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marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
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Aborted pacbio read correction #1629

Closed hidvegin closed 4 years ago

hidvegin commented 4 years ago

I have got a pacbio raw data for about 4Gbp plant genome with about 32x coverage. I use the canu 2.0. I used on cluster with only one node (48 CPU core and 126 GB ram)

Firstly, I tried only error correction on my raw data fastq file.

canu -correct -p lculinaris -d $HOME/output/canu_trim/lculinaris genomeSize=4.0g batMemory=124M -pacbio $HOME/input/pacbio_raw/LC001pacbio.fastq.gz

I got this output report from the SLURM:

-- Canu snapshot v2.0-development +375 changes (r9868 9492acc56ebe1ff0c7ee7b13ae1704a7db68dc5d)
--
-- Detected Java(TM) Runtime Environment '1.8.0_242' (from 'java') with -d64 support.
--
-- WARNING:
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.
-- WARNING:
--
-- Detected 48 CPUs and 126 gigabytes of memory.
-- Detected Slurm with 'sinfo' binary in /usr/bin/sinfo.
-- Detected Slurm with task IDs up to 511 allowed.
-- 
-- Found   2 hosts with  24 cores and   22 GB memory under Slurm control.
-- Found  48 hosts with  48 cores and  124 GB memory under Slurm control.
--
--                         (tag)Threads
--                (tag)Memory         |
--        (tag)             |         |  algorithm
--        -------  ----------  --------  -----------------------------
-- Grid:  meryl     24.000 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       16.000 GB   24 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   22.000 GB   16 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    24.000 GB   16 CPUs  (overlap detection)
-- Grid:  utgovl    24.000 GB   16 CPUs  (overlap detection)
-- Grid:  cor       24.000 GB    4 CPUs  (read correction)
-- Grid:  ovb        4.000 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       32.000 GB    1 CPU   (overlap store sorting)
-- Grid:  red       41.000 GB    8 CPUs  (read error detection)
-- Grid:  oea        8.000 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat        0.121 GB   32 CPUs  (contig construction with bogart)
-- Grid:  cns        -.--- GB    8 CPUs  (consensus)
-- Grid:  gfa       64.000 GB   32 CPUs  (GFA alignment and processing)
-- WARNING:
-- WARNING:  Option '-pacbio-raw <files>' is deprecated.
-- WARNING:  Use option '-pacbio <files>' in the future.
-- WARNING:
--
-- Found untrimmed raw PacBio CLR reads in the input files.
--
-- Generating assembly 'lculinaris' in '/mnt/stori/home/fk8jybr/output/canu_trim/lculinaris':
--    - only correct raw reads.
--
-- Parameters:
--
--  genomeSize        4000000000
--
--  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
--
----------------------------------------
-- Starting command on Tue Feb 25 15:35:39 2020 with 139526.173 GB free disk space

    cd .
    ./lculinaris.seqStore.sh \
    > ./lculinaris.seqStore.err 2>&1

-- Finished on Tue Feb 25 16:53:23 2020 (4664 seconds) with 139481.143 GB free disk space
----------------------------------------
----------------------------------------
-- Starting command on Tue Feb 25 16:53:26 2020 with 139481.106 GB free disk space

    cd .
    /mnt/stori/home/fk8jybr/canu/Linux-amd64/bin/sqStoreDumpMetaData \
      -S ./lculinaris.seqStore \
      -raw \
      -histogram \
      -lengths \
    > ./lculinaris.seqStore/readlengths-cor.dat \
    2> ./lculinaris.seqStore/readlengths-cor.err 

-- Finished on Tue Feb 25 16:53:34 2020 (8 seconds) with 139479.956 GB free disk space
----------------------------------------
--
-- WARNING: gnuplot failed.
--
----------------------------------------
----------------------------------------
-- Starting command on Tue Feb 25 16:53:34 2020 with 139479.956 GB free disk space

    cd .
    /mnt/stori/home/fk8jybr/canu/Linux-amd64/bin/sqStoreDumpMetaData \
      -S ./lculinaris.seqStore \
      -raw \
      -histogram \
    > ./lculinaris.seqStore/readlengths-cor.txt \
    2> ./lculinaris.seqStore/readlengths-cor.err 

