{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1299","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1299/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1299/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1299/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1299","id":145175565,"number":1299,"title":"Coverage calculation for the report fails with file not found","user":{"login":"lbeltrame","id":25192,"avatar_url":"https://avatars.githubusercontent.com/u/25192?v=3","gravatar_id":"","url":"https://api.github.com/users/lbeltrame","html_url":"https://github.com/lbeltrame","followers_url":"https://api.github.com/users/lbeltrame/followers","following_url":"https://api.github.com/users/lbeltrame/following{/other_user}","gists_url":"https://api.github.com/users/lbeltrame/gists{/gist_id}","starred_url":"https://api.github.com/users/lbeltrame/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbeltrame/subscriptions","organizations_url":"https://api.github.com/users/lbeltrame/orgs","repos_url":"https://api.github.com/users/lbeltrame/repos","events_url":"https://api.github.com/users/lbeltrame/events{/privacy}","received_events_url":"https://api.github.com/users/lbeltrame/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2016-04-01T13:01:47Z","updated_at":"2016-04-05T14:39:32Z","closed_at":"2016-04-05T14:39:32Z","body":"Apparently it tries to load a file that's not there:\r\n\r\n```\r\n[2016-04-01T12:18Z] Run coverage for 20724-IL-LY\r\n[2016-04-01T12:18Z] sambamba-depth: couldn't open file /scratch/bcbiotx/f183f606-f6f3-4979-a04b-8dfcc65ac580/tmp06vMsc/0425761_Covered.bed or find reference /scratch/bcbiotx/f183f606-f6f3-4979-a04b-8dfcc65ac580/tmp06vMsc/0425761_Covered.bed\r\n```\r\nThere are no references to that file in the `-commands.log` save for what I wrote, so I guess that's either not created, or deleted in the transaction before it's actually used.\r\n\r\nEDIT: In fact, I think that file is not even created. I wiped the `/scratch/bcbiotx` directory before, and no subfolders are being created when that command is run."},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/205837038","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1299#issuecomment-205837038","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1299","id":205837038,"user":{"login":"lpantano","id":1621788,"avatar_url":"https://avatars.githubusercontent.com/u/1621788?v=3","gravatar_id":"","url":"https://api.github.com/users/lpantano","html_url":"https://github.com/lpantano","followers_url":"https://api.github.com/users/lpantano/followers","following_url":"https://api.github.com/users/lpantano/following{/other_user}","gists_url":"https://api.github.com/users/lpantano/gists{/gist_id}","starred_url":"https://api.github.com/users/lpantano/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lpantano/subscriptions","organizations_url":"https://api.github.com/users/lpantano/orgs","repos_url":"https://api.github.com/users/lpantano/repos","events_url":"https://api.github.com/users/lpantano/events{/privacy}","received_events_url":"https://api.github.com/users/lpantano/received_events","type":"User","site_admin":false},"created_at":"2016-04-05T14:39:32Z","updated_at":"2016-04-05T14:39:32Z","body":"I checked and right now can detect '#' commented lines. I added the UCSC header keywords as well.\r\n\r\nthanks"}}