{"action":"created","issue":{"url":"https://api.github.com/repos/marbl/canu/issues/308","repository_url":"https://api.github.com/repos/marbl/canu","labels_url":"https://api.github.com/repos/marbl/canu/issues/308/labels{/name}","comments_url":"https://api.github.com/repos/marbl/canu/issues/308/comments","events_url":"https://api.github.com/repos/marbl/canu/issues/308/events","html_url":"https://github.com/marbl/canu/issues/308","id":193948876,"number":308,"title":"Get polyG/A/T reads after trimming","user":{"login":"WeichenZhou","id":15823356,"avatar_url":"https://avatars.githubusercontent.com/u/15823356?v=3","gravatar_id":"","url":"https://api.github.com/users/WeichenZhou","html_url":"https://github.com/WeichenZhou","followers_url":"https://api.github.com/users/WeichenZhou/followers","following_url":"https://api.github.com/users/WeichenZhou/following{/other_user}","gists_url":"https://api.github.com/users/WeichenZhou/gists{/gist_id}","starred_url":"https://api.github.com/users/WeichenZhou/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/WeichenZhou/subscriptions","organizations_url":"https://api.github.com/users/WeichenZhou/orgs","repos_url":"https://api.github.com/users/WeichenZhou/repos","events_url":"https://api.github.com/users/WeichenZhou/events{/privacy}","received_events_url":"https://api.github.com/users/WeichenZhou/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":17,"created_at":"2016-12-07T03:27:06Z","updated_at":"2016-12-29T16:23:26Z","closed_at":null,"body":"Dear Sir,\r\nI just started to use CANU and wanted to analyze Human Genome PacBio data.\r\nSo I used the scripts step by step as following:\r\ncorrecting..\r\n`./canu  useGrid=true gridEngine=\"pbs\" gridOptionsJobName=\"canu_test1\" gridEngineThreadsOption=\"-l nodes=3:ppn=4\" gridEngineMemoryOption=\"-l pmem=4gb,qos=flux,wall time=100:00:00\" gridOptions=\"-m abe -V -d . \"  -correct -d 16.12.05.canu_consensus -p wash genomeSize=3g -pacbio-raw SRR1.fastq`\r\nthen trimming..\r\n`./canu  useGrid=true gridEngine=\"pbs\" gridOptionsJobName=\"canu_test_trim1\" gridEngineThreadsOption=\"-l nodes=3:ppn=4\" gridEngineMemoryOption=\"-l pmem=4gb,qos=flux, walltime=100:00:00\" gridOptions=\"-m abe -V -d .\"  -trim -d 16.12.05.canu_consensus -p wash genomeSize=3g -pacbio-corrected wash.correctedReads.fasta.1.gz`\r\nThe corrected fasta.gz looks pretty good, which has 20k number of reads for this SRR1.fastq file. While the trimmed fasta.gz contains reads only having ployT/A/G, and the number decreases to 9k.\r\nBesides, SRR1.fastq is just one of 200 human genome PacBio sequencing files and has 50k raw reads.\r\nHave you ever met that problem before? I would appreciate if you can give some advice to handle this. Thank you so much!\r\n\r\nArthur"},"comment":{"url":"https://api.github.com/repos/marbl/canu/issues/comments/269654185","html_url":"https://github.com/marbl/canu/issues/308#issuecomment-269654185","issue_url":"https://api.github.com/repos/marbl/canu/issues/308","id":269654185,"user":{"login":"WeichenZhou","id":15823356,"avatar_url":"https://avatars.githubusercontent.com/u/15823356?v=3","gravatar_id":"","url":"https://api.github.com/users/WeichenZhou","html_url":"https://github.com/WeichenZhou","followers_url":"https://api.github.com/users/WeichenZhou/followers","following_url