{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/217","labels_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/217/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/217/comments","events_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/217/events","html_url":"https://github.com/PacificBiosciences/FALCON/issues/217","id":110081157,"number":217,"title":"error during 1-preads_ovl / p_merge_done step","user":{"login":"conte1","id":5486871,"avatar_url":"https://avatars.githubusercontent.com/u/5486871?v=3","gravatar_id":"","url":"https://api.github.com/users/conte1","html_url":"https://github.com/conte1","followers_url":"https://api.github.com/users/conte1/followers","following_url":"https://api.github.com/users/conte1/following{/other_user}","gists_url":"https://api.github.com/users/conte1/gists{/gist_id}","starred_url":"https://api.github.com/users/conte1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/conte1/subscriptions","organizations_url":"https://api.github.com/users/conte1/orgs","repos_url":"https://api.github.com/users/conte1/repos","events_url":"https://api.github.com/users/conte1/events{/privacy}","received_events_url":"https://api.github.com/users/conte1/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-10-06T19:22:32Z","updated_at":"2015-10-13T20:53:15Z","closed_at":"2015-10-13T20:53:15Z","body":"Hi,\r\n\r\nA couple of the p_merge jobs are failing with the following error:\r\n\r\n```\r\n...\r\nMerging 32 files totalling 42,378 records\r\nMerging 8 files totalling 517,039 records\r\nMerging 8 files totalling 423,228 records\r\nMerging 8 files totalling 388,383 records\r\nMerging 8 files totalling 392,336 records\r\nMerging 8 files totalling 376,861 records\r\nLAmerge: Cannot open ./L1.37.45.las for 'r'\r\nMerging 8 files totalling 388,468 records\r\nMerging 9 files totalling 452,664 records\r\nLAmerge: Cannot open ./L2.37.6.las for 'r'\r\n...\r\n```\r\nAnd so I am missing a couple of the 1-preads_olv .las files. I have tried to re-run each of these rp_000.sh jobs manually, but they just fail with the same error.\r\n\r\nDo I need to re-run the entire 1-preads_ovl step or is there a way to restart at the end of the \"da_done\" step?\r\n\r\nThanks,\r\nMatt"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/comments/147850467","html_url":"https://github.com/PacificBiosciences/FALCON/issues/217#issuecomment-147850467","issue_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/217","id":147850467,"user":{"login":"conte1","id":5486871,"avatar_url":"https://avatars.githubusercontent.com/u/5486871?v=3","gravatar_id":"","url":"https://api.github.com/users/conte1","html_url":"https://github.com/conte1","followers_url":"https://api.github.com/users/conte1/followers","following_url":"https://api.github.com/users/conte1/following{/other_user}","gists_url":"https://api.github.com/users/conte1/gists{/gist_id}","starred_url":"https://api.github.com/users/conte1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/conte1/subscriptions","organizations_url":"https://api.github.com/users/conte1/orgs","repos_url":"https://api.github.com/users/conte1/repos","events_url":"https://api.github.com/users/conte1/events{/privacy}","received_events_url":"https://api.github.com/users/conte1/received_events","type":"User","site_admin":false},"created_at":"2015-10-13T20:53:15Z","updated_at":"2015-10-13T20:53:15Z","body":"Hey guys,\r\n\r\nI was able to track down the problematic files in the 1-preads_ovl/job_* directories as there were a few .las files that were 0kb in size. I never did get any errors for those jobs, so I'm not sure why the failed. Re-running those couple rp_*.sh jobs fixed the problem and I was able to complete the assembly.\r\n\r\n-Matt"}}