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marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
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ERROR: Failed with signal INT. (rc=2) #1766

Closed Xuelei-Dai closed 4 years ago

Xuelei-Dai commented 4 years ago

Hello, When I run the canu in LSF cluster system, some small errors occurred as follows:

In Plant.err file content

-- Canu snapshot (snapshot)
--
-- 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 '1.8.0_72' (from 'java') with -d64 support.
-- Detected gnuplot version '4.2 patchlevel 6 ' (from 'gnuplot') and image format 'png'.
-- Detected 24 CPUs and 126 gigabytes of memory.
-- Limited to 125G gigabytes from maxMemory option.
-- Limited to 24 CPUs from maxThreads option.
-- Detected LSF with 'bsub' binary in /stor9000/apps/jhinno/unischeduler/jhlava/bin/linux-x86_64/bsub.
Invalid command <showconf> 

Usage: lsadmin [-h] [-V] [command] [command_options] [command_args]

    where 'command' is:

    reconfig    Reconfigure jhscheduler
    ckconfig    Check configuration files
    limrestart  Restart LIM (Load Information Manager)
    limstartup  Startup LIM (Load Information Manager)
    limshutdown Shut down LIM (Load Information Manager)
    limlock     Lock LIM on local host
    limunlock   Unlock LIM on local host
    resrestart  Restart RES (Remote Execution Server)
    resstartup  Startup RES (Remote Execution Server)
    resshutdown Shut down RES (Remote Execution Server)
    reslogon    Log tasks executed by RES
    reslogoff   RES log off
    limdebug    Debug LIM
    limtime     Debug LIM timing message
    resdebug    Debug RES
    restime     Debug RES timing message
    help        Get help on commands
    ?           Get help on commands
    quit        Quit
-- Warning: unknown memory units for grid engine LSF assuming KB
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 79.
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 84.
-- 
-- Found  71 hosts with  24 cores and   62 GB memory under LSF control.
-- Found   9 hosts with  32 cores and  125 GB memory under LSF control.
-- Found   1 host  with  16 cores and   62 GB memory under LSF control.
-- Found  42 hosts with  24 cores and  125 GB memory under LSF control.
-- Found  16 hosts with  28 cores and  251 GB memory under LSF control.
-- Found   2 hosts with  56 cores and 2019 GB memory under LSF control.
-- 
-- On LSF detected memory is requested in KB
-- 
--
--                     (tag)Threads
--            (tag)Memory         |
--        (tag)         |         |  algorithm
--        -------  ------  --------  -----------------------------
-- Grid:  meryl     20 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       12 GB    8 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   20 GB    8 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    16 GB    8 CPUs  (overlap detection)
-- Grid:  utgovl    16 GB    8 CPUs  (overlap detection)
-- Grid:  ovb        4 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       16 GB    1 CPU   (overlap store sorting)
-- Grid:  red       10 GB    4 CPUs  (read error detection)
-- Grid:  oea        4 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat      125 GB   16 CPUs  (contig construction with bogart)
-- Grid:  gfa       16 GB   16 CPUs  (GFA alignment and processing)
--
-- Found PacBio uncorrected reads in the input files.
--
-- Generating assembly 'Plant' in '/home/Plant/assembly/canu/Plant.polyploidy/Plant'
--
-- Parameters:
--
--  genomeSize        644000000
--
--  Overlap Generation Limits:
--    corOvlErrorRate 0.2400 ( 24.00%)
--    obtOvlErrorRate 0.0850 (  8.50%)
--    utgOvlErrorRate 0.0850 (  8.50%)
--
--  Overlap Processing Limits:
--    corErrorRate    0.3000 ( 30.00%)
--    obtErrorRate    0.0850 (  8.50%)
--    utgErrorRate    0.0850 (  8.50%)
--    cnsErrorRate    0.0850 (  8.50%)
--
--
-- BEGIN CORRECTION
--
----------------------------------------
-- Starting command on Thu Jul 23 20:50:06 2020 with 50719.493 GB free disk space

    cd .
    /home/anaconda2/libexec/bin/sqStoreCreate \
      -o ./Plant.seqStore.BUILDING \
      -minlength 1000 \
      ./Plant.seqStore.ssi \
    > ./Plant.seqStore.BUILDING.err 2>&1