":"https://api.github.com/users/WeichenZhou/following{/other_user}","gists_url":"https://api.github.com/users/WeichenZhou/gists{/gist_id}","starred_url":"https://api.github.com/users/WeichenZhou/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/WeichenZhou/subscriptions","organizations_url":"https://api.github.com/users/WeichenZhou/orgs","repos_url":"https://api.github.com/users/WeichenZhou/repos","events_url":"https://api.github.com/users/WeichenZhou/events{/privacy}","received_events_url":"https://api.github.com/users/WeichenZhou/received_events","type":"User","site_admin":false},"created_at":"2016-12-29T16:23:26Z","updated_at":"2016-12-29T16:23:26Z","body":"Thanks for your reply.\r\nThis morning I got another `canu.03.out`, and it says:\r\n```\r\n-- Canu v1.3 (+367 commits) r7983 fd38ffccd8674d78312d343b0717e0d6b55d823d.\r\n-- Detected Java(TM) Runtime Environment '1.8.0_111' (from 'java').\r\n-- Detected gnuplot version '4.6 patchlevel 2' (from 'gnuplot') and image format 'png'.\r\n-- Detected 40 CPUs and 1008 gigabytes of memory.\r\n-- Detecting PBS/Torque resources.\r\n-- \r\n-- Found   4 hosts with  16 cores and  125 GB memory under PBS/Torque control.\r\n-- Found 468 hosts with  16 cores and   62 GB memory under PBS/Torque control.\r\n-- Found 208 hosts with  24 cores and  125 GB memory under PBS/Torque control.\r\n-- Found   6 hosts with   8 cores and   47 GB memory under PBS/Torque control.\r\n-- Found   1 host  with  20 cores and   78 GB memory under PBS/Torque control.\r\n-- Found   4 hosts with  40 cores and 1007 GB memory under PBS/Torque control.\r\n-- Found 151 hosts with  20 cores and   94 GB memory under PBS/Torque control.\r\n-- Found   3 hosts with  20 cores and  251 GB memory under PBS/Torque control.\r\n-- Found   4 hosts with  32 cores and  503 GB memory under PBS/Torque control.\r\n-- Found   5 hosts with  32 cores and 1007 GB memory under PBS/Torque control.\r\n-- Found   1 host  with  56 cores and 1464 GB memory under PBS/Torque control.\r\n-- Found   1 host  with  56 cores and 1495 GB memory under PBS/Torque control.\r\n-- Found   6 hosts with  20 cores and   62 GB memory under PBS/Torque control.\r\n-- Found   5 hosts with  56 cores and 1511 GB memory under PBS/Torque control.\r\n-- Found 399 hosts with  12 cores and   47 GB memory under PBS/Torque control.\r\n-- Found   4 hosts with  16 cores and  251 GB memory under PBS/Torque control.\r\n--\r\n-- Allowed to run under grid control, and use up to  16 compute threads and  251 GB memory for stage 'bogart (unitigger)'.\r\n-- Allowed to run under grid control, and use up to   5 compute threads and   19 GB memory for stage 'mhap (overlapper)'.\r\n-- Allowed to run under grid control, and use up to   5 compute threads and   19 GB memory for stage 'mhap (overlapper)'.\r\n-- Allowed to run under grid control, and use up to   5 compute threads and   19 GB memory for stage 'mhap (overlapper)'.\r\n-- Allowed to run under grid control, and use up to   4 compute threads and   12 GB memory for stage 'read error detection (overlap error adjustment)'.\r\n-- Allowed to run under grid control, and use up to   1 compute thread  and    4 GB memory for stage 'overlap error adjustment'.\r\n-- Allowed to run under grid control, and use up to   8 compute threads and   78 GB memory for stage 'utgcns (consensus)'.