{"action":"created","issue":{"url":"https://api.github.com/repos/lucventurini/mikado/issues/117","repository_url":"https://api.github.com/repos/lucventurini/mikado","labels_url":"https://api.github.com/repos/lucventurini/mikado/issues/117/labels{/name}","comments_url":"https://api.github.com/repos/lucventurini/mikado/issues/117/comments","events_url":"https://api.github.com/repos/lucventurini/mikado/issues/117/events","html_url":"https://github.com/lucventurini/mikado/issues/117","id":318426924,"number":117,"title":"errors in prepare.log","user":{"login":"uncleflybfchen","id":38780054,"avatar_url":"https://avatars3.githubusercontent.com/u/38780054?v=4","gravatar_id":"","url":"https://api.github.com/users/uncleflybfchen","html_url":"https://github.com/uncleflybfchen","followers_url":"https://api.github.com/users/uncleflybfchen/followers","following_url":"https://api.github.com/users/uncleflybfchen/following{/other_user}","gists_url":"https://api.github.com/users/uncleflybfchen/gists{/gist_id}","starred_url":"https://api.github.com/users/uncleflybfchen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/uncleflybfchen/subscriptions","organizations_url":"https://api.github.com/users/uncleflybfchen/orgs","repos_url":"https://api.github.com/users/uncleflybfchen/repos","events_url":"https://api.github.com/users/uncleflybfchen/events{/privacy}","received_events_url":"https://api.github.com/users/uncleflybfchen/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-04-27T14:17:51Z","updated_at":"2018-05-11T02:36:23Z","closed_at":null,"author_association":"NONE","body":"Many thanks for providing Mikado software.\r\n\r\nI am using Mikado in our _de novo_ assembly project. I got the following error messages in prepare.log when running the mikado prepare steps. \r\n\r\n```\r\n2018-04-27 15:10:10,358 - prepare - checking.py:91 - ERROR - create_transcript - MainProcess -\r\nTraceback (most recent call last):\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/Mikado/preparation/checking.py\", line 78, in create_transcript\r\n    transcript_object.check_strand()\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/Mikado/transcripts/transcriptchecker.py\", line 159, in check_strand\r\n    assert self.exons[-1][1] - self.start + 1 == len(self.fasta_seq)\r\nAssertionError\r\n2018-04-27 15:10:10,360 - prepare - checking.py:91 - ERROR - create_transcript - MainProcess -\r\nTraceback (most recent call last):\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/Mikado/preparation/checking.py\", line 78, in create_transcript\r\n    transcript_object.check_strand()\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/Mikado/transcripts/transcriptchecker.py\", line 159, in check_strand\r\n    assert self.exons[-1][1] - self.start + 1 == len(self.fasta_seq)\r\nAssertionError\r\n2018-04-27 15:10:10,362 - prepare - checking.py:91 - ERROR - create_transcript - MainProcess -\r\nTraceback (most recent call last):\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/Mikado/preparation/checking.py\", line 78, in create_transcript\r\n    transcript_object.check_strand()\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/Mikado/transcripts/transcriptchecker.py\", line 159, in check_strand\r\n    assert self.exons[-1][1] - self.start + 1 == len(self.fasta_seq)\r\nAssertionError\r\n2018-04-27 15:10:10,363 - prepare - checking.py:91 - ERROR - create_transcript - MainProcess -\r\nTraceback (most recent call last):\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/Mikado/preparation/checking.py\", line 78, in create_transcript\r\n    transcript_object.check_strand()\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/Mikado/transcripts/transcriptchecker.py\", line 159, in check_strand\r\n    assert self.exons[-1][1] - self.start + 1 == len(self.fasta_seq)\r\nAssertionError\r\n2018-04-27 15:10:10,365 - prepare - checking.py:91 - ERROR - create_transcript - MainProcess -\r\nTraceback (most recent call last):\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/Mikado/preparation/checking.py\", line 78, in create_transcript\r\n    transcript_object.check_strand()\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/Mikado/transcripts/transcriptchecker.py\", line 159, in check_strand\r\n    assert self.exons[-1][1] - self.start + 1 == len(self.fasta_seq)\r\nAssertionError\r\n2018-04-27 15:10:10,378 - prepare - checking.py:91 - ERROR - create_transcript - MainProcess -\r\nTraceback (most recent call last):\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/Mikado/preparation/checking.py\", line 78, in create_transcript\r\n    transcript_object.check_strand()\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/Mikado/transcripts/transcriptchecker.py\", line 