-- Finished on Tue Feb 25 16:53:39 2020 (5 seconds) with 139479.937 GB free disk space
----------------------------------------
--
-- In sequence store './lculinaris.seqStore':
--   Found 16602048 reads.
--   Found 130133008970 bases (32.53 times coverage).
--    
--    G=130133008970                     sum of  ||               length     num
--    NG         length     index       lengths  ||                range    seqs
--    ----- ------------ --------- ------------  ||  ------------------- -------
--    00010        15899    602960  13013306386  ||       1000-5676      4169748|----------------------------
--    00020        12310   1544407  26026611074  ||       5677-10353     9556286|---------------------------------------------------------------
--    00030        10536   2695517  39039909482  ||      10354-15030     2122092|--------------
--    00040         9452   4003038  52053208351  ||      15031-19707      507514|----
--    00050         8640   5445065  65066507900  ||      19708-24384      148365|-
--    00060         7972   7014450  78079812011  ||      24385-29061       47939|-
--    00070         7394   8710214  91093107687  ||      29062-33738       17781|-
--    00080         6814  10540237 104106410693  ||      33739-38415        8418|-
--    00090         5497  12613562 117119710915  ||      38416-43092        5187|-
--    00100         1000  16602047 130133008970  ||      43093-47769        3608|-
--    001.000x            16602048 130133008970  ||      47770-52446        2655|-
--                                               ||      52447-57123        2092|-
--                                               ||      57124-61800        1784|-
--                                               ||      61801-66477        1464|-
--                                               ||      66478-71154        1216|-
--                                               ||      71155-75831        1030|-
--                                               ||      75832-80508         871|-
--                                               ||      80509-85185         741|-
--                                               ||      85186-89862         637|-
--                                               ||      89863-94539         453|-
--                                               ||      94540-99216         432|-
--                                               ||      99217-103893        333|-
--                                               ||     103894-108570        280|-
--                                               ||     108571-113247        238|-
--                                               ||     113248-117924        161|-
--                                               ||     117925-122601        129|-
--                                               ||     122602-127278        127|-
--                                               ||     127279-131955         76|-
--                                               ||     131956-136632         69|-
--                                               ||     136633-141309         56|-
--                                               ||     141310-145986         39|-
--                                               ||     145987-150663         44|-
--                                               ||     150664-155340         31|-
--                                               ||     155341-160017         17|-
--                                               ||     160018-164694         21|-
--                                               ||     164695-169371         21|-
--                                               ||     169372-174048         16|-
--                                               ||     174049-178725          9|-
--                                               ||     178726-183402         11|-
--                                               ||     183403-188079          8|-
--                                               ||     188080-192756         13|-
--                                               ||     192757-197433          8|-
--                                               ||     197434-202110          5|-
--                                               ||     202111-206787          4|-
--                                               ||     206788-211464          4|-
--                                               ||     211465-216141          6|-
--                                               ||     216142-220818          3|-
--                                               ||     220819-225495          2|-
--                                               ||     225496-230172          1|-
--                                               ||     230173-234849          3|-
--    
-- New report created.
----------------------------------------
-- Starting command on Tue Feb 25 16:53:39 2020 with 139479.937 GB free disk space

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

-- Finished on Tue Feb 25 16:54:17 2020 (38 seconds) with 139480.679 GB free disk space
----------------------------------------
--  segments   memory batches
--  -------- -------- -------
--        01 15.00 GB       1
--        02 14.50 GB       1
--        04 14.00 GB       1
--        06 14.00 GB       1
--        08 13.50 GB       1
--        12 13.50 GB       1
--        16 13.00 GB       1
--        20 13.00 GB       1
--        24 12.00 GB       1
--        32  8.01 GB       1
--        40  7.00 GB       1
--        48  6.00 GB       1
--        56  5.00 GB       1
--        64  4.01 GB       1
--        96  3.00 GB       1
--
--  For 16602048 reads with 130133008970 bases, limit to 1301 batches.
--  Will count kmers using 01 jobs, each using 17 GB and 8 threads.
--
-- Report changed.
-- Finished stage 'merylConfigure', reset canuIteration.
-- No change in report.
--
-- Running jobs.  First attempt out of 2.
--
-- 'meryl-count.jobSubmit-01.sh' -> job 388028 task 1.
--
----------------------------------------
-- Starting command on Tue Feb 25 16:54:18 2020 with 139480.679 GB free disk space

    cd /mnt/stori/home/fk8jybr/output/canu_trim/lculinaris
    sbatch \
      --depend=afterany:388028 \
      --cpus-per-task=1 \
      --mem-per-cpu=4g   \
      -D `pwd` \
      -J 'canu_lculinaris' \
      -o canu-scripts/canu.01.out  canu-scripts/canu.01.sh
Submitted batch job 388029

-- Finished on Tue Feb 25 16:54:18 2020 (in the blink of an eye) with 139480.679 GB free disk space
----------------------------------------

I got this error report from canu:

Found perl:
   /usr/bin/perl
   This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi

Found java:
   /mnt/stori/home/fk8jybr/.linuxbrew/bin/java
   openjdk version "1.8.0_242"

Found canu:
   /mnt/stori/home/fk8jybr/canu/Linux-amd64/bin/canu
   Canu snapshot v2.0-development +375 changes (r9868 9492acc56ebe1ff0c7ee7b13ae1704a7db68dc5d)