\r\n-- Allowed to run under grid control, and use up to   1 compute thread  and    3 GB memory for stage 'overlap store parallel bucketizer'.\r\n-- Allowed to run under grid control, and use up to   1 compute thread  and   32 GB memory for stage 'overlap store parallel sorting'.\r\n-- Allowed to run under grid control, and use up to   1 compute thread  and    3 GB memory for stage 'overlapper'.\r\n-- Allowed to run under grid control, and use up to   4 compute threads and   12 GB memory for stage 'overlapper'.\r\n-- Allowed to run under grid control, and use up to   4 compute threads and   12 GB memory for stage 'overlapper'.\r\n-- Allowed to run under grid control, and use up to  20 compute threads and   78 GB memory for stage 'meryl (k-mer counting)'.\r\n-- Allowed to run under grid control, and use up to   4 compute threads and   12 GB memory for stage 'falcon_sense (read correction)'.\r\n-- Allowed to run under grid control, and use up to   5 compute threads and   19 GB memory for stage 'minimap (overlapper)'.\r\n-- Allowed to run under grid control, and use up to   5 compute threads and   19 GB memory for stage 'minimap (overlapper)'.\r\n-- Allowed to run under grid control, and use up to   5 compute threads and   19 GB memory for stage 'minimap (overlapper)'.\r\n--\r\n-- This is canu parallel iteration #3, out of a maximum of 2 attempts.\r\n--\r\n-- Final error rates before starting pipeline:\r\n--   \r\n--   genomeSize          -- 3000000000\r\n--   errorRate           -- 0.015\r\n--   \r\n--   corOvlErrorRate     -- 0.045\r\n--   obtOvlErrorRate     -- 0.045\r\n--   utgOvlErrorRate     -- 0.045\r\n--   \r\n--   obtErrorRate        -- 0.045\r\n--   \r\n--   cnsErrorRate        -- 0.045\r\n--\r\n--\r\n-- BEGIN CORRECTION\r\n--\r\n--\r\n-- 1697 overlap store sorter jobs failed:\r\n--   job /home/arthurz/arthur_remflux_scratch/16.12.05.canu_consensus/correction/wash.ovlStore.BUILDING/0001 FAILED.\r\n--   job /home/arthurz/arthur_remflux_scratch/16.12.05.canu_consensus/correction/wash.ovlStore.BUILDING/0002 FAILED.\r\n--   job /home/arthurz/arthur_remflux_scratch/16.12.05.canu_consensus/correction/wash.ovlStore.BUILDING/0003 FAILED.\r\n--   job /home/arthurz/arthur_remflux_scratch/16.12.05.canu_consensus/correction/wash.ovlStore.BUILDING/0004 FAILED.\r\n......\r\n--   job /home/arthurz/arthur_remflux_scratch/16.12.05.canu_consensus/correction/wash.ovlStore.BUILDING/1698 FAILED.\r\n--   job /home/arthurz/arthur_remflux_scratch/16.12.05.canu_consensus/correction/wash.ovlStore.BUILDING/1699 FAILED.\r\n--\r\n================================================================================\r\nDon't panic, but a mostly harmless error occurred and canu failed.\r\n\r\ncanu failed with 'failed to overlapStoreSorter.  Made 2 attempts, jobs still failed'.\r\n```\r\n\r\nWhen I checked `/correction/wash.ovlStore.BUILDING`, there are 7284 files/directory inside, with very recent `N` & `N.index` files (0 bytes) and the same number of older `N`, `N.index`& `N.evalueLen` files (several G/M/K). Also, I checked the `/correction/wash.ovlStore.BUILDING/logs`, one of `2-sort.*.out`s says:\r\n\r\n```\r\nRunning job 1497 based on PBS_ARRAYID=1497 and offset=0.\r\nMax processes per user limited to 4127233, no increase possible.