-- Finished on Thu Jul 23 21:44:57 2020 (3291 seconds) with 50676.958 GB free disk space
----------------------------------------
--
-- In sequence store './Plant.seqStore':
--   Found 9868339 reads.
--   Found 181133116868 bases (281.26 times coverage).
--
--   Read length histogram (one '*' equals 22561.52 reads):
--        0   4999 1579307 **********************************************************************
--     5000   9999 1565453 *********************************************************************
--    10000  14999 1285604 ********************************************************
--    15000  19999 1207345 *****************************************************
--    20000  24999 1433857 ***************************************************************
--    25000  29999 1141368 **************************************************
--    30000  34999 709054 *******************************
--    35000  39999 415628 ******************
--    40000  44999 234661 **********
--    45000  49999 132018 *****
--    50000  54999  71957 ***
--    55000  59999  38093 *
--    60000  64999  21060 
--    65000  69999  12158 
--    70000  74999   7528 
--    75000  79999   4705 
--    80000  84999   3099 
--    85000  89999   2091 
--    90000  94999   1311 
--    95000  99999    799 
--   100000 104999    501 
--   105000 109999    294 
--   110000 114999    177 
--   115000 119999     90 
--   120000 124999     54 
--   125000 129999     48 
--   130000 134999     24 
--   135000 139999     25 
--   140000 144999      9 
--   145000 149999      4 
--   150000 154999      6 
--   155000 159999      3 
--   160000 164999      2 
--   165000 169999      3 
--   170000 174999      0 
--   175000 179999      0 
--   180000 184999      0 
--   185000 189999      0 
--   190000 194999      1 
--   195000 199999      0 
--   200000 204999      0 
--   205000 209999      0 
--   210000 214999      0 
--   215000 219999      0 
--   220000 224999      1 
--   225000 229999      0 
--   230000 234999      1 
----------------------------------------
-- Starting command on Thu Jul 23 21:47:08 2020 with 50676 GB free disk space

    cd correction/0-mercounts
    ./meryl-configure.sh \
    > ./meryl-configure.err 2>&1

-- Finished on Thu Jul 23 21:47:18 2020 (10 seconds) with 50676 GB free disk space
----------------------------------------
--  segments   memory batches
--  -------- -------- -------
--        01 15.50 GB       1
--        02 15.00 GB       1
--        04 14.50 GB       1
--        06 14.00 GB       1
--        08 14.00 GB       1
--        12 13.50 GB       1
--        16 13.50 GB       1
--        20 13.50 GB       1
--        24 13.00 GB       1
--        32 12.00 GB       1
--        40  8.01 GB       1
--        48  8.00 GB       1
--        56  7.00 GB       1
--        64  6.00 GB       1
--        96  4.00 GB       1
--
--  For 9868339 reads with 181133116868 bases, limit to 1811 batches.
--  Will count kmers using 01 jobs, each using 17 GB and 8 threads.
--
-- Finished stage 'merylConfigure', reset canuIteration.
--
-- Running jobs.  First attempt out of 2.
--
-- 'meryl-count.jobSubmit-01.sh' -> job ended(9705697) task 1.
--
----------------------------------------
-- Starting command on Thu Jul 23 21:47:19 2020 with 50676 GB free disk space

    cd /home/Plant/assembly/canu/Plant.polyploidy/Plant
    bsub \
      -w "ended(9705697)"  \
      -q jynodequeue \
      -M 4194304 \
      -R span[hosts=1] \
      -n 1 \
      -J 'canu_Plant' \
      -o canu-scripts/canu.01.out  canu-scripts/canu.01.sh

-- Finished on Thu Jul 23 21:47:21 2020 (2 seconds) with 50676 GB free disk space
----------------------------------------
-- Canu snapshot (snapshot)
--
-- 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 '1.8.0_72' (from 'java') with -d64 support.
-- Detected gnuplot version '4.2 patchlevel 6 ' (from 'gnuplot') and image format 'png'.
-- Detected 28 CPUs and 252 gigabytes of memory.
-- Limited to 256G gigabytes from maxMemory option.
-- Limited to 28 CPUs from maxThreads option.
-- Detected LSF with 'bsub' binary in /stor9000/apps/jhinno/unischeduler/jhlava/bin/linux-x86_64/bsub.
Invalid command <showconf> 

Usage: lsadmin [-h] [-V] [command] [command_options] [command_args]

    where 'command' is:

    reconfig    Reconfigure jhscheduler
    ckconfig    Check configuration files
    limrestart  Restart LIM (Load Information Manager)
    limstartup  Startup LIM (Load Information Manager)
    limshutdown Shut down LIM (Load Information Manager)
    limlock     Lock LIM on local host
    limunlock   Unlock LIM on local host
    resrestart  Restart RES (Remote Execution Server)
    resstartup  Startup RES (Remote Execution Server)
    resshutdown Shut down RES (Remote Execution Server)
    reslogon    Log tasks executed by RES
    reslogoff   RES log off
    limdebug    Debug LIM
    limtime     Debug LIM timing message
    resdebug    Debug RES
    restime     Debug RES timing message
    help        Get help on commands
    ?           Get help on commands
    quit        Quit
-- Warning: unknown memory units for grid engine LSF assuming KB
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 59.
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 77.
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 79.
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 81.
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 84.
-- 
-- Found  71 hosts with  24 cores and   62 GB memory under LSF control.
-- Found  39 hosts with  24 cores and  125 GB memory under LSF control.
-- Found   2 hosts with  56 cores and 2019 GB memory under LSF control.
-- Found   1 host  with  16 cores and   62 GB memory under LSF control.
-- Found   9 hosts with  32 cores and  125 GB memory under LSF control.
-- Found  16 hosts with  28 cores and  251 GB memory under LSF control.
-- 
-- On LSF detected memory is requested in KB
-- 
--
--                     (tag)Threads
--            (tag)Memory         |
--        (tag)         |         |  algorithm
--        -------  ------  --------  -----------------------------
-- Grid:  meryl     20 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       12 GB    8 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   20 GB    8 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    16 GB    8 CPUs  (overlap detection)
-- Grid:  utgovl    16 GB    8 CPUs  (overlap detection)
-- Grid:  ovb        4 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       16 GB    1 CPU   (overlap store sorting)
-- Grid:  red       10 GB    4 CPUs  (read error detection)
-- Grid:  oea        4 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat      256 GB   16 CPUs  (contig construction with bogart)
-- Grid:  gfa       16 GB   16 CPUs  (GFA alignment and processing)
--
-- In 'Plant.seqStore', found PacBio reads:
--   Raw:        9868339
--   Corrected:  0
--   Trimmed:    0
--
-- Generating assembly 'Plant' in '/home/Plant/assembly/canu/Plant.polyploidy/Plant'
--
-- Parameters:
--
--  genomeSize        644000000
--
--  Overlap Generation Limits:
--    corOvlErrorRate 0.2400 ( 24.00%)
--    obtOvlErrorRate 0.0850 (  8.50%)
--    utgOvlErrorRate 0.0850 (  8.50%)
--
--  Overlap Processing Limits:
--    corErrorRate    0.3000 ( 30.00%)
--    obtErrorRate    0.0850 (  8.50%)
--    utgErrorRate    0.0850 (  8.50%)
--    cnsErrorRate    0.0850 (  8.50%)
--
--
-- BEGIN CORRECTION
--
--
-- Creating overlap store correction/Plant.ovlStore using:
--    453 buckets
--    589 slices
--        using at most 15 GB memory each
--
-- Running jobs.  First attempt out of 2.
--
-- 'scripts/2-sort.jobSubmit-01.sh' -> job ended(9725013) tasks 1-8.
-- 'scripts/2-sort.jobSubmit-02.sh' -> job ended(9725014) task 10.
-- 'scripts/2-sort.jobSubmit-03.sh' -> job ended(9725015) task 13.
-- 'scripts/2-sort.jobSubmit-04.sh' -> job ended(9725016) task 15.
-- 'scripts/2-sort.jobSubmit-05.sh' -> job ended(9725017) task 18.
-- 'scripts/2-sort.jobSubmit-06.sh' -> job ended(9725018) task 20.
-- 'scripts/2-sort.jobSubmit-07.sh' -> job ended(9725019) task 22.
-- 'scripts/2-sort.jobSubmit-08.sh' -> job ended(9725020) tasks 24-26.
-- 'scripts/2-sort.jobSubmit-09.sh' -> job ended(9725021) task 28.
-- 'scripts/2-sort.jobSubmit-10.sh' -> job ended(9725022) tasks 31-32.
-- 'scripts/2-sort.jobSubmit-11.sh' -> job ended(9725023) task 34.
-- 'scripts/2-sort.jobSubmit-12.sh' -> job ended(9725024) tasks 36-40.
-- 'scripts/2-sort.jobSubmit-13.sh' -> job ended(9725025) task 42.
-- 'scripts/2-sort.jobSubmit-14.sh' -> job ended(9725026) task 44.
-- 'scripts/2-sort.jobSubmit-15.sh' -> job ended(9725027) task 46.
-- 'scripts/2-sort.jobSubmit-16.sh' -> job ended(9725028) tasks 48-50.
-- 'scripts/2-sort.jobSubmit-17.sh' -> job ended(9725029) task 52.
-- 'scripts/2-sort.jobSubmit-18.sh' -> job ended(9725030) task 54.
-- 'scripts/2-sort.jobSubmit-19.sh' -> job ended(9725031) tasks 58-59.
-- 'scripts/2-sort.jobSubmit-20.sh' -> job ended(9725032) tasks 61-63.
-- 'scripts/2-sort.jobSubmit-21.sh' -> job ended(9725033) tasks 66-67.
-- 'scripts/2-sort.jobSubmit-22.sh' -> job ended(9725034) tasks 69-71.
-- 'scripts/2-sort.jobSubmit-23.sh' -> job ended(9725035) task 73.
-- 'scripts/2-sort.jobSubmit-24.sh' -> job ended(9725036) tasks 78-82.
-- 'scripts/2-sort.jobSubmit-25.sh' -> job ended(9725037) tasks 84-89.
-- 'scripts/2-sort.jobSubmit-26.sh' -> job ended(9725038) task 95.
-- 'scripts/2-sort.jobSubmit-27.sh' -> job ended(9725039) task 97.
-- 'scripts/2-sort.jobSubmit-28.sh' -> job ended(9725040) tasks 101-103.
-- 'scripts/2-sort.jobSubmit-29.sh' -> job ended(9725041) tasks 108-112.
-- 'scripts/2-sort.jobSubmit-30.sh' -> job ended(9725042) tasks 114-116.
-- 'scripts/2-sort.jobSubmit-31.sh' -> job ended(9725043) task 118.
-- 'scripts/2-sort.jobSubmit-32.sh' -> job ended(9725044) tasks 120-121.
-- 'scripts/2-sort.jobSubmit-33.sh' -> job ended(9725045) tasks 123-124.
-- 'scripts/2-sort.jobSubmit-34.sh' -> job ended(9725046) tasks 127-129.
-- 'scripts/2-sort.jobSubmit-35.sh' -> job ended(9725047) tasks 132-139.
-- 'scripts/2-sort.jobSubmit-36.sh' -> job ended(9725048) task 142.
-- 'scripts/2-sort.jobSubmit-37.sh' -> job ended(9725049) tasks 144-145.
-- 'scripts/2-sort.jobSubmit-38.sh' -> job ended(9725050) tasks 148-171.
-- 'scripts/2-sort.jobSubmit-39.sh' -> job ended(9725051) tasks 173-178.
-- 'scripts/2-sort.jobSubmit-40.sh' -> job ended(9725052) tasks 184-186.
