{"action":"created","issue":{"url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/216","repository_url":"https://api.github.com/repos/davidemms/OrthoFinder","labels_url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/216/labels{/name}","comments_url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/216/comments","events_url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/216/events","html_url":"https://github.com/davidemms/OrthoFinder/issues/216","id":377307578,"node_id":"MDU6SXNzdWUzNzczMDc1Nzg=","number":216,"title":"\"IOError: [Errno 2] No such file or directory:\" while it does exist ","user":{"login":"ESDeutekom","id":39910765,"node_id":"MDQ6VXNlcjM5OTEwNzY1","avatar_url":"https://avatars3.githubusercontent.com/u/39910765?v=4","gravatar_id":"","url":"https://api.github.com/users/ESDeutekom","html_url":"https://github.com/ESDeutekom","followers_url":"https://api.github.com/users/ESDeutekom/followers","following_url":"https://api.github.com/users/ESDeutekom/following{/other_user}","gists_url":"https://api.github.com/users/ESDeutekom/gists{/gist_id}","starred_url":"https://api.github.com/users/ESDeutekom/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ESDeutekom/subscriptions","organizations_url":"https://api.github.com/users/ESDeutekom/orgs","repos_url":"https://api.github.com/users/ESDeutekom/repos","events_url":"https://api.github.com/users/ESDeutekom/events{/privacy}","received_events_url":"https://api.github.com/users/ESDeutekom/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-11-05T09:08:36Z","updated_at":"2018-11-06T10:48:01Z","closed_at":null,"author_association":"NONE","body":"Hi, \r\nI ran into a problem using Orthofinder  (v2.2.6) on a big dataset of 165 species with precomputed blast results (in the format orthofinder wants using the -op option). During the initial processing of the species, species 125 runs into problems and stops Orthofinder, with the error the file does not exist. I checked and it does exist. \r\n \r\nProcess Process-2:\r\nTraceback (most recent call last):\r\n  File \"multiprocessing/process.py\", line 258, in _bootstrap\r\n  File \"multiprocessing/process.py\", line 114, in run\r\n  File \"orthofinder/orthofinder.py\", line 484, in Worker_ProcessBlastHits\r\n  File \"orthofinder/orthofinder.py\", line 471, in ProcessBlastHits\r\n  File \"orthofinder/scripts/blast_file_processor.py\", line 61, in GetBLAST6Scores\r\nIOError: [Errno 2] No such file or directory:\"/home/myfilepath/\"\r\n\r\nFor the species before, B*.pic and BH*.pic files are generated. I ran orthofinder on two species from my set, to check if it ran through completely, and it does.\r\n\r\nIs there a way to rerun orthofinder from its last point (species 125) or do I have to redo all of that? It took a while.\r\nAnd what could the problem be? \r\nKind regards and thank you in advance, \r\n"},"comment":{"url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/comments/436210646","html_url":"https://github.com/davidemms/OrthoFinder/issues/216#issuecomment-436210646","issue_url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/216","id":436210646,"node_id":"MDEyOklzc3VlQ29tbWVudDQzNjIxMDY0Ng==","user":{"login":"davidemms","id":13098041,"node_id":"MDQ6VXNlcjEzMDk4MDQx","avatar_url":"https://avatars2.githubusercontent.com/u/13098041?v=4","gravatar_id":"","url":"https://api.github.com/users/davidemms","html_url":"https://github.com/davidemms","followers_url":"https://api.github.com/users/davidemms/followers","following_url":"https://api.github.com/users/davidemms/following{/other_user}","gists_url":"https://api.github.com/users/davidemms/gists{/gist_id}","starred_url":"https://api.github.com/users/davidemms/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidemms/subscriptions","organizations_url":"https://api.github.com/users/davidemms/orgs","repos_url":"https://api.github.com/users/davidemms/repos","events_url":"https://api.github.com/users/davidemms/events{/privacy}","received_events_url":"https://api.github.com/users/davidemms/received_events","type":"User","site_admin":false},"created_at":"2018-11-06T10:48:01Z","updated_at":"2018-11-06T10:48:01Z","author_association":"OWNER","body":"Hi\r\n\r\nUnfortunately you'll need to start again from the BLAST results. It will just overwrite the .pic files so you don't have to worry about them. \r\n\r\nProbably the best thing to try is a test of the problem file first. Comment out all the species in the SpeciesIDs.txt file with a '#' except for 125, 17 and two other species and run OrthoFinder on that reduced dataset. It will be pretty quick and would let you know if it was a temporary or a real issue with the Blast125_17.txt file. If that runs successfully then re-include all the species and run it on the full dataset. You can keep things a bit tidier by deleting all the new files produced by the test run (OrthoFinder_v2.2.7_graph.txt, clusters*, Orthogroups*, Statistics* etc) before starting the full run.\r\n\r\nAll the best\r\nDavid"}}
{"actor":{"display_login":"davidemms"}}