{"action":"created","issue":{"url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/145","repository_url":"https://api.github.com/repos/davidemms/OrthoFinder","labels_url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/145/labels{/name}","comments_url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/145/comments","events_url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/145/events","html_url":"https://github.com/davidemms/OrthoFinder/issues/145","id":308586440,"number":145,"title":"orthofinder \"freezes\" within the first minute of run, when using many species","user":{"login":"assafwww","id":16415223,"avatar_url":"https://avatars3.githubusercontent.com/u/16415223?v=4","gravatar_id":"","url":"https://api.github.com/users/assafwww","html_url":"https://github.com/assafwww","followers_url":"https://api.github.com/users/assafwww/followers","following_url":"https://api.github.com/users/assafwww/following{/other_user}","gists_url":"https://api.github.com/users/assafwww/gists{/gist_id}","starred_url":"https://api.github.com/users/assafwww/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/assafwww/subscriptions","organizations_url":"https://api.github.com/users/assafwww/orgs","repos_url":"https://api.github.com/users/assafwww/repos","events_url":"https://api.github.com/users/assafwww/events{/privacy}","received_events_url":"https://api.github.com/users/assafwww/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-03-26T14:04:20Z","updated_at":"2018-04-27T14:56:57Z","closed_at":null,"author_association":"NONE","body":"Dear Orthofinder developers,\r\n\r\nI'm encountering a problem when running Orthofinder with more than few fasta files.\r\nBasically, within the first minute of run, orthofinder creates in workingDirectory:\r\n* blast databases (BlastDBSpecies*.* files)\r\n* SpeciesIDs.txt , SequenceIDs.txt\r\n* species*.fa fasta files\r\nBut then it does not proceed to the next step (running blast, and producing Blast*_*.txt files).\r\nIn my case the problem happens with 14 species, but the program seems to complete fine with 4 species (giving all expected files and dirs, and completing apparently without any errors).\r\n\r\nI'm using a slurm cloud, and call the program as so:\r\n```\r\n\r\nsbatch -N1 -n56 --ntasks-per-node=56 --mem=760000 -p q \\\r\n\t-o $dirIn/out.out -e $dirIn/err.err \\\r\n\t--wrap \"python $orthofinder -f \\\"$dirIn\" -t 56\"\r\n```\r\n\r\nthanks in advance,\r\nAssaf\r\n"},"comment":{"url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/comments/384995710","html_url":"https://github.com/davidemms/OrthoFinder/issues/145#issuecomment-384995710","issue_url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/145","id":384995710,"user":{"login":"davidemms","id":13098041,"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":"2018-04-27T14:56:57Z","updated_at":"2018-04-27T14:56:57Z","author_association":"OWNER","body":"Hi Assaf\r\n\r\nHave you got any further information on this? It would be helpful to see the OrthoFinder output printed to screen for this (I think slurm puts this in a file). Did the system administrator have any extra information? Would you be able to find out if any processes are running after it appears to halt? \r\n\r\nAlso, could you try it with the latest version of OrthoFinder. OrthoFinder creates some worker processes at the beginning (it reduces the memory usage caused by process forking which is important for large analyses). These processes need to be terminated correctly at the end of a run. It could be that the run failed but that these processes weren't terminated causing it to hanf=g. This should be resolved in the latest version.\r\n\r\nThanks\r\nDavid "}}
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