-- 'scripts/2-sort.jobSubmit-41.sh' -> job ended(9725053) task 188.
-- 'scripts/2-sort.jobSubmit-42.sh' -> job ended(9725054) tasks 190-193.
-- 'scripts/2-sort.jobSubmit-43.sh' -> job ended(9725055) task 195.
-- 'scripts/2-sort.jobSubmit-44.sh' -> job ended(9725056) task 197.
-- 'scripts/2-sort.jobSubmit-45.sh' -> job ended(9725057) task 201.
-- 'scripts/2-sort.jobSubmit-46.sh' -> job ended(9725058) task 203.
-- 'scripts/2-sort.jobSubmit-47.sh' -> job ended(9725059) tasks 206-207.
-- 'scripts/2-sort.jobSubmit-48.sh' -> job ended(9725060) tasks 209-214.
-- 'scripts/2-sort.jobSubmit-49.sh' -> job ended(9725061) task 216.
-- 'scripts/2-sort.jobSubmit-50.sh' -> job ended(9725062) tasks 218-221.
-- 'scripts/2-sort.jobSubmit-51.sh' -> job ended(9725063) task 223.
-- 'scripts/2-sort.jobSubmit-52.sh' -> job ended(9725064) tasks 225-227.
-- 'scripts/2-sort.jobSubmit-53.sh' -> job ended(9725065) tasks 229-231.
-- 'scripts/2-sort.jobSubmit-54.sh' -> job ended(9725066) tasks 233-235.
-- 'scripts/2-sort.jobSubmit-55.sh' -> job ended(9725067) task 238.
-- 'scripts/2-sort.jobSubmit-56.sh' -> job ended(9725068) tasks 240-248.
-- 'scripts/2-sort.jobSubmit-57.sh' -> job ended(9725069) tasks 253-254.
-- 'scripts/2-sort.jobSubmit-58.sh' -> job ended(9725070) tasks 256-263.
-- 'scripts/2-sort.jobSubmit-59.sh' -> job ended(9725071) task 265.
-- 'scripts/2-sort.jobSubmit-60.sh' -> job ended(9725072) tasks 267-268.
-- 'scripts/2-sort.jobSubmit-61.sh' -> job ended(9725073) tasks 271-273.
-- 'scripts/2-sort.jobSubmit-62.sh' -> job ended(9725074) task 275.
-- 'scripts/2-sort.jobSubmit-63.sh' -> job ended(9725075) tasks 278-284.
-- 'scripts/2-sort.jobSubmit-64.sh' -> job ended(9725076) task 288.
-- 'scripts/2-sort.jobSubmit-65.sh' -> job ended(9725077) tasks 291-292.
-- 'scripts/2-sort.jobSubmit-66.sh' -> job ended(9725078) tasks 294-297.
-- 'scripts/2-sort.jobSubmit-67.sh' -> job ended(9725079) tasks 299-300.
-- 'scripts/2-sort.jobSubmit-68.sh' -> job ended(9725080) task 304.
-- 'scripts/2-sort.jobSubmit-69.sh' -> job ended(9725081) task 306.
-- 'scripts/2-sort.jobSubmit-70.sh' -> job ended(9725082) tasks 308-313.
-- 'scripts/2-sort.jobSubmit-71.sh' -> job ended(9725083) tasks 318-319.
-- 'scripts/2-sort.jobSubmit-72.sh' -> job ended(9725084) tasks 322-324.
-- 'scripts/2-sort.jobSubmit-73.sh' -> job ended(9725085) task 326.
-- 'scripts/2-sort.jobSubmit-74.sh' -> job ended(9725086) tasks 328-354.
-- 'scripts/2-sort.jobSubmit-75.sh' -> job ended(9725087) tasks 356-358.
-- 'scripts/2-sort.jobSubmit-76.sh' -> job ended(9725088) task 361.
-- 'scripts/2-sort.jobSubmit-77.sh' -> job ended(9725089) tasks 364-365.
-- 'scripts/2-sort.jobSubmit-78.sh' -> job ended(9725521) tasks 367-369.
-- 'scripts/2-sort.jobSubmit-79.sh' -> job ended(9725532) task 372.
-- 'scripts/2-sort.jobSubmit-80.sh' -> job ended(9725533) tasks 374-375.
-- 'scripts/2-sort.jobSubmit-81.sh' -> job ended(9725534) tasks 377-379.
-- 'scripts/2-sort.jobSubmit-82.sh' -> job ended(9725535) task 381.
-- 'scripts/2-sort.jobSubmit-83.sh' -> job ended(9725536) tasks 383-384.
-- 'scripts/2-sort.jobSubmit-84.sh' -> job ended(9725537) task 386.
-- 'scripts/2-sort.jobSubmit-85.sh' -> job ended(9725538) task 388.
-- 'scripts/2-sort.jobSubmit-86.sh' -> job ended(9725539) tasks 390-395.
-- 'scripts/2-sort.jobSubmit-87.sh' -> job ended(9725540) tasks 397-398.
-- 'scripts/2-sort.jobSubmit-88.sh' -> job ended(9725541) tasks 403-404.
-- 'scripts/2-sort.jobSubmit-89.sh' -> job ended(9725542) tasks 406-421.
-- 'scripts/2-sort.jobSubmit-90.sh' -> job ended(9725543) task 423.
-- 'scripts/2-sort.jobSubmit-91.sh' -> job ended(9725544) task 425.
-- 'scripts/2-sort.jobSubmit-92.sh' -> job ended(9725545) tasks 427-428.
-- 'scripts/2-sort.jobSubmit-93.sh' -> job ended(9725575) task 432.
-- 'scripts/2-sort.jobSubmit-94.sh' -> job ended(9725576) tasks 434-435.
-- 'scripts/2-sort.jobSubmit-95.sh' -> job ended(9725577) tasks 437-441.
-- 'scripts/2-sort.jobSubmit-96.sh' -> job ended(9725578) tasks 443-444.
-- 'scripts/2-sort.jobSubmit-97.sh' -> job ended(9725608) tasks 450-453.
-- 'scripts/2-sort.jobSubmit-98.sh' -> job ended(9725638) task 455.
-- 'scripts/2-sort.jobSubmit-99.sh' -> job ended(9725639) tasks 457-464.
-- 'scripts/2-sort.jobSubmit-100.sh' -> job ended(9725642) tasks 467-468.
-- 'scripts/2-sort.jobSubmit-101.sh' -> job ended(9725645) tasks 471-474.
-- 'scripts/2-sort.jobSubmit-102.sh' -> job ended(9725677) task 476.
-- 'scripts/2-sort.jobSubmit-103.sh' -> job ended(9725680) tasks 478-482.
-- 'scripts/2-sort.jobSubmit-104.sh' -> job ended(9725744) task 485.
-- 'scripts/2-sort.jobSubmit-105.sh' -> job ended(9725804) tasks 487-488.
-- 'scripts/2-sort.jobSubmit-106.sh' -> job ended(9725805) task 491.
-- 'scripts/2-sort.jobSubmit-107.sh' -> job ended(9725806) tasks 496-508.
-- 'scripts/2-sort.jobSubmit-108.sh' -> job ended(9725807) task 514.
-- 'scripts/2-sort.jobSubmit-109.sh' -> job ended(9725808) task 517.
-- 'scripts/2-sort.jobSubmit-110.sh' -> job ended(9725809) tasks 519-521.
-- 'scripts/2-sort.jobSubmit-111.sh' -> job ended(9725810) tasks 523-525.
-- 'scripts/2-sort.jobSubmit-112.sh' -> job ended(9725811) tasks 527-529.
-- 'scripts/2-sort.jobSubmit-113.sh' -> job ended(9725812) task 531.
-- 'scripts/2-sort.jobSubmit-114.sh' -> job ended(9726166) task 533.
-- 'scripts/2-sort.jobSubmit-115.sh' -> job ended(9726411) task 535.
-- 'scripts/2-sort.jobSubmit-116.sh' -> job ended(9726412) task 538.
-- 'scripts/2-sort.jobSubmit-117.sh' -> job ended(9726414) tasks 540-541.
-- 'scripts/2-sort.jobSubmit-118.sh' -> job ended(9726477) tasks 543-550.
-- 'scripts/2-sort.jobSubmit-119.sh' -> job ended(9726478) tasks 553-559.
-- 'scripts/2-sort.jobSubmit-120.sh' -> job ended(9726480) tasks 561-565.
-- 'scripts/2-sort.jobSubmit-121.sh' -> job ended(9726484) tasks 567-571.
-- 'scripts/2-sort.jobSubmit-122.sh' -> job ended(9726485) tasks 573-574.
-- 'scripts/2-sort.jobSubmit-123.sh' -> job ended(9726647) task 577.
-- 'scripts/2-sort.jobSubmit-124.sh' -> job ended(9726680) tasks 579-587.
--
----------------------------------------
-- Starting command on Sat Jul 25 12:16:59 2020 with 39482.466 GB free disk space

