{"action":"created","issue":{"url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/174","repository_url":"https://api.github.com/repos/davidemms/OrthoFinder","labels_url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/174/labels{/name}","comments_url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/174/comments","events_url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/174/events","html_url":"https://github.com/davidemms/OrthoFinder/issues/174","id":333705060,"node_id":"MDU6SXNzdWUzMzM3MDUwNjA=","number":174,"title":"add species fails after blast searches complete: duplicate sequence ID","user":{"login":"l-yampolsky","id":8876981,"node_id":"MDQ6VXNlcjg4NzY5ODE=","avatar_url":"https://avatars2.githubusercontent.com/u/8876981?v=4","gravatar_id":"","url":"https://api.github.com/users/l-yampolsky","html_url":"https://github.com/l-yampolsky","followers_url":"https://api.github.com/users/l-yampolsky/followers","following_url":"https://api.github.com/users/l-yampolsky/following{/other_user}","gists_url":"https://api.github.com/users/l-yampolsky/gists{/gist_id}","starred_url":"https://api.github.com/users/l-yampolsky/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/l-yampolsky/subscriptions","organizations_url":"https://api.github.com/users/l-yampolsky/orgs","repos_url":"https://api.github.com/users/l-yampolsky/repos","events_url":"https://api.github.com/users/l-yampolsky/events{/privacy}","received_events_url":"https://api.github.com/users/l-yampolsky/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-06-19T14:45:38Z","updated_at":"2018-06-27T08:42:57Z","closed_at":null,"author_association":"NONE","body":"Updated version of the issue:\r\n\r\nI am still having trouble running OF by dropping / adding species to previously completed analysis.\r\n\r\nBlast searches completed successfully. So now I am starting it with -b option. And get the following:\r\n\r\nERROR: /WorkingDirectory/SequenceIDs.txt contains a duplicate ID. The IDs for the orthogroups in /WorkingDirectory/clusters_OrthoFinder_v2.2.0_I1.5_2.txt_id_pairs.txt will not be replaced with the sequence accessions. If /WorkingDirectory/SequenceIDs.txt was prepared manually then please check the IDs are correct. \r\nERROR: An error occurred, please review error messages for more information.\r\n2018-06-19 19:42:46 : Written final scores for species 6 to graph file\r\n2018-06-19 19:42:47 : Written final scores for species 0 to graph file\r\n2018-06-19 19:42:48 : Written final scores for species 7 to graph file\r\n2018-06-19 19:42:49 : Written final scores for species 2 to graph file\r\n2018-06-19 19:42:49 : Written final scores for species 1 to graph file\r\n\r\nOn a couple of runs it proceeds to various steps of writing to graph file, but then invariably dies.\r\n\r\nAgain, would be very grateful for suggestions of what may be going wrong.\r\n\r\nLev Yampolsky\r\n"},"comment":{"url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/comments/400591587","html_url":"https://github.com/davidemms/OrthoFinder/issues/174#issuecomment-400591587","issue_url":"https://api.github.com/repos/davidemms/OrthoFinder/issues/174","id":400591587,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMDU5MTU4Nw==","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":"2018-06-27T08:42:57Z","updated_at":"2018-06-27T08:42:57Z","author_association":"OWNER","body":"Hi\r\n\r\nIt sounds like you probably didn't revert the files to their previous state. Judging from the error message, perhaps there was a newline at the end of the file?"}}
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