{"action":"created","issue":{"url":"https://api.github.com/repos/cancerit/BRASS/issues/73","repository_url":"https://api.github.com/repos/cancerit/BRASS","labels_url":"https://api.github.com/repos/cancerit/BRASS/issues/73/labels{/name}","comments_url":"https://api.github.com/repos/cancerit/BRASS/issues/73/comments","events_url":"https://api.github.com/repos/cancerit/BRASS/issues/73/events","html_url":"https://github.com/cancerit/BRASS/issues/73","id":349428910,"node_id":"MDU6SXNzdWUzNDk0Mjg5MTA=","number":73,"title":"Brass produces output but returns code 255","user":{"login":"edawson","id":2595153,"node_id":"MDQ6VXNlcjI1OTUxNTM=","avatar_url":"https://avatars2.githubusercontent.com/u/2595153?v=4","gravatar_id":"","url":"https://api.github.com/users/edawson","html_url":"https://github.com/edawson","followers_url":"https://api.github.com/users/edawson/followers","following_url":"https://api.github.com/users/edawson/following{/other_user}","gists_url":"https://api.github.com/users/edawson/gists{/gist_id}","starred_url":"https://api.github.com/users/edawson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/edawson/subscriptions","organizations_url":"https://api.github.com/users/edawson/orgs","repos_url":"https://api.github.com/users/edawson/repos","events_url":"https://api.github.com/users/edawson/events{/privacy}","received_events_url":"https://api.github.com/users/edawson/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":8,"created_at":"2018-08-10T08:49:31Z","updated_at":"2018-10-12T12:50:55Z","closed_at":null,"author_association":"NONE","body":"I ran brass.pl on the hcc test data provided [here](https://github.com/ohsu-comp-bio/wdl-pcawg-sanger-cgp-workflow) and the CGP bundle for BRASS >= v6. I get the following files back:\r\n\r\n    HCC1143.insert_size_distr \r\n    HCC1143_vs_HCC1143_BL.inversions.pdf\r\n    HCC1143_vs_HCC1143_BL.r2\r\n    HCC1143_vs_HCC1143_BL.groups\r\n    HCC1143_vs_HCC1143_BL.is_fb_artefact.txt\r\n    HCC1143_vs_HCC1143_BL.r3\r\n    HCC1143_vs_HCC1143_BL.groups.filtered.bedpe\r\n    HCC1143_vs_HCC1143_BL.ngscn.abs_cn.bg\r\n    HCC1143_vs_HCC1143_BL.r4\r\n    HCC1143_vs_HCC1143_BL.groups.filtered.bedpe.preclean\r\n    HCC1143_vs_HCC1143_BL.ngscn.diagnostic_plots.pdf  tmpBrass\r\n    HCC1143_vs_HCC1143_BL.groups.filtered.bedpenohead\r\n    HCC1143_vs_HCC1143_BL.ngscn.segments.abs_cn.bg\r\n\r\nbut the return code that gets sent to the workflow engine is 255, indicating some sort of failure.\r\n\r\nAre there any docs I missed on the correct full set of outputs? I'm having trouble debugging what failed because there's no stdout/stderr output."},"comment":{"url":"https://api.github.com/repos/cancerit/BRASS/issues/comments/429314553","html_url":"https://github.com/cancerit/BRASS/issues/73#issuecomment-429314553","issue_url":"https://api.github.com/repos/cancerit/BRASS/issues/73","id":429314553,"node_id":"MDEyOklzc3VlQ29tbWVudDQyOTMxNDU1Mw==","user":{"login":"sb43","id":8640169,"node_id":"MDQ6VXNlcjg2NDAxNjk=","avatar_url":"https://avatars1.githubusercontent.com/u/8640169?v=4","gravatar_id":"","url":"https://api.github.com/users/sb43","html_url":"https://github.com/sb43","followers_url":"https://api.github.com/users/sb43/followers","following_url":"https://api.github.com/users/sb43/following{/other_user}","gists_url":"https://api.github.com/users/sb43/gists{/gist_id}","starred_url":"https://api.github.com/users/sb43/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sb43/subscriptions","organizations_url":"https://api.github.com/users/sb43/orgs","repos_url":"https://api.github.com/users/sb43/repos","events_url":"https://api.github.com/users/sb43/events{/privacy}","received_events_url":"https://api.github.com/users/sb43/received_events","type":"User","site_admin":false},"created_at":"2018-10-12T12:50:55Z","updated_at":"2018-10-12T12:50:55Z","author_association":"MEMBER","body":"Added UNLINK=>0 if --noclean flag is set"}}
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