    cd /home/Plant/assembly/canu/Plant.polyploidy/Plant
    bsub \
      -w "ended(9725013)&&ended(9725014)&&ended(9725015)&&ended(9725016)&&ended(9725017)&&ended(9725018)&&ended(9725019)&&ended(9725020)&&ended(9725021)&&ended(9725022)&&ended(9725023)&&ended(9725024)&&ended(9725025)&&ended(9725026)&&ended(9725027)&&ended(9725028)&&ended(9725029)&&ended(9725030)&&ended(9725031)&&ended(9725032)&&ended(9725033)&&ended(9725034)&&ended(9725035)&&ended(9725036)&&ended(9725037)&&ended(9725038)&&ended(9725039)&&ended(9725040)&&ended(9725041)&&ended(9725042)&&ended(9725043)&&ended(9725044)&&ended(9725045)&&ended(9725046)&&ended(9725047)&&ended(9725048)&&ended(9725049)&&ended(9725050)&&ended(9725051)&&ended(9725052)&&ended(9725053)&&ended(9725054)&&ended(9725055)&&ended(9725056)&&ended(9725057)&&ended(9725058)&&ended(9725059)&&ended(9725060)&&ended(9725061)&&ended(9725062)&&ended(9725063)&&ended(9725064)&&ended(9725065)&&ended(9725066)&&ended(9725067)&&ended(9725068)&&ended(9725069)&&ended(9725070)&&ended(9725071)&&ended(9725072)&&ended(9725073)&&ended(9725074)&&ended(9725075)&&ended(9725076)&&ended(9725077)&&ended(9725078)&&ended(9725079)&&ended(9725080)&&ended(9725081)&&ended(9725082)&&ended(9725083)&&ended(9725084)&&ended(9725085)&&ended(9725086)&&ended(9725087)&&ended(9725088)&&ended(9725089)&&ended(9725521)&&ended(9725532)&&ended(9725533)&&ended(9725534)&&ended(9725535)&&ended(9725536)&&ended(9725537)&&ended(9725538)&&ended(9725539)&&ended(9725540)&&ended(9725541)&&ended(9725542)&&ended(9725543)&&ended(9725544)&&ended(9725545)&&ended(9725575)&&ended(9725576)&&ended(9725577)&&ended(9725578)&&ended(9725608)&&ended(9725638)&&ended(9725639)&&ended(9725642)&&ended(9725645)&&ended(9725677)&&ended(9725680)&&ended(9725744)&&ended(9725804)&&ended(9725805)&&ended(9725806)&&ended(9725807)&&ended(9725808)&&ended(9725809)&&ended(9725810)&&ended(9725811)&&ended(9725812)&&ended(9726166)&&ended(9726411)&&ended(9726412)&&ended(9726414)&&ended(9726477)&&ended(9726478)&&ended(9726480)&&ended(9726484)&&ended(9726485)&&ended(9726647)&&ended(9726680)"  \
      -q mem128queue \
      -M 4194304 \
      -R span[hosts=1] \
      -n 1 \
      -J 'canu_Plant' \
      -o canu-scripts/canu.05.out  canu-scripts/canu.05.sh

