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marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
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Read correction jobs failed, tried 2 times, giving up. #1605

Closed LesterWYoung closed 4 years ago

LesterWYoung commented 4 years ago

Hi,

I used canu -p PMKlongBACs -d PMKbacs-raw-reads genomeSize=150k gridOptionsmeryl="--mem-per-cpu=12g" -pacbio-raw PMK_PacBio_reads.fasta.gz , submitted via slurm.

This is the canu.out file:

Found perl:
   /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/perl/5.22.4/bin/perl
   This is perl 5, version 22, subversion 4 (v5.22.4) built for x86_64-linux-thread-multi

Found java:
   /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/java/13.0.1/bin/java
   openjdk version "13.0.1" 2019-10-15

Found canu:
   /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc7.3/canu/1.9/bin/canu
   Canu 1.9

-- Canu 1.9
--
-- CITATIONS
--
-- Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM.
-- Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
-- Genome Res. 2017 May;27(5):722-736.
-- http://doi.org/10.1101/gr.215087.116
-- 
-- Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM, Kingan SB, Hiendleder S, Williams JL, Smith TPL, Phillippy AM.
-- De novo assembly of haplotype-resolved genomes with trio binning.
-- Nat Biotechnol. 2018
-- https//doi.org/10.1038/nbt.4277
-- 
-- Read and contig alignments during correction, consensus and GFA building use:
--   Šošic M, Šikic M.
--   Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance.
--   Bioinformatics. 2017 May 1;33(9):1394-1395.
--   http://doi.org/10.1093/bioinformatics/btw753
-- 
-- Overlaps are generated using:
--   Berlin K, et al.
--   Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.
--   Nat Biotechnol. 2015 Jun;33(6):623-30.
--   http://doi.org/10.1038/nbt.3238
-- 
--   Myers EW, et al.
--   A Whole-Genome Assembly of Drosophila.
--   Science. 2000 Mar 24;287(5461):2196-204.
--   http://doi.org/10.1126/science.287.5461.2196
-- 
-- Corrected read consensus sequences are generated using an algorithm derived from FALCON-sense:
--   Chin CS, et al.
--   Phased diploid genome assembly with single-molecule real-time sequencing.
--   Nat Methods. 2016 Dec;13(12):1050-1054.
--   http://doi.org/10.1038/nmeth.4035
-- 
-- Contig consensus sequences are generated using an algorithm derived from pbdagcon:
--   Chin CS, et al.
--   Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
--   Nat Methods. 2013 Jun;10(6):563-9
--   http://doi.org/10.1038/nmeth.2474
-- 
-- CONFIGURE CANU
--
-- Detected Java(TM) Runtime Environment '13.0.1' (from '/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/java/13.0.1/bin/java') without -d64 support.
-- Detected gnuplot version '5.0 patchlevel 3   ' (from 'gnuplot') and image format 'png'.
-- Detected 32 CPUs and 126 gigabytes of memory.
-- Detected Slurm with 'sinfo' binary in /opt/software/slurm/bin/sinfo.
-- Detected Slurm with task IDs up to 9999 allowed.
-- 
-- Found 640 hosts with  32 cores and  124 GB memory under Slurm control.
-- Found 672 hosts with  48 cores and  187 GB memory under Slurm control.
-- Found  94 hosts with  32 cores and  250 GB memory under Slurm control.
-- Found   4 hosts with  48 cores and  375 GB memory under Slurm control.
-- Found  24 hosts with  32 cores and  502 GB memory under Slurm control.
-- Found   4 hosts with  32 cores and 3021 GB memory under Slurm control.
-- Found 115 hosts with  24 cores and  124 GB memory under Slurm control.
-- Found  24 hosts with  32 cores and 1510 GB memory under Slurm control.
-- Found  32 hosts with  24 cores and  250 GB memory under Slurm control.
--
--                     (tag)Threads
--            (tag)Memory         |
--        (tag)         |         |  algorithm
--        -------  ------  --------  -----------------------------
-- Grid:  meryl     12 GB    4 CPUs  (k-mer counting)
-- Grid:  hap        8 GB    4 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap    6 GB    8 CPUs  (overlap detection with mhap)