-- Canu snapshot v2.0-development +375 changes (r9868 9492acc56ebe1ff0c7ee7b13ae1704a7db68dc5d)
--
-- Detected Java(TM) Runtime Environment '1.8.0_242' (from 'java') with -d64 support.
--
-- WARNING:
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.
-- WARNING:
--
-- Detected 48 CPUs and 126 gigabytes of memory.
-- Detected Slurm with 'sinfo' binary in /usr/bin/sinfo.
-- Detected Slurm with task IDs up to 511 allowed.
-- 
-- Found   2 hosts with  24 cores and   22 GB memory under Slurm control.
-- Found  48 hosts with  48 cores and  124 GB memory under Slurm control.
--
--                         (tag)Threads
--                (tag)Memory         |
--        (tag)             |         |  algorithm
--        -------  ----------  --------  -----------------------------
-- Grid:  meryl     24.000 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       16.000 GB   24 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   22.000 GB   16 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    24.000 GB   16 CPUs  (overlap detection)
-- Grid:  utgovl    24.000 GB   16 CPUs  (overlap detection)
-- Grid:  cor       24.000 GB    4 CPUs  (read correction)
-- Grid:  ovb        4.000 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       32.000 GB    1 CPU   (overlap store sorting)
-- Grid:  red       41.000 GB    8 CPUs  (read error detection)
-- Grid:  oea        8.000 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat        0.121 GB   32 CPUs  (contig construction with bogart)
-- Grid:  cns        -.--- GB    8 CPUs  (consensus)
-- Grid:  gfa       64.000 GB   32 CPUs  (GFA alignment and processing)
--
-- In 'lculinaris.seqStore', found PacBio CLR reads:
--   PacBio CLR:               1
--
--   Raw:                      1
--
-- Generating assembly 'lculinaris' in '/mnt/stori/home/fk8jybr/output/canu_trim/lculinaris':
--    - only correct raw reads.
--
-- Parameters:
--
--  genomeSize        4000000000
--
--  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.
--
-- Kmer counting (meryl-count) jobs failed, tried 2 times, giving up.
--   job lculinaris.01.meryl FAILED.
--

ABORT:
ABORT: Canu snapshot v2.0-development +375 changes (r9868 9492acc56ebe1ff0c7ee7b13ae1704a7db68dc5d)
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:

Error log from the meryl-count job:

Found perl:
   /usr/bin/perl
   This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi

Found java:
   /mnt/stori/home/fk8jybr/.linuxbrew/bin/java
   openjdk version "1.8.0_242"

Found canu:
   /mnt/stori/home/fk8jybr/canu/Linux-amd64/bin/canu
   Canu snapshot v2.0-development +375 changes (r9868 9492acc56ebe1ff0c7ee7b13ae1704a7db68dc5d)

Running job 1 based on SLURM_ARRAY_TASK_ID=1 and offset=0.
sqStore_loadMetadata()-- Using 'raw' 0x01 reads.
Enabling 8 threads.

Counting 121 (estimated) billion canonical 16-mers from 1 input file:
    canu-seqStore: ../../lculinaris.seqStore

SIMPLE MODE
-----------

  16-mers
    -> 4294967296 entries for counts up to 65535.
    -> 64 Gbits memory used

  130133008970 input bases
    -> expected max count of 520532035, needing 14 extra bits.
    -> 56 Gbits memory used

  15 GB memory needed

COMPLEX MODE
------------

prefix     # of   struct   kmers/    segs/      min     data    total
  bits   prefix   memory   prefix   prefix   memory   memory   memory
------  -------  -------  -------  -------  -------  -------  -------
     1     2  P    58 MB    60 GM  3757 kS   128 kB   469 GB   469 GB
     2     4  P    56 MB    30 GM  1817 kS   256 kB   454 GB   454 GB
     3     8  P    54 MB    15 GM   878 kS   512 kB   439 GB   439 GB
     4    16  P    53 MB  7756 MM   424 kS  1024 kB   424 GB   424 GB
     5    32  P    51 MB  3878 MM   204 kS  2048 kB   409 GB   409 GB
     6    64  P    49 MB  1939 MM    98 kS  4096 kB   393 GB   393 GB
     7   128  P    47 MB   969 MM    47 kS  8192 kB   378 GB   378 GB
     8   256  P    45 MB   484 MM    22 kS    16 MB   363 GB   363 GB
     9   512  P    43 MB   242 MM    10 kS    32 MB   348 GB   348 GB
    10  1024  P    41 MB   121 MM  5333  S    64 MB   333 GB   333 GB
    11  2048  P    40 MB    60 MM  2546  S   128 MB   318 GB   318 GB
    12  4096  P    38 MB    30 MM  1212  S   256 MB   303 GB   303 GB
    13  8192  P    36 MB    15 MM   576  S   512 MB   288 GB   288 GB
    14    16 kP    35 MB  7756 kM   273  S  1024 MB   273 GB   273 GB
    15    32 kP    35 MB  3878 kM   129  S  2048 MB   258 GB   258 GB
    16    64 kP    37 MB  1939 kM    61  S  4096 MB   244 GB   244 GB
    17   128 kP    43 MB   969 kM    29  S  8192 MB   232 GB   232 GB
    18   256 kP    56 MB   484 kM    14  S    16 GB   224 GB   224 GB  Best Value!
    19   512 kP    84 MB   242 kM     7  S    32 GB   224 GB   224 GB
    20  1024 kP   136 MB   121 kM     3  S    64 GB   192 GB   192 GB
    21  2048 kP   256 MB    60 kM     2  S   128 GB   256 GB   256 GB
    22  4096 kP   480 MB    30 kM     1  S   256 GB   256 GB   256 GB
    23  8192 kP   960 MB    15 kM     1  S   512 GB   512 GB   512 GB
    24    16 MP  1920 MB  7757  M     1  S  1024 GB  1024 GB  1025 GB
    25    32 MP  3840 MB  3879  M     1  S  2048 GB  2048 GB  2051 GB
    26    64 MP  7680 MB  1940  M     1  S  4096 GB  4096 GB  4103 GB

