{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/pbalign/issues/34","repository_url":"https://api.github.com/repos/PacificBiosciences/pbalign","labels_url":"https://api.github.com/repos/PacificBiosciences/pbalign/issues/34/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/pbalign/issues/34/comments","events_url":"https://api.github.com/repos/PacificBiosciences/pbalign/issues/34/events","html_url":"https://github.com/PacificBiosciences/pbalign/issues/34","id":158585684,"number":34,"title":"ERROR, could not read pulse metrics for SMRTSequence","user":{"login":"guleiathms","id":12107732,"avatar_url":"https://avatars.githubusercontent.com/u/12107732?v=3","gravatar_id":"","url":"https://api.github.com/users/guleiathms","html_url":"https://github.com/guleiathms","followers_url":"https://api.github.com/users/guleiathms/followers","following_url":"https://api.github.com/users/guleiathms/following{/other_user}","gists_url":"https://api.github.com/users/guleiathms/gists{/gist_id}","starred_url":"https://api.github.com/users/guleiathms/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/guleiathms/subscriptions","organizations_url":"https://api.github.com/users/guleiathms/orgs","repos_url":"https://api.github.com/users/guleiathms/repos","events_url":"https://api.github.com/users/guleiathms/events{/privacy}","received_events_url":"https://api.github.com/users/guleiathms/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-06-06T01:16:24Z","updated_at":"2016-06-06T16:56:25Z","closed_at":null,"body":"Not sure I reopened this issue.\r\n\r\nI met this error when I run the smrtanalysis_2.3.0.140936 with patch 5 for 28 movies (28 ...p0.1.bax.h5, p0.2.bax.h5, p0.3.bax.h5), and got\r\n```\r\n2016-06-05 01:19:23,470 [ERROR] BlasrService returned a non-zero exit status. [INFO] 2016-06-04T16:09:37 [blasr] started.\r\nERROR, could not read pulse metrics for SMRTSequence m140929_122654_42139_c100719602550000001823155305141594_s1_p0/92444\r\n```\r\nin the align.log.\r\n\r\nThen I run the same pipeline for that potential problematic moive (m140929_122654_42139_c100719602550000001823155305141594_s1_p0), but no error reported, with exit code 0:\r\n```\r\nTask 1 completed at Fri Jun 3 20:51:02 EDT 2016\r\nAlignment Complete\r\nTask 2 completed at Fri Jun 3 20:51:02 EDT 2016\r\n[INFO] 2016-06-03T20:51:05 [loadPulses] started.\r\nloading 199520 alignments for movie 1\r\nloading 199520 alignments for movie 1\r\nloading 199520 alignments for movie 1\r\nloading 163226 alignments for movie 2\r\nloading 163226 alignments for movie 2\r\nloading 163226 alignments for movie 2\r\n[INFO] 2016-06-03T21:52:34 [loadPulses] ended.\r\nTask 3 completed at Fri Jun 3 21:52:34 EDT 2016\r\nLoadPulses Complete\r\nTask 4 completed at Fri Jun 3 21:52:34 EDT 2016\r\nFinished on Sat Jun 4 01:52:34 UTC 2016\r\nTask align with nproc 8 with exit code 0.\r\n```\r\n\r\nSo what's going on when I run the pipeline with 28 movies together?"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/pbalign/issues/comments/224019395","html_url":"https://github.com/PacificBiosciences/pbalign/issues/34#issuecomment-224019395","issue_url":"https://api.github.com/repos/PacificBiosciences/pbalign/issues/34","id":224019395,"user":{"login":"ylipacbio","id":3189673,"avatar_url":"https://avatars.githubusercontent.com/u/3189673?v=3","gravatar_id":"","url":"https://api.github.com/users/ylipacbio","html_url":"https://github.com/ylipacbio","followers_url":"https://api.github.com/users/ylipacbio/followers","following_url":"https://api.github.com/users/ylipacbio/following{/other_user}","gists_url":"https://api.github.com/users/ylipacbio/gists{/gist_id}","starred_url":"https://api.github.com/users/ylipacbio/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ylipacbio/subscriptions","organizations_url":"https://api.github.com/users/ylipacbio/orgs","repos_url":"https://api.github.com/users/ylipacbio/repos","events_url":"https://api.github.com/users/ylipacbio/events{/privacy}","received_events_url":"https://api.github.com/users/ylipacbio/received_events","type":"User","site_admin":false},"created_at":"2016-06-06T16:56:25Z","updated_at":"2016-06-06T16:56:25Z","body":"The issue that guleiathms observed does seem to be related with blasr version. \r\n\r\nThere was a bug in blasr_libcpp which caused blasr to raise this error when any (non-mandatory) QV is missing and this bug should have been fixed.\r\n\r\nWould you please check that blasr used in two pipelines identical?\r\n\r\nIn addition, the following command helps to duplicate this error quickly:\r\n```\r\nblasr m140929_122654_42139_c100719602550000001823155305141594_s1_p0.fofn ref.fasta -holeNumbers 92000-100000 \r\n```"}}
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