{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/pbccs/issues/42","labels_url":"https://api.github.com/repos/PacificBiosciences/pbccs/issues/42/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/pbccs/issues/42/comments","events_url":"https://api.github.com/repos/PacificBiosciences/pbccs/issues/42/events","html_url":"https://github.com/PacificBiosciences/pbccs/issues/42","id":99727976,"number":42,"title":"Fix Performance Regression","user":{"login":"evolvedmicrobe","id":1330626,"avatar_url":"https://avatars.githubusercontent.com/u/1330626?v=3","gravatar_id":"","url":"https://api.github.com/users/evolvedmicrobe","html_url":"https://github.com/evolvedmicrobe","followers_url":"https://api.github.com/users/evolvedmicrobe/followers","following_url":"https://api.github.com/users/evolvedmicrobe/following{/other_user}","gists_url":"https://api.github.com/users/evolvedmicrobe/gists{/gist_id}","starred_url":"https://api.github.com/users/evolvedmicrobe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/evolvedmicrobe/subscriptions","organizations_url":"https://api.github.com/users/evolvedmicrobe/orgs","repos_url":"https://api.github.com/users/evolvedmicrobe/repos","events_url":"https://api.github.com/users/evolvedmicrobe/events{/privacy}","received_events_url":"https://api.github.com/users/evolvedmicrobe/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-08-07T20:48:17Z","updated_at":"2015-08-08T01:34:38Z","closed_at":null,"body":"From Liz.\r\n\r\nVersion/build when this occurred: 0.0.1 (internal build)\r\n\r\nOverview: new CCS is very slow. A single movie (three .bax.h5 combined to a bam\r\nfile) takes almost a day to finish on 12 CPUs.\r\n\r\n\r\nSteps to reproduce\r\n\r\ndirectory:\r\n/home/UNIXHOME/etseng/projects2015/internal_Ting_Maize/smrtpipe/BC_rerun_4to6kb_newCCS\r\n\r\nThe .bax.h5 files were first converted bam per movie (see: bax2bam.sh)\r\n\r\nThen CCS was called using the following parameters:\r\n\r\n`ccs --minLength 300 --minPasses 0 --minPredictedAccuracy 0.75 --numThreads 12\r\n--minZScore -999999 --maxDropFrac 1.0`\r\n\r\nNOTE: the ridiculous minZScore and maxDropFrac are intentional. We are trying\r\nto get as much CCS as possible to look at some stats.\r\n\r\nEach ccs job is submitted to SGE (ex: qsub -pe smp 12 cmd_1).\r\n\r\nI did not explicitly time since I didn't know that was going to be an issue,\r\nbut the jobs were all submitted (and started) on Aug 5 2PM.\r\n\r\nYou can look at the <movie>.ccs.report timestamp to see when it finished.\r\n\r\n\r\nAug  7 05:32\r\nm150520_052201_42141_c100722061910000001823149204301510_s1_p0.ccs.report\r\nAug  7 03:41\r\nm150520_140510_42141_c100722061910000001823149204301512_s1_p0.ccs.report\r\nAug  6 13:42\r\nm150520_234644_42141_c100722061910000001823149204301513_s1_p0.ccs.report\r\nAug  6 08:12\r\nm150521_040756_42141_c100722061910000001823149204301514_s1_p0.ccs.report\r\nAug  6 19:08\r\nm150521_083055_42141_c100722061910000001823149204301515_s1_p0.ccs.report\r\nAug  6 13:42\r\nm150521_125225_42141_c100722061910000001823149204301517_s1_p0.ccs.report\r\n\r\n\r\nSo some of the took about a day and two of them took 1.5 days.\r\n"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/pbccs/issues/comments/128879645","html_url":"https://github.com/PacificBiosciences/pbccs/issues/42#issuecomment-128879645","issue_url":"https://api.github.com/repos/PacificBiosciences/pbccs/issues/42","id":128879645,"user":{"login":"nlhepler","id":38372,"avatar_url":"https://avatars.githubusercontent.com/u/38372?v=3","gravatar_id":"","url":"https://api.github.com/users/nlhepler","html_url":"https://github.com/nlhepler","followers_url":"https://api.github.com/users/nlhepler/followers","following_url":"https://api.github.com/users/nlhepler/following{/other_user}","gists_url":"https://api.github.com/users/nlhepler/gists{/gist_id}","starred_url":"https://api.github.com/users/nlhepler/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nlhepler/subscriptions","organizations_url":"https://api.github.com/users/nlhepler/orgs","repos_url":"https://api.github.com/users/nlhepler/repos","events_url":"https://api.github.com/users/nlhepler/events{/privacy}","received_events_url":"https://api.github.com/users/nlhepler/received_events","type":"User","site_admin":false},"created_at":"2015-08-08T01:34:38Z","updated_at":"2015-08-08T01:34:38Z","body":"Ohhhh, for 0- and 1-pass ZMWs the model will perfectly match the observations, leading to super-high z-scores."}}