FINAL CONFIGURATION
-------------------

Configured simple mode for 15.000 GB memory per batch, and up to 1 batch.

Loading kmers from '../../lculinaris.seqStore' into buckets.
Increasing to 17-bit storage (for kmer 0x0000000000000000).
Increasing to 18-bit storage (for kmer 0x0000000000000000).
Increasing to 19-bit storage (for kmer 0x0000000000000000).
Increasing to 20-bit storage (for kmer 0x0000000000000000).
Increasing to 21-bit storage (for kmer 0x0000000000000000).
Increasing to 22-bit storage (for kmer 0x0000000000000000).
Increasing to 23-bit storage (for kmer 0x0000000000000000).
Increasing to 24-bit storage (for kmer 0x0000000000000000).
Increasing to 25-bit storage (for kmer 0x0000000000000000).
Increasing to 26-bit storage (for kmer 0x0000000000000000).
Increasing to 27-bit storage (for kmer 0x0000000000000000).
slurmstepd: error: *** JOB 388030 ON cn01 CANCELLED AT 2020-02-25T18:54:58 DUE TO TIME LIMIT ***

Can you help me with this issue?

skoren commented 4 years ago

The issue is that your grid has a default time limit which was exceeded:

slurmstepd: error: *** JOB 388030 ON cn01 CANCELLED AT 2020-02-25T18:54:58 DUE TO TIME LIMIT ***

which looks to be about 2 hrs based on the job start time and the time it was cancelled. As listed on the FAQ (https://canu.readthedocs.io/en/latest/faq.html#how-do-i-run-canu-on-my-slurm-sge-pbs-lsf-torque-system), Canu does not specify time as part of its submit commands, you need to add the gridOptions parameter to explicitly request a longer time limit, given your genome size I'd say 3-4 days (or longer if your grid allows it).

On another note, there is no 2.0 release, you're running an untested commit. I would recommend staying with the 1.9 release for production assembly which you can get from the releases page.

hidvegin commented 4 years ago

Thank you for your answer. I tried it your suggestion about gridOptions parameter. I tried to set 7 days because this is the maxiumu what I can allocate in the SLURM. I try the 2.0-develop version only for test. I asked the administrator of HPC cluster that install the canu v1.9 version. I have to wait for it. Until that I test the v2.0.

hidvegin commented 4 years ago

I tried re-run the canu v2.0 with your suggestions. This was the parameter:

canu -correct -p lculinaris -d $HOME/output/canu_trim/lculinaris2 genomeSize=4.0g batMemory=124g batThreads=48 gridOptions="--time=6-00:00:00 --partition=prod --account ID" -pacbio $HOME/input/pacbio_raw/LC001pacbio.fastq.gz

Several days after I get this outputs from canu and erro message:

Found perl:
   /usr/bin/perl
   This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi

Found java:
   /mnt/stori/home/fk8jybr/.linuxbrew/bin/java
   openjdk version "1.8.0_242"

Found canu:
   /mnt/stori/home/fk8jybr/canu/Linux-amd64/bin/canu
   Canu snapshot v2.0-development +375 changes (r9868 9492acc56ebe1ff0c7ee7b13ae1704a7db68dc5d)

