{"action":"created","issue":{"url":"https://api.github.com/repos/ding-lab/MuSiC2/issues/5","repository_url":"https://api.github.com/repos/ding-lab/MuSiC2","labels_url":"https://api.github.com/repos/ding-lab/MuSiC2/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/ding-lab/MuSiC2/issues/5/comments","events_url":"https://api.github.com/repos/ding-lab/MuSiC2/issues/5/events","html_url":"https://github.com/ding-lab/MuSiC2/issues/5","id":187644283,"number":5,"title":"Command music2 bmr calc-covg fails","user":{"login":"kjnousia","id":22838472,"avatar_url":"https://avatars.githubusercontent.com/u/22838472?v=3","gravatar_id":"","url":"https://api.github.com/users/kjnousia","html_url":"https://github.com/kjnousia","followers_url":"https://api.github.com/users/kjnousia/followers","following_url":"https://api.github.com/users/kjnousia/following{/other_user}","gists_url":"https://api.github.com/users/kjnousia/gists{/gist_id}","starred_url":"https://api.github.com/users/kjnousia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kjnousia/subscriptions","organizations_url":"https://api.github.com/users/kjnousia/orgs","repos_url":"https://api.github.com/users/kjnousia/repos","events_url":"https://api.github.com/users/kjnousia/events{/privacy}","received_events_url":"https://api.github.com/users/kjnousia/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-11-07T07:42:05Z","updated_at":"2016-12-02T21:48:41Z","closed_at":null,"body":"The command requires optional argument \"cmd-list-file\" and the argument is given the resulted script is not run. The error message:\r\n... not found in ../Data/Music/covG/output/roi_covgs. please make a command list file to run calcRoiCovg !"},"comment":{"url":"https://api.github.com/repos/ding-lab/MuSiC2/issues/comments/264571614","html_url":"https://github.com/ding-lab/MuSiC2/issues/5#issuecomment-264571614","issue_url":"https://api.github.com/repos/ding-lab/MuSiC2/issues/5","id":264571614,"user":{"login":"MHBailey","id":8783135,"avatar_url":"https://avatars.githubusercontent.com/u/8783135?v=3","gravatar_id":"","url":"https://api.github.com/users/MHBailey","html_url":"https://github.com/MHBailey","followers_url":"https://api.github.com/users/MHBailey/followers","following_url":"https://api.github.com/users/MHBailey/following{/other_user}","gists_url":"https://api.github.com/users/MHBailey/gists{/gist_id}","starred_url":"https://api.github.com/users/MHBailey/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MHBailey/subscriptions","organizations_url":"https://api.github.com/users/MHBailey/orgs","repos_url":"https://api.github.com/users/MHBailey/repos","events_url":"https://api.github.com/users/MHBailey/events{/privacy}","received_events_url":"https://api.github.com/users/MHBailey/received_events","type":"User","site_admin":false},"created_at":"2016-12-02T21:48:41Z","updated_at":"2016-12-02T21:48:41Z","body":"Sorry for the delay. \r\n\r\nI would check on two different aspects.\r\n1) Make sure that you normal-tumor pairs are tab delimited. \r\ne.g. --normal-tumor-bam-pair=\"ID<\\t>normal.bam<\\t>tumor.bam\"\r\n\r\nOr you could start with a command similar to this. (This should generate a cmd_list_file for you)\r\n2)music2 bmr calc-covg --bam-list <your-file-name> --output-dir . --reference-sequence refseq.fa --roi-file roi_file --cmd-prefix <your system prefix. (e.g. if LSF then you'd put bsub)> --cmd-list-file cmd_list_file\r\n\r\n\r\n\r\n\r\n"}}
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