{"action":"created","issue":{"url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/102","repository_url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit","labels_url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/102/labels{/name}","comments_url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/102/comments","events_url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/102/events","html_url":"https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/102","id":339492611,"node_id":"MDU6SXNzdWUzMzk0OTI2MTE=","number":102,"title":"transMap file in wrong location","user":{"login":"nbedelman","id":13751276,"node_id":"MDQ6VXNlcjEzNzUxMjc2","avatar_url":"https://avatars3.githubusercontent.com/u/13751276?v=4","gravatar_id":"","url":"https://api.github.com/users/nbedelman","html_url":"https://github.com/nbedelman","followers_url":"https://api.github.com/users/nbedelman/followers","following_url":"https://api.github.com/users/nbedelman/following{/other_user}","gists_url":"https://api.github.com/users/nbedelman/gists{/gist_id}","starred_url":"https://api.github.com/users/nbedelman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nbedelman/subscriptions","organizations_url":"https://api.github.com/users/nbedelman/orgs","repos_url":"https://api.github.com/users/nbedelman/repos","events_url":"https://api.github.com/users/nbedelman/events{/privacy}","received_events_url":"https://api.github.com/users/nbedelman/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2018-07-09T15:14:33Z","updated_at":"2018-07-12T19:42:18Z","closed_at":null,"author_association":"NONE","body":"I just got the following error during the hgmDriverTask part of the pipeline:\r\n\r\n> ERROR: [pid 32423] Worker Worker(salt=829794966, workers=400, host=holy2a09304.rc.fas.harvard.edu, username=nedelman, pid=29363) failed    Task: HgmDriverTask for transMap\r\n> Traceback (most recent call last):\r\n>   File \"/n/home09/nedelman/.conda/envs/CAT/lib/python2.7/site-packages/luigi/worker.py\", line 194, in run\r\n>     new_deps = self._run_get_new_deps()\r\n>   File \"/n/home09/nedelman/.conda/envs/CAT/lib/python2.7/site-packages/luigi/worker.py\", line 131, in _run_get_new_deps\r\n>     task_gen = self.task.run()\r\n>   File \"/n/mallet_lab/edelman/software/Comparative-Annotation-Toolkit/cat/__init__.py\", line 1725, in run\r\n>     df = parse_hgm_gtf(hgm_args.gtf_out_files[genome], genome)\r\n>   File \"/n/mallet_lab/edelman/software/Comparative-Annotation-Toolkit/cat/hgm.py\", line 227, in parse_hgm_gtf\r\n>     with open(hgm_out) as infile:\r\n> IOError: [Errno 2] No such file or directory: '/n/regal/mallet_lab/edelman/18Genomes/results/annotation/heliconiiniAlignment/cat_work/hgm/transMap/Dryas_iulia_helico3.gtf'\r\n\r\nThe directory `cat_work/hgm/transMap/` is  empty, but the file `Dryas_iulia_helico3.gtf` does exist in the directory `cat_work/transMap`. Would it work to just copy the files in `cat_work/transMap` to `cat_work/hgm/transMap/` ? Similarly, the directory `cat_work/hgm/augTM` is empty, but there are many files in `cat_work/augustus` that have augTM in their filename. Should I copy those over as well?\r\nThanks!"},"comment":{"url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/comments/404628019","html_url":"https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/102#issuecomment-404628019","issue_url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/102","id":404628019,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNDYyODAxOQ==","user":{"login":"nbedelman","id":13751276,"node_id":"MDQ6VXNlcjEzNzUxMjc2","avatar_url":"https://avatars3.githubusercontent.com/u/13751276?v=4","gravatar_id":"","url":"https://api.github.com/users/nbedelman","html_url":"https://github.com/nbedelman","followers_url":"https://api.github.com/users/nbedelman/followers","following_url":"https://api.github.com/users/nbedelman/following{/other_user}","gists_url":"https://api.github.com/users/nbedelman/gists{/gist_id}","starred_url":"https://api.github.com/users/nbedelman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nbedelman/subscriptions","organizations_url":"https://api.github.com/users/nbedelman/orgs","repos_url":"https://api.github.com/users/nbedelman/repos","events_url":"https://api.github.com/users/nbedelman/events{/privacy}","received_events_url":"https://api.github.com/users/nbedelman/received_events","type":"User","site_admin":false},"created_at":"2018-07-12T19:42:18Z","updated_at":"2018-07-12T19:42:18Z","author_association":"NONE","body":"weird, this time we just get\r\n\r\n`Traceback (most recent call last):\r\n  File \"/n/home09/nedelman/.conda/envs/CAT/lib/python2.7/site-packages/luigi/worker.py\", line 194, in run\r\n    new_deps = self._run_get_new_deps()\r\n  File \"/n/home09/nedelman/.conda/envs/CAT/lib/python2.7/site-packages/luigi/worker.py\", line 131, in _run_get_new_deps\r\n    task_gen = self.task.run()\r\n  File \"/n/mallet_lab/edelman/software/Comparative-Annotation-Toolkit/cat/__init__.py\", line 1725, in run\r\n    df = parse_hgm_gtf(hgm_args.gtf_out_files[genome], genome)\r\n  File \"/n/mallet_lab/edelman/software/Comparative-Annotation-Toolkit/cat/hgm.py\", line 238, in parse_hgm_gtf\r\n    with open(hgm_out) as infile:\r\nIOError: [Errno 2] No such file or directory: '/n/regal/mallet_lab/edelman/18Genomes/results/annotation/heliconiiniAlignment/cat_work/hgm/transMap/Dryas_iulia_helico3.gtf'`\r\n\r\nThe only file in `/n/regal/mallet_lab/edelman/18Genomes/results/annotation/heliconiiniAlignment/cat_work/hgm/transMap/ ` is one called fofn, attached here.\r\n\r\n\r\n[fofn.txt](https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/files/2190051/fofn.txt)\r\n"}}
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