-- Canu snapshot v2.0-development +375 changes (r9868 9492acc56ebe1ff0c7ee7b13ae1704a7db68dc5d)
--
-- Detected Java(TM) Runtime Environment '1.8.0_242' (from 'java') with -d64 support.
--
-- WARNING:
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.
-- WARNING:
--
-- Detected 48 CPUs and 126 gigabytes of memory.
-- Detected Slurm with 'sinfo' binary in /usr/bin/sinfo.
-- Detected Slurm with task IDs up to 511 allowed.
-- 
-- Found   2 hosts with  24 cores and   22 GB memory under Slurm control.
-- Found  48 hosts with  48 cores and  124 GB memory under Slurm control.
--
--                         (tag)Threads
--                (tag)Memory         |
--        (tag)             |         |  algorithm
--        -------  ----------  --------  -----------------------------
-- Grid:  meryl     24.000 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       16.000 GB   24 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   22.000 GB   16 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    24.000 GB   16 CPUs  (overlap detection)
-- Grid:  utgovl    24.000 GB   16 CPUs  (overlap detection)
-- Grid:  cor       24.000 GB    4 CPUs  (read correction)
-- Grid:  ovb        4.000 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       32.000 GB    1 CPU   (overlap store sorting)
-- Grid:  red       41.000 GB    8 CPUs  (read error detection)
-- Grid:  oea        8.000 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat      124.000 GB   48 CPUs  (contig construction with bogart)
-- Grid:  cns        -.--- GB    8 CPUs  (consensus)
-- Grid:  gfa       64.000 GB   32 CPUs  (GFA alignment and processing)
--
-- In 'lculinaris.seqStore', found PacBio CLR reads:
--   PacBio CLR:               1
--
--   Raw:                      1
--
-- Generating assembly 'lculinaris' in '/mnt/stori/home/fk8jybr/output/canu_trim/lculinaris2':
--    - only correct raw reads.
--
-- Parameters:
--
--  genomeSize        4000000000
--
--  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.
-- Found 1 Kmer counting (meryl) outputs.
-- No change in report.
-- Finished stage 'cor-merylCountCheck', reset canuIteration.
-- No change in report.
--
-- Running jobs.  First attempt out of 2.
--
-- 'meryl-process.jobSubmit-01.sh' -> job 388050 task 1.
--
----------------------------------------
-- Starting command on Thu Feb 27 03:52:01 2020 with 139449.46 GB free disk space

    cd /mnt/stori/home/fk8jybr/output/canu_trim/lculinaris2
    sbatch \
      --depend=afterany:388050 \
      --cpus-per-task=1 \
      --mem-per-cpu=4g \
      --time=6-00:00:00 \
      --partition=prod \
      --account denolen  \
      -D `pwd` \
      -J 'canu_lculinaris' \
      -o canu-scripts/canu.02.out  canu-scripts/canu.02.sh
Submitted batch job 388051

-- Finished on Thu Feb 27 03:52:01 2020 (lickety-split) with 139449.46 GB free disk space
----------------------------------------

Found perl:
   /usr/bin/perl
   This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi

Found java:
   /mnt/stori/home/fk8jybr/.linuxbrew/bin/java
   openjdk version "1.8.0_242"

Found canu:
   /mnt/stori/home/fk8jybr/canu/Linux-amd64/bin/canu
   Canu snapshot v2.0-development +375 changes (r9868 9492acc56ebe1ff0c7ee7b13ae1704a7db68dc5d)