\r\n\r\nMax open files limited to 32768, no increase possible.\r\n\r\nFound 590709 overlaps from '/home/arthurz/arthur_remflux_scratch/16.12.05.canu_consensus/correction/wash.ovlStore.BUILDING/bucket0004/sliceSizes'.\r\nFound 1950949 overlaps from '/home/arthurz/arthur_remflux_scratch/16.12.05.canu_consensus/correction/wash.ovlStore.BUILDING/bucket0008/sliceSizes'.\r\nFound 1997091 overlaps from '/home/arthurz/arthur_remflux_scratch/16.12.05.canu_consensus/correction/wash.ovlStore.BUILDING/bucket0012/sliceSizes'.\r\n......\r\nFound 25177598 overlaps from '/home/arthurz/arthur_remflux_scratch/16.12.05.canu_consensus/correction/wash.ovlStore.BUILDING/bucket0401/sliceSizes'.\r\nOverlaps need 3.77 GB memory, allowed to use up to (via -M) 4 GB.\r\nLoading 590709 overlaps from '/home/arthurz/arthur_remflux_scratch/16.12.05.canu_consensus/correction/wash.ovlStore.BUILDING/bucket0004/slice1497'.\r\nLoading 1950949 overlaps from '/home/arthurz/arthur_remflux_scratch/16.12.05.canu_consensus/correction/wash.ovlStore.BUILDING/bucket0008/slice1497'.\r\nLoading 1997091 overlaps from '/home/arthurz/arthur_remflux_scratch/16.12.05.canu_consensus/correction/wash.ovlStore.BUILDING/bucket0012/slice1497'.\r\n......\r\nLoading 25177598 overlaps from '/home/arthurz/arthur_remflux_scratch/16.12.05.canu_consensus/correction/wash.ovlStore.BUILDING/bucket0401/slice1497'.\r\nSorting.\r\nWriting output.\r\nWriting 101183081 overlaps.\r\n\r\nFailed with 'Segmentation fault'\r\n\r\nBacktrace (mangled):\r\n\r\n/home/arthurz/app/canu/Linux-amd64/bin/ovStoreSorter[0x4058fd]\r\n/lib64/libpthread.so.0(+0xf100)[0x2aed9fc30100]\r\n/home/arthurz/app/canu/Linux-amd64/bin/ovStoreSorter[0x40ff4a]\r\n/home/arthurz/app/canu/Linux-amd64/bin/ovStoreSorter[0x40f329]\r\n/home/arthurz/app/canu/Linux-amd64/bin/ovStoreSorter[0x40d4ab]\r\n/home/arthurz/app/canu/Linux-amd64/bin/ovStoreSorter[0x402b08]\r\n/lib64/libc.so.6(__libc_start_main+0xf5)[0x2aed9fe5eb15]\r\n/home/arthurz/app/canu/Linux-amd64/bin/ovStoreSorter[0x403189]\r\n\r\nBacktrace (demangled):\r\n\r\n[0] /home/arthurz/app/canu/Linux-amd64/bin/ovStoreSorter() [0x4058fd]\r\n[1] /lib64/libpthread.so.0::(null) + 0xf100  [0x2aed9fc30100]\r\n[2] /home/arthurz/app/canu/Linux-amd64/bin/ovStoreSorter() [0x40ff4a]\r\n[3] /home/arthurz/app/canu/Linux-amd64/bin/ovStoreSorter() [0x40f329]\r\n[4] /home/arthurz/app/canu/Linux-amd64/bin/ovStoreSorter() [0x40d4ab]\r\n[5] /home/arthurz/app/canu/Linux-amd64/bin/ovStoreSorter() [0x402b08]\r\n[6] /lib64/libc.so.6::(null) + 0xf5  [0x2aed9fe5eb15]\r\n[7] /home/arthurz/app/canu/Linux-amd64/bin/ovStoreSorter() [0x403189]\r\n\r\nGDB:\r\n\r\n\r\n/var/spool/torque/mom_priv/jobs/21853805-1497.nyx.arc-ts.umich.edu.SC: line 78:  1518 Segmentation fault      (core dumped) $bin/ovStoreSorter -deletelate -M 4 -O /home/arthurz/arthur_remflux_scratch/16.12.05.canu_consensus/correction/wash.ovlStore.BUILDING -G /home/arthurz/arthur_remflux_scratch/16.12.05.canu_consensus/correction/wash.gkpStore -F 1736 -job $jobid 407\r\nFailure.\r\n```\r\nSo I saw a 'Segmentation fault' here. It is because of not enough memory? I think it was assigned at least 64GB (in 4 cores), but the log said 'Overlaps need 3.77 GB memory, allowed to use up to (via -M) 4 GB'.\r\n\r\nThank you so much!/Arthur"}}
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