159, in check_strand\r\n    assert self.exons[-1][1] - self.start + 1 == len(self.fasta_seq)\r\nAssertionError\r\n\r\n```\r\n```\r\n2018-04-27 15:15:06,820 - prepare - checking.py:91 - ERROR - create_transcript - MainProcess -\r\nTraceback (most recent call last):\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/Mikado/preparation/checking.py\", line 78, in create_transcript\r\n    transcript_object.check_strand()\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/Mikado/transcripts/transcriptchecker.py\", line 159, in check_strand\r\n    assert self.exons[-1][1] - self.start + 1 == len(self.fasta_seq)\r\nAssertionError\r\n\r\n```\r\n```\r\n2018-04-27 15:15:54,844 - prepare - prepare.py:435 - ERROR - prepare - MainProcess - Coordinates (Sequence.start=437 and Sequence.end=436) imply a different length than Sequence.seq (len=0). Did you modify Sequence.seq?\r\nTraceback (most recent call last):\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/Mikado/preparation/prepare.py\", line 433, in prepare\r\n    perform_check(sorter(shelf_stacks), shelf_stacks, args, logger)\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/Mikado/preparation/prepare.py\", line 163, in perform_check\r\n    str(args.json_conf[\"reference\"][\"genome\"][chrom][key[0]-1:key[1]]),\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/pyfaidx/__init__.py\", line 784, in __getitem__\r\n    return self._fa.get_seq(self.name, start + 1, stop)[::step]\r\n  File \"/home/bfc/.local/lib/python3.5/site-packages/pyfaidx/__init__.py\", line 135, in __getitem__\r\n    % (self.start, self.end, len(self.seq)))\r\nValueError: Coordinates (Sequence.start=437 and Sequence.end=436) imply a different length than Sequence.seq (len=0). Did you modify Sequence.seq?\r\n2018-04-27 15:15:54,856 - prepare - prepare.py:437 - ERROR - prepare - MainProcess - Mikado has encountered an error, exiting\r\n2018-04-27 15:15:55,044 - prepare - prepare.py:447 - INFO - prepare - MainProcess - Finished\r\n\r\n```\r\n\r\n- Are these errors related to my environments?\r\n- How can I fix these errors?\r\n- Although some errors occured, I still got two files, mikado_prepared.fasta and mikado_prepared.gtf. Can I still use these two files in the following steps?\r\n\r\nThanks a lot\r\n"},"comment":{"url":"https://api.github.com/repos/lucventurini/mikado/issues/comments/388242250","html_url":"https://github.com/lucventurini/mikado/issues/117#issuecomment-388242250","issue_url":"https://api.github.com/repos/lucventurini/mikado/issues/117","id":388242250,"user":{"login":"lucventurini","id":8897821,"avatar_url":"https://avatars0.githubusercontent.com/u/8897821?v=4","gravatar_id":"","url":"https://api.github.com/users/lucventurini","html_url":"https://github.com/lucventurini","followers_url":"https://api.github.com/users/lucventurini/followers","following_url":"https://api.github.com/users/lucventurini/following{/other_user}","gists_url":"https://api.github.com/users/lucventurini/gists{/gist_id}","starred_url":"https://api.github.com/users/lucventurini/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lucventurini/subscriptions","organizations_url":"https://api.github.com/users/lucventurini/orgs","repos_url":"https://api.github.com/users/lucventurini/repos","events_url":"https://api.github.com/users/lucventurini/events{/privacy}","received_events_url":"https://api.github.com/users/lucventurini/received_events","type":"User","site_admin":false},"created_at":"2018-05-11T02:36:23Z","updated_at":"2018-05-11T02:36:23Z","author_association":"OWNER","body":"Dear @uncleflybfchen,\r\n                                     many apologies for the late reply.\r\nYou have two different errors here:\r\n- In the first case, Mikado is complaining that the length of the FASTA sequence is different from the expected length of the DNA fragment. This is bizarre, and I cannot fathom the origin of the mistake like this. I will try to make the error message more informative.\r\n- In the second case, Mikado is complaining that some transcripts have at least one exon with an expected length of 0 base pairs. This is, of course, invalid, and throws Mikado again into an error.\r\n\r\nI would not trust the mikado_prepared files, as they are most probably corrupt and/or incomplete. I have just released a new version of Mikado, which unfortunately does not take care of the issue. I can, however, modify the code in the development branch so that it will sidestep the issue and report something more informative. I will let you know when it is ready.\r\n"}}
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