-- Canu snapshot v2.0-development +375 changes (r9868 9492acc56ebe1ff0c7ee7b13ae1704a7db68dc5d)
--
-- Detected Java(TM) Runtime Environment '1.8.0_242' (from 'java') with -d64 support.
--
-- WARNING:
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.
-- WARNING:
--
-- Detected 48 CPUs and 126 gigabytes of memory.
-- Detected Slurm with 'sinfo' binary in /usr/bin/sinfo.
-- Detected Slurm with task IDs up to 511 allowed.
-- 
-- Found   2 hosts with  24 cores and   22 GB memory under Slurm control.
-- Found  48 hosts with  48 cores and  124 GB memory under Slurm control.
--
--                         (tag)Threads
--                (tag)Memory         |
--        (tag)             |         |  algorithm
--        -------  ----------  --------  -----------------------------
-- Grid:  meryl     24.000 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       16.000 GB   24 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   22.000 GB   16 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    24.000 GB   16 CPUs  (overlap detection)
-- Grid:  utgovl    24.000 GB   16 CPUs  (overlap detection)
-- Grid:  cor       24.000 GB    4 CPUs  (read correction)
-- Grid:  ovb        4.000 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       32.000 GB    1 CPU   (overlap store sorting)
-- Grid:  red       41.000 GB    8 CPUs  (read error detection)
-- Grid:  oea        8.000 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat      124.000 GB   48 CPUs  (contig construction with bogart)
-- Grid:  cns        -.--- GB    8 CPUs  (consensus)
-- Grid:  gfa       64.000 GB   32 CPUs  (GFA alignment and processing)
--
-- In 'lculinaris.seqStore', found PacBio CLR reads:
--   PacBio CLR:               1
--
--   Raw:                      1
--
-- Generating assembly 'lculinaris' in '/mnt/stori/home/fk8jybr/output/canu_trim/lculinaris2':
--    - only correct raw reads.
--
-- Parameters:
--
--  genomeSize        4000000000
--
--  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.
-- Meryl finished successfully.  Kmer frequency histogram:
--
-- WARNING: gnuplot failed.
--
----------------------------------------
--
--  16-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1         0                                                                        0.0000 0.0000
--       2-     2  64126708 ****************                                                       0.0306 0.0010
--       3-     4 169270722 *******************************************                            0.0692 0.0029
--       5-     7 258298328 ******************************************************************     0.1542 0.0090
--       8-    11 273347908 ********************************************************************** 0.2713 0.0222
--      12-    16 242748348 **************************************************************         0.3920 0.0424
--      17-    22 201336966 ***************************************************                    0.4998 0.0683
--      23-    29 162750551 *****************************************                              0.5903 0.0979
--      30-    37 130158672 *********************************                                      0.6641 0.1298
--      38-    46 103801910 **************************                                             0.7236 0.1627
--      47-    56  82789664 *********************                                                  0.7713 0.1956
--      57-    67  66296011 ****************                                                       0.8096 0.2279
--      68-    79  53401713 *************                                                          0.8404 0.2590
--      80-    92  43321562 ***********                                                            0.8652 0.2888
--      93-   106  35361532 *********                                                              0.8855 0.3171
--     107-   121  29075935 *******                                                                0.9020 0.3439
--     122-   137  24055121 ******                                                                 0.9157 0.3691
--     138-   154  20033667 *****                                                                  0.9270 0.3928
--     155-   172  16792932 ****                                                                   0.9364 0.4152
--     173-   191  14151421 ***                                                                    0.9443 0.4361
--     192-   211  12007133 ***                                                                    0.9510 0.4558
--     212-   232  10240165 **                                                                     0.9567 0.4743
--     233-   254   8778255 **                                                                     0.9615 0.4917
--     255-   277   7558987 *                                                                      0.9657 0.5080
--     278-   301   6548117 *                                                                      0.9693 0.5234
--     302-   326   5700869 *                                                                      0.9724 0.5380
--     327-   352   4986015 *                                                                      0.9751 0.5517
--     353-   379   4377721 *                                                                      0.9774 0.5646
--     380-   407   3856902                                                                        0.9795 0.5769
--     408-   436   3406540                                                                        0.9814 0.5886
--     437-   466   3027570                                                                        0.9830 0.5996
--     467-   497   2695673                                                                        0.9844 0.6101
--     498-   529   2403736                                                                        0.9857 0.6201
--     530-   562   2157183                                                                        0.9868 0.6295
--     563-   596   1935784                                                                        0.9879 0.6386
--     597-   631   1742844                                                                        0.9888 0.6472
--     632-   667   1573870                                                                        0.9896 0.6554
--     668-   704   1427589                                                                        0.9904 0.6633
--     705-   742   1297292                                                                        0.9910 0.6708
--     743-   781   1181074                                                                        0.9917 0.6780
--     782-   821   1078513                                                                        0.9922 0.6849
--
--           0 (max occurrences)
-- 129844687695 (total mers, non-unique)
--  2094348602 (distinct mers, non-unique)
--           0 (unique mers)
-- Report changed.
-- Finished stage 'meryl-process', reset canuIteration.
--
-- Removing meryl database 'correction/0-mercounts/lculinaris.ms16'.
--
-- OVERLAPPER (mhap) (correction)
--
-- Set corMhapSensitivity=normal based on read coverage of 32.
--
-- PARAMETERS: hashes=512, minMatches=3, threshold=0.78
--
-- Given 19.8 GB, can fit 59400 reads per block.
-- For 281 blocks, set stride to 70 blocks.
-- Logging partitioning to 'correction/1-overlapper/partitioning.log'.
-- Configured 280 mhap precompute jobs.
-- Configured 697 mhap overlap jobs.
-- No change in report.
-- Finished stage 'cor-mhapConfigure', reset canuIteration.
-- No change in report.
--
-- Running jobs.  First attempt out of 2.
--
-- 'precompute.jobSubmit-01.sh' -> job 388052 tasks 1-280.
--
----------------------------------------
-- Starting command on Thu Feb 27 03:55:19 2020 with 139463.895 GB free disk space

    cd /mnt/stori/home/fk8jybr/output/canu_trim/lculinaris2
    sbatch \
      --depend=afterany:388052 \
      --cpus-per-task=1 \
      --mem-per-cpu=4g \
      --time=6-00:00:00 \
      --partition=prod \
      --account denolen  \
      -D `pwd` \
      -J 'canu_lculinaris' \
      -o canu-scripts/canu.03.out  canu-scripts/canu.03.sh
Submitted batch job 388053

-- Finished on Thu Feb 27 03:55:20 2020 (one second) with 139463.135 GB free disk space
----------------------------------------

Found perl:
   /usr/bin/perl
   This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi

Found java:
   /mnt/stori/home/fk8jybr/.linuxbrew/bin/java
   openjdk version "1.8.0_242"

Found canu:
   /mnt/stori/home/fk8jybr/canu/Linux-amd64/bin/canu
   Canu snapshot v2.0-development +375 changes (r9868 9492acc56ebe1ff0c7ee7b13ae1704a7db68dc5d)