-- Grid:  obtovl     4 GB    8 CPUs  (overlap detection)
-- Grid:  utgovl     4 GB    8 CPUs  (overlap detection)
-- Grid:  cor        8 GB    4 CPUs  (read correction)
-- Grid:  ovb        4 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs        8 GB    1 CPU   (overlap store sorting)
-- Grid:  red       15 GB    4 CPUs  (read error detection)
-- Grid:  oea        8 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat       16 GB    4 CPUs  (contig construction with bogart)
-- Grid:  cns      --- GB    4 CPUs  (consensus)
-- Grid:  gfa       16 GB    4 CPUs  (GFA alignment and processing)
--
-- In 'PMKlongBACs.seqStore', found PacBio reads:
--   Raw:        595311
--   Corrected:  0
--   Trimmed:    0
--
-- Generating assembly 'PMKlongBACs' in '/scratch/lwy304/Sep2019_PacBio/PMKbacs-raw-reads'
--
-- Parameters:
--
--  genomeSize        150000
--
--  Overlap Generation Limits:
--    corOvlErrorRate 0.2400 ( 24.00%)
--    obtOvlErrorRate 0.0450 (  4.50%)
--    utgOvlErrorRate 0.0450 (  4.50%)
--
--  Overlap Processing Limits:
--    corErrorRate    0.3000 ( 30.00%)
--    obtErrorRate    0.0450 (  4.50%)
--    utgErrorRate    0.0450 (  4.50%)
--    cnsErrorRate    0.0750 (  7.50%)
--
--
-- BEGIN CORRECTION
--
-- No change in report.
-- Set corMinCoverage=4 based on read coverage of 60294.
--
-- Read correction jobs failed, tried 2 times, giving up.
--   job 2-correction/results/0001.cns FAILED.
--   job 2-correction/results/0002.cns FAILED.
--   job 2-correction/results/0003.cns FAILED.
--   job 2-correction/results/0004.cns FAILED.
--   job 2-correction/results/0005.cns FAILED.
--   job 2-correction/results/0006.cns FAILED.
--   job 2-correction/results/0007.cns FAILED.
--   job 2-correction/results/0008.cns FAILED.
--   job 2-correction/results/0009.cns FAILED.
--   job 2-correction/results/0010.cns FAILED.
--   job 2-correction/results/0011.cns FAILED.
--   job 2-correction/results/0012.cns FAILED.
--   job 2-correction/results/0013.cns FAILED.
--   job 2-correction/results/0014.cns FAILED.
--   job 2-correction/results/0015.cns FAILED.
--   job 2-correction/results/0016.cns FAILED.
--   job 2-correction/results/0017.cns FAILED.
--   job 2-correction/results/0018.cns FAILED.
--   job 2-correction/results/0019.cns FAILED.
--   job 2-correction/results/0020.cns FAILED.
--   job 2-correction/results/0021.cns FAILED.
--   job 2-correction/results/0022.cns FAILED.
--   job 2-correction/results/0023.cns FAILED.
--   job 2-correction/results/0024.cns FAILED.
--   job 2-correction/results/0025.cns FAILED.
--   job 2-correction/results/0026.cns FAILED.
--   job 2-correction/results/0027.cns FAILED.
--   job 2-correction/results/0028.cns FAILED.
--   job 2-correction/results/0029.cns FAILED.
--   job 2-correction/results/0030.cns FAILED.
--   job 2-correction/results/0031.cns FAILED.
--   job 2-correction/results/0032.cns FAILED.
--   job 2-correction/results/0033.cns FAILED.
--   job 2-correction/results/0034.cns FAILED.
--

ABORT:
ABORT: Canu 1.9
ABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.
ABORT: Try restarting.  If that doesn't work, ask for help.
ABORT:

and this is in correction/2-correction/correctReads.34889512_1.out

Found perl:
   /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/perl/5.22.4/bin/perl
   This is perl 5, version 22, subversion 4 (v5.22.4) built for x86_64-linux-thread-multi

Found java:
   /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/java/13.0.1/bin/java
   openjdk version "13.0.1" 2019-10-15

Found canu:
   /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc7.3/canu/1.9/bin/canu
   Canu 1.9

Running job 1 based on SLURM_ARRAY_TASK_ID=1 and offset=0.
slurmstepd: error: *** JOB 34889515 ON cdr544 CANCELLED AT 2020-01-21T22:17:52 DUE TO TIME LIMIT ***
skoren commented 4 years ago

Your grid is killing these jobs for exceeding a time limit, Canu does not request an explicit time so you'll have to add gridOptions="--time=240:00:00 or similar (depending on what time limit maximum your grid allows) to allow the jobs to complete.

skoren commented 4 years ago

Idle