{"action":"created","issue":{"url":"https://api.github.com/repos/marbl/canu/issues/67","repository_url":"https://api.github.com/repos/marbl/canu","labels_url":"https://api.github.com/repos/marbl/canu/issues/67/labels{/name}","comments_url":"https://api.github.com/repos/marbl/canu/issues/67/comments","events_url":"https://api.github.com/repos/marbl/canu/issues/67/events","html_url":"https://github.com/marbl/canu/issues/67","id":140940739,"number":67,"title":"canu failed with 'failed to precompute mhap indices.  Made 2 attempts, jobs still failed'.","user":{"login":"hjjansen","id":8056295,"avatar_url":"https://avatars.githubusercontent.com/u/8056295?v=3","gravatar_id":"","url":"https://api.github.com/users/hjjansen","html_url":"https://github.com/hjjansen","followers_url":"https://api.github.com/users/hjjansen/followers","following_url":"https://api.github.com/users/hjjansen/following{/other_user}","gists_url":"https://api.github.com/users/hjjansen/gists{/gist_id}","starred_url":"https://api.github.com/users/hjjansen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hjjansen/subscriptions","organizations_url":"https://api.github.com/users/hjjansen/orgs","repos_url":"https://api.github.com/users/hjjansen/repos","events_url":"https://api.github.com/users/hjjansen/events{/privacy}","received_events_url":"https://api.github.com/users/hjjansen/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-03-15T11:12:01Z","updated_at":"2016-03-15T11:29:51Z","closed_at":null,"body":"When run locally Canu fails in the mhap precompute stage with 1 finished job and 4 to compute. \r\nThe same data was used on the same machine in canu v1.0 to produce assemblies 1 to 7 without any problem.  After installation of Canu v1.1 (+16 commits) r7394 a57a2edacb17f7dd842f32e2ef58f22953394b05 Canu stops with this message: \"canu failed with 'failed to precompute mhap indices.  Made 2 attempts, jobs still failed'.\"\r\n\r\nIn the correction/1-overlapper folder I can find the precompute.out files.\r\n/assembly8/correction/1-overlapper/precompute.000001.out is finished and looks like this:\r\n```\r\nDumping reads from 1 to 9000 (inclusive).\r\nStarting mhap precompute.\r\nRunning with these settings:\r\nVersion = 1.5b1\r\nBuild time = 01/22/2015 12:04 PM\r\n--filter-threshold = 5.0E-6\r\n--help = false\r\n--max-seq-size = 100000\r\n--max-shift = 0.2\r\n--min-store-length = 499\r\n--no-self = false\r\n--num-hashes = 768\r\n--num-min-matches = 2\r\n--num-threads = 8\r\n--pacbio_experimental = false\r\n--pacbio_fast = false\r\n--pacbio_sensitive = false\r\n--store-full-id = false\r\n--threshold = 0.04\r\n--version = false\r\n--weighted = true\r\n-f = /mnt/data3/minion_data/zfg150502/assembly8/correction/0-mercounts/zfg150502_assembly8.ms16.frequentMers.ignore\r\n-h = false\r\n-k = 16\r\n-p = /mnt/data3/minion_data/zfg150502/assembly8/correction/1-overlapper/blocks/000001.fasta\r\n-q = /mnt/data3/minion_data/zfg150502/assembly8/correction/1-overlapper/blocks\r\n-s =\r\n\r\nReading in filter file /mnt/data3/minion_data/zfg150502/assembly8/correction/0-mercounts/zfg150502_assembly8.ms16.frequentMers.ignore.\r\nTime (s) to read filter file: 0.019249216\r\nProcessing FASTA files for binary compression...\r\nCurrent # sequences loaded and processed from file: 5000...\r\nCurrent # sequences loaded and processed from file: 10000...\r\n```\r\n\r\n\r\n/assembly8/correction/1-overlapper/precompute.000002.out fails and looks like this\r\n```\r\nERROR:  AS_MAX_READS_BITS in store = 41, differs from executable = 37\r\nERROR:  AS_MAX_READLEN_BITS in store = 17, differs from executable = 21\r\nERROR:\r\nERROR:  Can't open store '/mnt/data3/minion_data/zfg150502/assembly8/correction/zfg150502_assembly8.gkpStore': parameters in src/AS_global.H are incompatible with the store.\r\nmv: cannot stat ‘/mnt/data3/minion_data/zfg150502/assembly8/correction/1-overlapper/blocks/000002.fasta’: No such file or directory\r\nFailed to extract fasta.\r\n\r\n```\r\nThe zfg150502_assembly8.gkpStore was made successfully according to /assembly8/correction/zfg150502_assembly8.gkpStore.err which looked like this:\r\n```\r\nStarting file '/mnt/data3/minion_data/zfg150502/assembly8/correction/zfg150502_assembly8.gkpStore.gkp'.\r\n\r\n  Loading reads from '/mnt/data3/minion_data/zfg150502/zfg150502_allruns_2d.fastq'\r\n    Processed 207180 lines.\r\n    Loaded 331948384 bp from:\r\n      41436 FASTQ format reads (331948384 bp).\r\n    WARNING: 532 reads (1.2839%) with 318121 bp (0.0957%) were too short (< 1000bp) and were ignored.\r\n\r\nFinished with:\r\n  0 warnings (bad base or qv, too short, too long)\r\n\r\nLoaded into store:\r\n  331948384 bp.\r\n  40904 reads.\r\n\r\nSkipped (too short):\r\n  318121 bp (0.0957%).\r\n  532 reads (1.2839%).\r\n\r\n\r\ngatekeeperCreate finished successfully.\r\n```\r\n\r\nI'm not sure how to proceed to solve this error. Any guidance is appreciated.\r\n\r\nHans Jansen"},"comment":{"url":"https://api.github.com/repos/marbl/canu/issues/comments/196775492","html_url":"https://github.com/marbl/canu/issues/67#issuecomment-196775492","issue_url":"https://api.github.com/repos/marbl/canu/issues/67","id":196775492,"user":{"login":"JohnUrban","id":7783314,"avatar_url":"https://avatars.githubusercontent.com/u/7783314?v=3","gravatar_id":"","url":"https://api.github.com/users/JohnUrban","html_url":"https://github.com/JohnUrban","followers_url":"https://api.github.com/users/JohnUrban/followers","following_url":"https://api.github.com/users/JohnUrban/following{/other_user}","gists_url":"https://api.github.com/users/JohnUrban/gists{/gist_id}","starred_url":"https://api.github.com/users/JohnUrban/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JohnUrban/subscriptions","organizations_url":"https://api.github.com/users/JohnUrban/orgs","repos_url":"https://api.github.com/users/JohnUrban/repos","events_url":"https://api.github.com/users/JohnUrban/events{/privacy}","received_events_url":"https://api.github.com/users/JohnUrban/received_events","type":"User","site_admin":false},"created_at":"2016-03-15T11:29:51Z","updated_at":"2016-03-15T11:29:51Z","body":"Did you update Canu in the middle of an assembly?"}}