-- Canu snapshot v2.0-development +375 changes (r9868 9492acc56ebe1ff0c7ee7b13ae1704a7db68dc5d)
--
-- Detected Java(TM) Runtime Environment '1.8.0_242' (from 'java') with -d64 support.
--
-- WARNING:
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.
-- WARNING:
--
-- Detected 48 CPUs and 126 gigabytes of memory.
-- Detected Slurm with 'sinfo' binary in /usr/bin/sinfo.
-- Detected Slurm with task IDs up to 511 allowed.
-- 
-- Found   2 hosts with  24 cores and   22 GB memory under Slurm control.
-- Found  48 hosts with  48 cores and  124 GB memory under Slurm control.
--
--                         (tag)Threads
--                (tag)Memory         |
--        (tag)             |         |  algorithm
--        -------  ----------  --------  -----------------------------
-- Grid:  meryl     24.000 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       16.000 GB   24 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   22.000 GB   16 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    24.000 GB   16 CPUs  (overlap detection)
-- Grid:  utgovl    24.000 GB   16 CPUs  (overlap detection)
-- Grid:  cor       24.000 GB    4 CPUs  (read correction)
-- Grid:  ovb        4.000 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       32.000 GB    1 CPU   (overlap store sorting)
-- Grid:  red       41.000 GB    8 CPUs  (read error detection)
-- Grid:  oea        8.000 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat      124.000 GB   48 CPUs  (contig construction with bogart)
-- Grid:  cns        -.--- GB    8 CPUs  (consensus)
-- Grid:  gfa       64.000 GB   32 CPUs  (GFA alignment and processing)
--
-- In 'lculinaris.seqStore', found PacBio CLR reads:
--   PacBio CLR:               1
--
--   Raw:                      1
--
-- Generating assembly 'lculinaris' in '/mnt/stori/home/fk8jybr/output/canu_trim/lculinaris2':
--    - only correct raw reads.
--
-- Parameters:
--
--  genomeSize        4000000000
--
--  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.
--
-- OVERLAPPER (mhap) (correction) complete, not rewriting scripts.
--
-- All 280 mhap precompute jobs finished successfully.
-- No change in report.
-- Finished stage 'cor-mhapPrecomputeCheck', reset canuIteration.
-- No change in report.
--
-- Running jobs.  First attempt out of 2.
--
-- 'mhap.jobSubmit-01.sh' -> job 388333 tasks 1-511.
-- 'mhap.jobSubmit-02.sh' -> job 388334 tasks 512-697.
--
----------------------------------------
-- Starting command on Thu Feb 27 09:26:33 2020 with 139143.537 GB free disk space

    cd /mnt/stori/home/fk8jybr/output/canu_trim/lculinaris2
    sbatch \
      --depend=afterany:388333:388334 \
      --cpus-per-task=1 \
      --mem-per-cpu=4g \
      --time=6-00:00:00 \
      --partition=prod \
      --account denolen  \
      -D `pwd` \
      -J 'canu_lculinaris' \
      -o canu-scripts/canu.04.out  canu-scripts/canu.04.sh
Submitted batch job 388335

-- Finished on Thu Feb 27 09:26:33 2020 (furiously fast) with 139143.537 GB free disk space
----------------------------------------

Found perl:
   /usr/bin/perl
   This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi

Found java:
   /mnt/stori/home/fk8jybr/.linuxbrew/bin/java
   openjdk version "1.8.0_242"

Found canu:
   /mnt/stori/home/fk8jybr/canu/Linux-amd64/bin/canu
   Canu snapshot v2.0-development +375 changes (r9868 9492acc56ebe1ff0c7ee7b13ae1704a7db68dc5d)

