{"action":"created","issue":{"url":"https://api.github.com/repos/BradnerLab/pipeline/issues/49","labels_url":"https://api.github.com/repos/BradnerLab/pipeline/issues/49/labels{/name}","comments_url":"https://api.github.com/repos/BradnerLab/pipeline/issues/49/comments","events_url":"https://api.github.com/repos/BradnerLab/pipeline/issues/49/events","html_url":"https://github.com/BradnerLab/pipeline/issues/49","id":103585829,"number":49,"title":"Unhandled exception: pthread_attr_setstacksize: Invalid argument","user":{"login":"davidhoover","id":4984669,"avatar_url":"https://avatars.githubusercontent.com/u/4984669?v=3","gravatar_id":"","url":"https://api.github.com/users/davidhoover","html_url":"https://github.com/davidhoover","followers_url":"https://api.github.com/users/davidhoover/followers","following_url":"https://api.github.com/users/davidhoover/following{/other_user}","gists_url":"https://api.github.com/users/davidhoover/gists{/gist_id}","starred_url":"https://api.github.com/users/davidhoover/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidhoover/subscriptions","organizations_url":"https://api.github.com/users/davidhoover/orgs","repos_url":"https://api.github.com/users/davidhoover/repos","events_url":"https://api.github.com/users/davidhoover/events{/privacy}","received_events_url":"https://api.github.com/users/davidhoover/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"jdimatteo","id":3752732,"avatar_url":"https://avatars.githubusercontent.com/u/3752732?v=3","gravatar_id":"","url":"https://api.github.com/users/jdimatteo","html_url":"https://github.com/jdimatteo","followers_url":"https://api.github.com/users/jdimatteo/followers","following_url":"https://api.github.com/users/jdimatteo/following{/other_user}","gists_url":"https://api.github.com/users/jdimatteo/gists{/gist_id}","starred_url":"https://api.github.com/users/jdimatteo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdimatteo/subscriptions","organizations_url":"https://api.github.com/users/jdimatteo/orgs","repos_url":"https://api.github.com/users/jdimatteo/repos","events_url":"https://api.github.com/users/jdimatteo/events{/privacy}","received_events_url":"https://api.github.com/users/jdimatteo/received_events","type":"User","site_admin":false},"milestone":null,"comments":3,"created_at":"2015-08-27T20:13:48Z","updated_at":"2015-08-28T13:47:39Z","closed_at":null,"body":"I've compiled and installed bamliquidator, but my initial tests are giving an ominous error:\r\n\r\n$ bamliquidator_batch.py bam_links\r\nLiquidating bam_links/D1JF9ACXX_MN23.bam (file 1 of 2)\r\nERROR\tUnhandled exception: pthread_attr_setstacksize: Invalid argument\r\nLiquidation completed: 0.022893 seconds, 163940971 reads, 7120.021162 millions of reads per second\r\nTraceback (most recent call last):\r\n  File \"/usr/local/apps/bamliquidator/pipeline/bamliquidator_internal/bamliquidatorbatch/bamliquidator_batch.py\", line 532, in <module>\r\n    main()\r\n  File \"/usr/local/apps/bamliquidator/pipeline/bamliquidator_internal/bamliquidatorbatch/bamliquidator_batch.py\", line 503, in main\r\n    not args.quiet, args.number_of_threads, args.black_list)\r\n  File \"/usr/local/apps/bamliquidator/pipeline/bamliquidator_internal/bamliquidatorbatch/bamliquidator_batch.py\", line 256, in __init__\r\n    self.batch(extension, sense)\r\n  File \"/usr/local/apps/bamliquidator/pipeline/bamliquidator_internal/bamliquidatorbatch/bamliquidator_batch.py\", line 205, in batch\r\n    raise Exception(\"%s failed with exit code %d\" % (self.executable_path, return_code))\r\nException: /usr/local/apps/bamliquidator/pipeline/bamliquidator_internal/bamliquidator_bins failed with exit code 4"},"comment":{"url":"https://api.github.com/repos/BradnerLab/pipeline/issues/comments/135779285","html_url":"https://github.com/BradnerLab/pipeline/issues/49#issuecomment-135779285","issue_url":"https://api.github.com/repos/BradnerLab/pipeline/issues/49","id":135779285,"user":{"login":"jdimatteo","id":3752732,"avatar_url":"https://avatars.githubusercontent.com/u/3752732?v=3","gravatar_id":"","url":"https://api.github.com/users/jdimatteo","html_url":"https://github.com/jdimatteo","followers_url":"https://api.github.com/users/jdimatteo/followers","following_url":"https://api.github.com/users/jdimatteo/following{/other_user}","gists_url":"https://api.github.com/users/jdimatteo/gists{/gist_id}","starred_url":"https://api.github.com/users/jdimatteo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdimatteo/subscriptions","organizations_url":"https://api.github.com/users/jdimatteo/orgs","repos_url":"https://api.github.com/users/jdimatteo/repos","events_url":"https://api.github.com/users/jdimatteo/events{/privacy}","received_events_url":"https://api.github.com/users/jdimatteo/received_events","type":"User","site_admin":false},"created_at":"2015-08-28T13:47:39Z","updated_at":"2015-08-28T13:47:39Z","body":"@davidhoover can you please try this command and post the output?\r\n\r\n`bamliquidator_batch.py --skip_plot -n 1 04032013_D1L57ACXX_4.TTAGGC.hg18.bwt.sorted.bam`\r\n\r\nAs far as I know, you are the first person to run bamliquidator on CentOS.  I think I should be able to fix the issues you are running into by Monday morning."}}