-- Finished on Sat Jul 25 12:17:10 2020 (12 seconds) with 39482.466 GB free disk space
----------------------------------------
-- Canu snapshot (snapshot)
--
-- 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 '1.8.0_72' (from 'java') with -d64 support.
-- Detected gnuplot version '4.2 patchlevel 6 ' (from 'gnuplot') and image format 'png'.
-- Detected 28 CPUs and 252 gigabytes of memory.
-- Limited to 256G gigabytes from maxMemory option.
-- Limited to 28 CPUs from maxThreads option.
-- Detected LSF with 'bsub' binary in /stor9000/apps/jhinno/unischeduler/jhlava/bin/linux-x86_64/bsub.
Invalid command <showconf> 

Usage: lsadmin [-h] [-V] [command] [command_options] [command_args]

    where 'command' is:

    reconfig    Reconfigure jhscheduler
    ckconfig    Check configuration files
    limrestart  Restart LIM (Load Information Manager)
    limstartup  Startup LIM (Load Information Manager)
    limshutdown Shut down LIM (Load Information Manager)
    limlock     Lock LIM on local host
    limunlock   Unlock LIM on local host
    resrestart  Restart RES (Remote Execution Server)
    resstartup  Startup RES (Remote Execution Server)
    resshutdown Shut down RES (Remote Execution Server)
    reslogon    Log tasks executed by RES
    reslogoff   RES log off
    limdebug    Debug LIM
    limtime     Debug LIM timing message
    resdebug    Debug RES
    restime     Debug RES timing message
    help        Get help on commands
    ?           Get help on commands
    quit        Quit
-- Warning: unknown memory units for grid engine LSF assuming KB
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 59.
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 77.
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 79.
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 81.
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 84.
-- 
-- Found  16 hosts with  28 cores and  251 GB memory under LSF control.
-- Found   9 hosts with  32 cores and  125 GB memory under LSF control.
-- Found  71 hosts with  24 cores and   62 GB memory under LSF control.
-- Found   1 host  with  16 cores and   62 GB memory under LSF control.
-- Found   2 hosts with  56 cores and 2019 GB memory under LSF control.
-- Found  39 hosts with  24 cores and  125 GB memory under LSF control.
-- 
-- On LSF detected memory is requested in KB
-- 
--
--                     (tag)Threads
--            (tag)Memory         |
--        (tag)         |         |  algorithm
--        -------  ------  --------  -----------------------------
-- Grid:  meryl     20 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       12 GB    8 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   20 GB    8 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    16 GB    8 CPUs  (overlap detection)
-- Grid:  utgovl    16 GB    8 CPUs  (overlap detection)
-- Grid:  ovb        4 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       16 GB    1 CPU   (overlap store sorting)
-- Grid:  red       10 GB    4 CPUs  (read error detection)
-- Grid:  oea        4 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat      256 GB   16 CPUs  (contig construction with bogart)
-- Grid:  gfa       16 GB   16 CPUs  (GFA alignment and processing)
--
-- In 'Plant.seqStore', found PacBio reads:
--   Raw:        9868339
--   Corrected:  0
--   Trimmed:    0
--
-- Generating assembly 'Plant' in '/home/Plant/assembly/canu/Plant.polyploidy/Plant'
--
-- Parameters:
--
--  genomeSize        644000000
--
--  Overlap Generation Limits:
--    corOvlErrorRate 0.2400 ( 24.00%)
--    obtOvlErrorRate 0.0850 (  8.50%)
--    utgOvlErrorRate 0.0850 (  8.50%)
--
--  Overlap Processing Limits:
--    corErrorRate    0.3000 ( 30.00%)
--    obtErrorRate    0.0850 (  8.50%)
--    utgErrorRate    0.0850 (  8.50%)
--    cnsErrorRate    0.0850 (  8.50%)
--
--
-- BEGIN CORRECTION
--
-- Set corMinCoverage=4 based on read coverage of 281.
-- Global filter scores will be estimated.
-- Computing correction layouts.
----------------------------------------
-- Starting command on Sun Jul 26 19:41:11 2020 with 49181.295 GB free disk space

