{"action":"created","issue":{"url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/151","repository_url":"https://api.github.com/repos/davidemms/OrthoFinder","labels_url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/151/labels{/name}","comments_url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/151/comments","events_url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/151/events","html_url":"https://github.com/davidemms/OrthoFinder/issues/151","id":311171175,"number":151,"title":"Failed to execute script orthofinder","user":{"login":"sejmodha","id":6159960,"avatar_url":"https://avatars0.githubusercontent.com/u/6159960?v=4","gravatar_id":"","url":"https://api.github.com/users/sejmodha","html_url":"https://github.com/sejmodha","followers_url":"https://api.github.com/users/sejmodha/followers","following_url":"https://api.github.com/users/sejmodha/following{/other_user}","gists_url":"https://api.github.com/users/sejmodha/gists{/gist_id}","starred_url":"https://api.github.com/users/sejmodha/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sejmodha/subscriptions","organizations_url":"https://api.github.com/users/sejmodha/orgs","repos_url":"https://api.github.com/users/sejmodha/repos","events_url":"https://api.github.com/users/sejmodha/events{/privacy}","received_events_url":"https://api.github.com/users/sejmodha/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2018-04-04T10:23:49Z","updated_at":"2018-04-23T23:28:58Z","closed_at":null,"author_association":"NONE","body":"Hi There,\r\n\r\nI get the following error with ExampleData with OrthoFinder 2.2.1\r\n\r\n```\r\n\r\nOrthoFinder version 2.2.1 Copyright (C) 2014 David Emms\r\n\r\n16 thread(s) for highly parallel tasks (BLAST searches etc.)\r\n1 thread(s) for OrthoFinder algorithm\r\n\r\nChecking required programs are installed\r\n----------------------------------------\r\nTest can run \"makeblastdb -help\" - ok\r\nTest can run \"blastp -help\" - ok\r\nTest can run \"mcl -h\" - ok\r\nTest can run \"fastme -i /home/software/OrthoFinder-2.2.1/ExampleData/SimpleTest.phy -o /home/software/OrthoFinder-2.2.1/ExampleData/SimpleTest.tre\" - ok\r\n\r\nDividing up work for BLAST for parallel processing\r\n--------------------------------------------------\r\n2018-04-04 11:17:22 : Creating Blast database 1 of 4\r\n2018-04-04 11:17:22 : Creating Blast database 2 of 4\r\n2018-04-04 11:17:22 : Creating Blast database 3 of 4\r\n2018-04-04 11:17:22 : Creating Blast database 4 of 4\r\n\r\nRunning BLAST all-versus-all\r\n----------------------------\r\nUsing 16 thread(s)\r\n2018-04-04 11:17:22 : This may take some time....\r\n2018-04-04 11:17:22 : Done 0 of 16\r\n\r\nRunning OrthoFinder algorithm\r\n-----------------------------\r\n2018-04-04 11:17:43 : Initial processing of each species\r\n2018-04-04 11:17:44 : Initial processing of species 0 complete\r\n2018-04-04 11:17:44 : Initial processing of species 1 complete\r\n2018-04-04 11:17:44 : Initial processing of species 2 complete\r\n2018-04-04 11:17:45 : Initial processing of species 3 complete\r\n2018-04-04 11:17:49 : Connected putatitive homologs\r\n2018-04-04 11:17:49 : Written final scores for species 0 to graph file\r\n2018-04-04 11:17:50 : Written final scores for species 1 to graph file\r\n2018-04-04 11:17:50 : Written final scores for species 2 to graph file\r\n2018-04-04 11:17:50 : Written final scores for species 3 to graph file\r\n2018-04-04 11:17:50 : Ran MCL\r\n\r\nWriting orthogroups to file\r\n---------------------------\r\nOrthogroups have been written to tab-delimited files:\r\n   /home/software/OrthoFinder-2.2.1/ExampleData/Results_Apr04/Orthogroups.csv\r\n   /home/software/OrthoFinder-2.2.1/ExampleData/Results_Apr04/Orthogroups.txt (OrthoMCL format)\r\n   /home/software/OrthoFinder-2.2.1/ExampleData/Results_Apr04/Orthogroups_UnassignedGenes.csv\r\n2018-04-04 11:17:50 : Done orthogroups\r\n\r\nAnalysing Orthogroups\r\n=====================\r\n\r\nCalculating gene distances\r\n--------------------------\r\n2018-04-04 11:17:53 : Done\r\n\r\nInferring gene and species trees\r\n--------------------------------\r\n2018-04-04 11:17:57 : Done 0 of 314\r\n2018-04-04 11:17:57 : Done 100 of 314\r\n2018-04-04 11:17:57 : Done 200 of 314\r\n2018-04-04 11:17:58 : Done 300 of 314\r\n\r\n280 trees had all species present and will be used by STAG to infer the species tree\r\n\r\nERROR: No trees found in directory\r\nTraceback (most recent call last):\r\n  File \"orthofinder/orthofinder.py\", line 1549, in <module>\r\n  File \"orthofinder/orthofinder.py\", line 1398, in GetOrthologues\r\n  File \"orthofinder/scripts/orthologues.py\", line 996, in OrthologuesWorkflow\r\n  File \"orthofinder/scripts/orthologues.py\", line 447, in RunAnalysis\r\n  File \"orthofinder/scripts/stag.py\", line 252, in Run_ForOrthoFinder\r\n  File \"orthofinder/scripts/stag.py\", line 237, in InferSpeciesTree\r\n  File \"orthofinder/scripts/consensus_tree.py\", line 249, in ConsensusTree\r\n  File \"orthofinder/scripts/consensus_tree.py\", line 152, in GetAllSplits\r\nException\r\nFailed to execute script orthofinder\r\n```"},"comment":{"url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/comments/383754339","html_url":"https://github.com/davidemms/OrthoFinder/issues/151#issuecomment-383754339","issue_url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/151","id":383754339,"user":{"login":"caonetto","id":25968988,"avatar_url":"https://avatars3.githubusercontent.com/u/25968988?v=4","gravatar_id":"","url":"https://api.github.com/users/caonetto","html_url":"https://github.com/caonetto","followers_url":"https://api.github.com/users/caonetto/followers","following_url":"https://api.github.com/users/caonetto/following{/other_user}","gists_url":"https://api.github.com/users/caonetto/gists{/gist_id}","starred_url":"https://api.github.com/users/caonetto/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/caonetto/subscriptions","organizations_url":"https://api.github.com/users/caonetto/orgs","repos_url":"https://api.github.com/users/caonetto/repos","events_url":"https://api.github.com/users/caonetto/events{/privacy}","received_events_url":"https://api.github.com/users/caonetto/received_events","type":"User","site_admin":false},"created_at":"2018-04-23T23:28:58Z","updated_at":"2018-04-23T23:28:58Z","author_association":"NONE","body":"Thanks Rebecca,\r\nYes, I am having the same issue, my output is the same as Rebecca with four folders, Distances_SpeciesTree, s_ids, SpeciesTrees_ids , Trees_ids and Distances, however my  Distances_SpeciesTree, s_ids has files in it.\r\n\r\nAny ideas?\r\n\r\nthanks,\r\n\r\nCris"}}
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