users/fbemm/repos","events_url":"https://api.github.com/users/fbemm/events{/privacy}","received_events_url":"https://api.github.com/users/fbemm/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":16,"created_at":"2017-08-29T06:12:48Z","updated_at":"2017-08-29T13:34:41Z","closed_at":null,"body":"Looks like I am missing a filtered transMap. I guess its the filtered reference file that is missing.\r\n\r\n```\r\nERROR: [pid 6921] Worker Worker(salt=242344154, workers=16, host=burrito, username=fbemm, pid=6142) failed    ToilTask: AugustusDriverTask for PRET_male using batchSystem singleMachine\r\nTraceback (most recent call last):\r\n  File \"/ebio/abt6_projects9/abt6_software/bin/Comparative-Annotation-Toolkit/env/local/lib/python2.7/site-packages/luigi/worker.py\", line 191, in run\r\n    new_deps = self._run_get_new_deps()\r\n  File \"/ebio/abt6_projects9/abt6_software/bin/Comparative-Annotation-Toolkit/env/local/lib/python2.7/site-packages/luigi/worker.py\", line 129, in _run_get_new_deps\r\n    task_gen = self.task.run()\r\n  File \"/ebio/abt6_projects9/abt6_software/bin/Comparative-Annotation-Toolkit/cat/__init__.py\", line 1336, in run\r\n    coding_gp = self.extract_coding_genes(augustus_args)\r\n  File \"/ebio/abt6_projects9/abt6_software/bin/Comparative-Annotation-Toolkit/cat/__init__.py\", line 1328, in extract_coding_genes\r\n    raise InvalidInputException('Unable to extract coding transcripts from the filtered transMap genePred.')\r\nInvalidInputException: Unable to extract coding transcripts from the filtered transMap genePred.\r\nINFO: Informed scheduler that task   AugustusDriverTask_False_True_True_4447b51b96   has status   FAILED\r\n```\r\n\r\nThis is how the transMap folder looks like:\r\n\r\n```\r\n-rw-r--r--  1 16338199 Aug 28 17:49 PRET_male.filtered.gp\r\n-rw-r--r--  1 15470773 Aug 28 17:49 PRET_male.filtered.psl\r\n-rw-r--r--  1 34966020 Aug 28 13:05 PRET_male.gp\r\n-rw-r--r--  1 404793692 Aug 28 17:50 PRET_male.gtf\r\n-rw-r--r--  1 37093028 Aug 28 13:05 PRET_male.psl\r\n```\r\nThis is how the reference folder looks like:\r\n\r\n```\r\n-rw-r--r--  1 9180428 Aug 28 11:37 PRET_female.bed\r\n-rw-r--r--  1 166259086 Aug 28 11:38 PRET_female.fa\r\n-rw-r--r--  1 11 Aug 28 11:38 PRET_female.fa.flat\r\n-rw-r--r--  1 1303172 Aug 28 11:38 PRET_female.fa.gdx\r\n-rw-r--r--  1 16730618 Aug 28 11:37 PRET_female.gp\r\n-rw-r--r--  1 25215265 Aug 28 11:37 PRET_female.gp_attrs\r\n-rw-r--r--  2 224116964 Aug 28 11:37 PRET_female.gtf\r\n-rw-r--r--  1 15266811 Aug 28 11:37 PRET_female.psl\r\n```\r\n\r\nLet me know where the PRET_female.filtered.gp should appear and I can start tracking what is going on. Might be that this is related to what we did yesterday and the file was just not created because I restarted CAT.\r\n\r\nThanks,\r\nFelix"},"comment":{"url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/comments/325665350","html_url":"https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/65#issuecomment-325665350","issue_url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/65","id":325665350,"user":{"login":"ifiddes","id":7818077,"avatar_url":"https://avatars2.githubusercontent.com/u/7818077?v=4","gravatar_id":"","url":"https://api.github.com/users/ifiddes","html_url":"https://github.com/ifiddes","followers_url":"https://api.github.com/users/ifiddes/followers","following_url":"https://api.github.com/users/ifiddes/following{/other_user}","gists_url":"https://api.github.com/users/ifiddes/gists{/gist_id}","starred_url":"https://api.github.com/users/ifiddes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ifiddes/subscriptions","organizations_url":"https://api.github.com/users/ifiddes/orgs","repos_url":"https://api.github.com/users/ifiddes/repos","events_url":"https://api.github.com/users/ifiddes/events{/privacy}","received_events_url":"https://api.github.com/users/ifiddes/received_events","type":"User","site_admin":false},"created_at":"2017-08-29T13:34:41Z","updated_at":"2017-08-29T13:34:41Z","body":"Yes, the modules are separate and the output you are generating now will be fine."}}
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