    cd correction
    /home/anaconda2/libexec/bin/generateCorrectionLayouts \
      -S ../Plant.seqStore \
      -O  ./Plant.ovlStore \
      -C  ./Plant.corStore.WORKING \
      -eC 200 \
    > ./Plant.corStore.err 2>&1

-- Finished on Sun Jul 26 19:41:17 2020 (6 seconds) with 49181.295 GB free disk space
----------------------------------------

ERROR:
ERROR:  Failed with signal INT.  (rc=2)
ERROR:

ABORT:
ABORT: Canu snapshot (snapshot)
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:
ABORT:   failed to generate correction layouts.
ABORT:
ABORT: Disk space available:  49181.295 GB
ABORT:
ABORT: Last 50 lines of the relevant log file (correction/Plant.corStore.err):
ABORT:
ABORT:   
ABORT:   Failed with 'Interrupt'; backtrace (libbacktrace):
ABORT:   utility/system-stackTrace.C::89 in _Z17AS_UTL_catchCrashiP7siginfoPv()
ABORT:   (null)::0 in (null)()
ABORT:   (null)::0 in (null)()
ABORT:   (null)::0 in (null)()
ABORT:   (null)::0 in (null)()
ABORT:   (null)::0 in (null)()
ABORT:   utility/files.C::118 in _Z12loadFromFilePvPKcmmP8_IO_FILEb()
ABORT:   utility/files.H::163 in loadFromFile<sqRead>()
ABORT:   utility/files.H::107 in AS_UTL_loadFile<sqRead>()
ABORT:   stores/sqStoreConstructor.C::55 in _ZN7sqStore20sqStore_loadMetadataEv()
ABORT:   stores/sqStoreConstructor.C::190 in _ZN7sqStoreC2EPKcS1_12sqStore_modej()
ABORT:   stores/sqStoreConstructor.C::335 in _ZN7sqStore12sqStore_openEPKc12sqStore_modej()
ABORT:   correction/generateCorrectionLayouts.C::306 in main()
ABORT:   (null)::0 in (null)()
ABORT:   (null)::0 in (null)()
ABORT:
-- Canu snapshot (snapshot)
--
-- 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 '1.8.0_72' (from 'java') with -d64 support.
-- Detected gnuplot version '4.2 patchlevel 6 ' (from 'gnuplot') and image format 'png'.
-- Detected 24 CPUs and 126 gigabytes of memory.
-- Limited to 256G gigabytes from maxMemory option.
-- Limited to 28 CPUs from maxThreads option.
-- Detected LSF with 'bsub' binary in /stor9000/apps/jhinno/unischeduler/jhlava/bin/linux-x86_64/bsub.
Invalid command <showconf> 

Usage: lsadmin [-h] [-V] [command] [command_options] [command_args]

    where 'command' is:

