{"action":"created","issue":{"url":"https://api.github.com/repos/Illumina/manta/issues/25","labels_url":"https://api.github.com/repos/Illumina/manta/issues/25/labels{/name}","comments_url":"https://api.github.com/repos/Illumina/manta/issues/25/comments","events_url":"https://api.github.com/repos/Illumina/manta/issues/25/events","html_url":"https://github.com/Illumina/manta/issues/25","id":122174127,"number":25,"title":"large cohorts crash GenerateSVCandidates due running out of file handles","user":{"login":"hguturu","id":2645632,"avatar_url":"https://avatars.githubusercontent.com/u/2645632?v=3","gravatar_id":"","url":"https://api.github.com/users/hguturu","html_url":"https://github.com/hguturu","followers_url":"https://api.github.com/users/hguturu/followers","following_url":"https://api.github.com/users/hguturu/following{/other_user}","gists_url":"https://api.github.com/users/hguturu/gists{/gist_id}","starred_url":"https://api.github.com/users/hguturu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hguturu/subscriptions","organizations_url":"https://api.github.com/users/hguturu/orgs","repos_url":"https://api.github.com/users/hguturu/repos","events_url":"https://api.github.com/users/hguturu/events{/privacy}","received_events_url":"https://api.github.com/users/hguturu/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-12-15T01:51:49Z","updated_at":"2015-12-15T16:33:02Z","closed_at":null,"body":"Attempting to run the GenerateSVCandidates stage using lots of --align-file results in  \r\nFATAL_ERROR: GenerateSVCandidates EXCEPTION: BAM/CRAM index is not available for file: test.bam\r\n...caught in program.run()\r\n\r\nTried with 64 samples and it fails sometimes (possible due to OS having some fluctuation of files open).\r\n\r\nBest solution may be to free handles beyond a certain limit (likely a performance hit due to open/closing files and loading the bam index)."},"comment":{"url":"https://api.github.com/repos/Illumina/manta/issues/comments/164819587","html_url":"https://github.com/Illumina/manta/issues/25#issuecomment-164819587","issue_url":"https://api.github.com/repos/Illumina/manta/issues/25","id":164819587,"user":{"login":"ctsa","id":1349103,"avatar_url":"https://avatars.githubusercontent.com/u/1349103?v=3","gravatar_id":"","url":"https://api.github.com/users/ctsa","html_url":"https://github.com/ctsa","followers_url":"https://api.github.com/users/ctsa/followers","following_url":"https://api.github.com/users/ctsa/following{/other_user}","gists_url":"https://api.github.com/users/ctsa/gists{/gist_id}","starred_url":"https://api.github.com/users/ctsa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ctsa/subscriptions","organizations_url":"https://api.github.com/users/ctsa/orgs","repos_url":"https://api.github.com/users/ctsa/repos","events_url":"https://api.github.com/users/ctsa/events{/privacy}","received_events_url":"https://api.github.com/users/ctsa/received_events","type":"User","site_admin":false},"created_at":"2015-12-15T16:33:02Z","updated_at":"2015-12-15T16:33:02Z","body":"Thanks for reporting.. this is a tricky case - firstly the design of all the tools assumes that we can jointly sweep over the reads from all samples. Secondly we haven't tested the call quality of multi-sample at larger than family scale, so it might be premature to facilitate this workflow.\r\n\r\nSetting aside the latter question for the moment -- 64 sounds like a surprisingly low limit, is this something you can `uname` your way out of?"}}