{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/411","repository_url":"https://api.github.com/repos/PacificBiosciences/FALCON","labels_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/411/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/411/comments","events_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/411/events","html_url":"https://github.com/PacificBiosciences/FALCON/issues/411","id":164580426,"number":411,"title":"LAcheck fails when level-1 is missing","user":{"login":"pb-cdunn","id":12086299,"avatar_url":"https://avatars.githubusercontent.com/u/12086299?v=3","gravatar_id":"","url":"https://api.github.com/users/pb-cdunn","html_url":"https://github.com/pb-cdunn","followers_url":"https://api.github.com/users/pb-cdunn/followers","following_url":"https://api.github.com/users/pb-cdunn/following{/other_user}","gists_url":"https://api.github.com/users/pb-cdunn/gists{/gist_id}","starred_url":"https://api.github.com/users/pb-cdunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pb-cdunn/subscriptions","organizations_url":"https://api.github.com/users/pb-cdunn/orgs","repos_url":"https://api.github.com/users/pb-cdunn/repos","events_url":"https://api.github.com/users/pb-cdunn/events{/privacy}","received_events_url":"https://api.github.com/users/pb-cdunn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2016-07-08T17:41:54Z","updated_at":"2016-07-27T14:55:47Z","closed_at":null,"body":"```sh\r\n[INFO] 2016-07-08 10:40:20,953Z Extracted from stderr\r\n[INFO] 2016-07-08 10:40:20,954Z + LAsort -v raw_reads.1.raw_reads.1.C0 raw_reads.1.raw_reads.1.N0 raw_reads.1.raw_reads.1.C1 raw_reads.1.raw_reads.1.N1 raw_reads.1.raw_reads.1.C2 raw_reads.1.raw_reads.1.N2 raw_reads.1.raw_reads.1.C3 raw_reads.1.raw_reads.1.N3\r\n[INFO] 2016-07-08 10:40:20,954Z + LAmerge -v L1.1.1 raw_reads.1.raw_reads.1.C0.S raw_reads.1.raw_reads.1.N0.S raw_reads.1.raw_reads.1.C1.S raw_reads.1.raw_reads.1.N1.S raw_reads.1.raw_reads.1.C2.S raw_reads.1.raw_reads.1.N2.S raw_reads.1.raw_reads.1.C3.S raw_reads.1.raw_reads.1.N3.S\r\n[INFO] 2016-07-08 10:40:20,954Z LAcheck -vS raw_reads raw_reads.1\r\n[INFO] 2016-07-08 10:40:20,954Z + LAcheck -vS raw_reads raw_reads.1\r\n[INFO] 2016-07-08 10:40:20,954Z Usage: LAcheck [-vS] <src1:db|dam> [ <src2:db|dam> ] <align:las> ...\r\n```\r\nObviously, we should run\r\n  LAcheck -vS raw_reads L1.1.1\r\n\r\n* https://bugzilla.nanofluidics.com/show_bug.cgi?id=33690\r\n* http://jenkins:8080/job/Ubuntu1404_Mainline_SA3_hgap4_pipe_falcon_fake/306/console"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/comments/235611518","html_url":"https://github.com/PacificBiosciences/FALCON/issues/411#issuecomment-235611518","issue_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/411","id":235611518,"user":{"login":"pb-cdunn","id":12086299,"avatar_url":"https://avatars.githubusercontent.com/u/12086299?v=3","gravatar_id":"","url":"https://api.github.com/users/pb-cdunn","html_url":"https://github.com/pb-cdunn","followers_url":"https://api.github.com/users/pb-cdunn/followers","following_url":"https://api.github.com/users/pb-cdunn/following{/other_user}","gists_url":"https://api.github.com/users/pb-cdunn/gists{/gist_id}","starred_url":"https://api.github.com/users/pb-cdunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pb-cdunn/subscriptions","organizations_url":"https://api.github.com/users/pb-cdunn/orgs","repos_url":"https://api.github.com/users/pb-cdunn/repos","events_url":"https://api.github.com/users/pb-cdunn/events{/privacy}","received_events_url":"https://api.github.com/users/pb-cdunn/received_events","type":"User","site_admin":false},"created_at":"2016-07-27T14:55:47Z","updated_at":"2016-07-27T14:55:47Z","body":"> is the nblock=1 problem specific to pbsmrtpipe jobs? Is the difference from the HPC.daligner vs. pbsmrtpipe scatter-gather?\r\n\r\nIn practice, yes. Your if-statement happens to work here because we are parsing the entire output of **HPC.daligner**.\r\n\r\nHowever, the **pbsmrtpipe** version first separates the bash-script into scripts for each group of chunks (where each group can run on a single machine). Then, when we run a \"chunked task\", it is possible that the derived bash-script for that group has only 1 daligner job, even thought the DB has multiple blocks.\r\n\r\nI will drop the pbsmrtpipe version this week, switching to HGAP5 (our pypeflow version) permanently. It is better to fix whatever problems occur there iteratively than to maintain two workflows, and I've been told for months that this is ok. It's time to pull the trigger.\r\n\r\nI'm also about to push a messy change which fixes this specific problem in pbsmrtpipe."}}
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