    reconfig    Reconfigure jhscheduler
    ckconfig    Check configuration files
    limrestart  Restart LIM (Load Information Manager)
    limstartup  Startup LIM (Load Information Manager)
    limshutdown Shut down LIM (Load Information Manager)
    limlock     Lock LIM on local host
    limunlock   Unlock LIM on local host
    resrestart  Restart RES (Remote Execution Server)
    resstartup  Startup RES (Remote Execution Server)
    resshutdown Shut down RES (Remote Execution Server)
    reslogon    Log tasks executed by RES
    reslogoff   RES log off
    limdebug    Debug LIM
    limtime     Debug LIM timing message
    resdebug    Debug RES
    restime     Debug RES timing message
    help        Get help on commands
    ?           Get help on commands
    quit        Quit
-- Warning: unknown memory units for grid engine LSF assuming KB
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 59.
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 77.
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 79.
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 81.
Argument "-" isn't numeric in int at /home/anaconda2/libexec/bin/../lib/site_perl/canu/Grid_LSF.pm line 152, <F> line 84.
-- 
-- Found  71 hosts with  24 cores and   62 GB memory under LSF control.
-- Found  39 hosts with  24 cores and  125 GB memory under LSF control.
-- Found  16 hosts with  28 cores and  251 GB memory under LSF control.
-- Found   2 hosts with  56 cores and 2019 GB memory under LSF control.
-- Found   1 host  with  16 cores and   62 GB memory under LSF control.
-- Found   9 hosts with  32 cores and  125 GB memory under LSF control.
-- 
-- On LSF detected memory is requested in KB
-- 
--
--                     (tag)Threads
--            (tag)Memory         |
--        (tag)         |         |  algorithm
--        -------  ------  --------  -----------------------------
-- Grid:  meryl     20 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       12 GB    8 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   20 GB    8 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    16 GB    8 CPUs  (overlap detection)
-- Grid:  utgovl    16 GB    8 CPUs  (overlap detection)
-- Grid:  ovb        4 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       16 GB    1 CPU   (overlap store sorting)
-- Grid:  red       10 GB    4 CPUs  (read error detection)
-- Grid:  oea        4 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat      256 GB   16 CPUs  (contig construction with bogart)
-- Grid:  gfa       16 GB   16 CPUs  (GFA alignment and processing)
--
-- In 'Plant.seqStore', found PacBio reads:
--   Raw:        9868339
--   Corrected:  0
--   Trimmed:    0
--
-- Generating assembly 'Plant' in '/home/Plant/assembly/canu/Plant.polyploidy/Plant'
--
-- Parameters:
--
--  genomeSize        644000000
--
--  Overlap Generation Limits:
--    corOvlErrorRate 0.2400 ( 24.00%)
--    obtOvlErrorRate 0.0850 (  8.50%)
--    utgOvlErrorRate 0.0850 (  8.50%)
--
--  Overlap Processing Limits:
--    corErrorRate    0.3000 ( 30.00%)
--    obtErrorRate    0.0850 (  8.50%)
--    utgErrorRate    0.0850 (  8.50%)
--    cnsErrorRate    0.0850 (  8.50%)
--
--
-- BEGIN CORRECTION
--
-- Set corMinCoverage=4 based on read coverage of 281.
-- Global filter scores will be estimated.
-- Computing correction layouts.
----------------------------------------
-- Starting command on Sun Jul 26 19:43:01 2020 with 49181.291 GB free disk space

    cd correction
    /home/anaconda2/libexec/bin/generateCorrectionLayouts \
      -S ../Plant.seqStore \
      -O  ./Plant.ovlStore \
      -C  ./Plant.corStore.WORKING \
      -eC 200 \
    > ./Plant.corStore.err 2>&1

-- Finished on Mon Jul 27 09:14:31 2020 (48690 seconds, fashionably late) with 49185.421 GB free disk space
----------------------------------------

ERROR:
ERROR:  Failed with signal INT.  (rc=2)
ERROR:

ABORT:
ABORT: Canu snapshot (snapshot)
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:
ABORT:   failed to generate correction layouts.
ABORT:
ABORT: Disk space available:  49185.421 GB
ABORT:
ABORT: Last 50 lines of the relevant log file (correction/Plant.corStore.err):
ABORT:
ABORT:   
ABORT:   Failed with 'Interrupt'; backtrace (libbacktrace):
ABORT:   utility/system-stackTrace.C::89 in _Z17AS_UTL_catchCrashiP7siginfoPv()
ABORT:   (null)::0 in (null)()
ABORT:   (null)::0 in (null)()
ABORT:   (null)::0 in (null)()
ABORT:   (null)::0 in (null)()
ABORT:   (null)::0 in (null)()
ABORT:   utility/files.C::118 in _Z12loadFromFilePvPKcmmP8_IO_FILEb()
ABORT:   utility/files.H::163 in loadFromFile<unsigned int>()
ABORT:   stores/ovStoreFile.C::354 in _ZN6ovFile10readBufferEv()
ABORT:   stores/ovStoreFile.C::391 in _ZN6ovFile11readOverlapEP9ovOverlap()
ABORT:   stores/ovStore.C::288 in _ZN7ovStore19loadOverlapsForReadEjRP9ovOverlapRj()
ABORT:   correction/generateCorrectionLayouts.C::343 in main()
ABORT:   (null)::0 in (null)()
ABORT:   (null)::0 in (null)()
ABORT:
skoren commented 4 years ago

Signal INT typically means the job was killed by the system. Most likely there was a timeout for the job on your cluster. Re-run Canu with the same parameters/folder but add gridOptionsExecutive="<whatever parameters LSF uses to request time for max allowed on your system>".

Xuelei-Dai commented 4 years ago

Thank you for your rapidly reply. I want to sure the parameters gridOptionsExecutive="" is ok ? Or add the time gridOptionsExecutive="--time=280:00:00" , or some other format?

skoren commented 4 years ago

You want the time like your second option, apparently GitHub didn't like the <> in my original comment.

skoren commented 4 years ago

Any update?

skoren commented 4 years ago

Idle, grid config issue.