-- Canu snapshot v2.0-development +375 changes (r9868 9492acc56ebe1ff0c7ee7b13ae1704a7db68dc5d)
--
-- Detected Java(TM) Runtime Environment '1.8.0_242' (from 'java') with -d64 support.
--
-- WARNING:
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.
-- WARNING:
--
-- Detected 48 CPUs and 126 gigabytes of memory.
-- Detected Slurm with 'sinfo' binary in /usr/bin/sinfo.
-- Detected Slurm with task IDs up to 511 allowed.
-- 
-- Found   2 hosts with  24 cores and   22 GB memory under Slurm control.
-- Found  48 hosts with  48 cores and  124 GB memory under Slurm control.
--
--                         (tag)Threads
--                (tag)Memory         |
--        (tag)             |         |  algorithm
--        -------  ----------  --------  -----------------------------
-- Grid:  meryl     24.000 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       16.000 GB   24 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   22.000 GB   16 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    24.000 GB   16 CPUs  (overlap detection)
-- Grid:  utgovl    24.000 GB   16 CPUs  (overlap detection)
-- Grid:  cor       24.000 GB    4 CPUs  (read correction)
-- Grid:  ovb        4.000 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       32.000 GB    1 CPU   (overlap store sorting)
-- Grid:  red       41.000 GB    8 CPUs  (read error detection)
-- Grid:  oea        8.000 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat      124.000 GB   48 CPUs  (contig construction with bogart)
-- Grid:  cns        -.--- GB    8 CPUs  (consensus)
-- Grid:  gfa       64.000 GB   32 CPUs  (GFA alignment and processing)
--
-- In 'lculinaris.seqStore', found PacBio CLR reads:
--   PacBio CLR:               1
--
--   Raw:                      1
--
-- Generating assembly 'lculinaris' in '/mnt/stori/home/fk8jybr/output/canu_trim/lculinaris2':
--    - only correct raw reads.
--
-- Parameters:
--
--  genomeSize        4000000000
--
--  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.
--
-- OVERLAPPER (mhap) (correction) complete, not rewriting scripts.
--
--
-- Mhap overlap jobs failed, retry.
--   job correction/1-overlapper/results/000247.ovb FAILED.
--   job correction/1-overlapper/results/000304.ovb FAILED.
--   job correction/1-overlapper/results/000305.ovb FAILED.
--   job correction/1-overlapper/results/000307.ovb FAILED.
--   job correction/1-overlapper/results/000308.ovb FAILED.
--   job correction/1-overlapper/results/000322.ovb FAILED.
--   job correction/1-overlapper/results/000323.ovb FAILED.
--   job correction/1-overlapper/results/000325.ovb FAILED.
--   job correction/1-overlapper/results/000326.ovb FAILED.
--   job correction/1-overlapper/results/000327.ovb FAILED.
--   job correction/1-overlapper/results/000328.ovb FAILED.
--   job correction/1-overlapper/results/000329.ovb FAILED.
--   job correction/1-overlapper/results/000331.ovb FAILED.
--   job correction/1-overlapper/results/000332.ovb FAILED.
--   job correction/1-overlapper/results/000333.ovb FAILED.
--   job correction/1-overlapper/results/000334.ovb FAILED.
--   job correction/1-overlapper/results/000335.ovb FAILED.
--   job correction/1-overlapper/results/000336.ovb FAILED.
--   job correction/1-overlapper/results/000337.ovb FAILED.
--   job correction/1-overlapper/results/000338.ovb FAILED.
--   job correction/1-overlapper/results/000339.ovb FAILED.
--   job correction/1-overlapper/results/000340.ovb FAILED.
--   job correction/1-overlapper/results/000341.ovb FAILED.
--   job correction/1-overlapper/results/000342.ovb FAILED.
--   job correction/1-overlapper/results/000343.ovb FAILED.
--   job correction/1-overlapper/results/000344.ovb FAILED.
--   job correction/1-overlapper/results/000345.ovb FAILED.
--   job correction/1-overlapper/results/000346.ovb FAILED.
--   job correction/1-overlapper/results/000347.ovb FAILED.
--   job correction/1-overlapper/results/000348.ovb FAILED.
--   job correction/1-overlapper/results/000349.ovb FAILED.
--   job correction/1-overlapper/results/000350.ovb FAILED.
--   job correction/1-overlapper/results/000351.ovb FAILED.
--   job correction/1-overlapper/results/000353.ovb FAILED.
--   job correction/1-overlapper/results/000354.ovb FAILED.
--   job correction/1-overlapper/results/000355.ovb FAILED.
--   job correction/1-overlapper/results/000357.ovb FAILED.
--   job correction/1-overlapper/results/000358.ovb FAILED.
--
-- No change in report.
--
-- Running jobs.  Second attempt out of 2.
--
-- 'mhap.jobSubmit-01.sh' -> job 389042 task 247.
-- 'mhap.jobSubmit-02.sh' -> job 389043 tasks 304-305.
-- 'mhap.jobSubmit-03.sh' -> job 389044 tasks 307-308.
-- 'mhap.jobSubmit-04.sh' -> job 389045 tasks 322-323.
-- 'mhap.jobSubmit-05.sh' -> job 389046 tasks 325-329.
-- 'mhap.jobSubmit-06.sh' -> job 389047 tasks 331-351.
-- 'mhap.jobSubmit-07.sh' -> job 389048 tasks 353-355.
-- 'mhap.jobSubmit-08.sh' -> job 389049 tasks 357-358.
--
----------------------------------------
-- Starting command on Mon Mar  2 10:56:00 2020 with 129760.222 GB free disk space

    cd /mnt/stori/home/fk8jybr/output/canu_trim/lculinaris2
    sbatch \
      --depend=afterany:389042:389043:389044:389045:389046:389047:389048:389049 \
      --cpus-per-task=1 \
      --mem-per-cpu=5g \
      --time=6-00:00:00 \
      --partition=prod \
      --account denolen  \
      -D `pwd` \
      -J 'canu_lculinaris' \
      -o canu-scripts/canu.05.out  canu-scripts/canu.05.sh
Submitted batch job 389050

-- Finished on Mon Mar  2 10:56:00 2020 (furiously fast) with 129760.215 GB free disk space
----------------------------------------

Found perl:
   /usr/bin/perl
   This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi

Found java:
   /mnt/stori/home/fk8jybr/.linuxbrew/bin/java
   openjdk version "1.8.0_242"

Found canu:
   /mnt/stori/home/fk8jybr/canu/Linux-amd64/bin/canu
   Canu snapshot v2.0-development +375 changes (r9868 9492acc56ebe1ff0c7ee7b13ae1704a7db68dc5d)

-- Canu snapshot v2.0-development +375 changes (r9868 9492acc56ebe1ff0c7ee7b13ae1704a7db68dc5d)
--
-- Detected Java(TM) Runtime Environment '1.8.0_242' (from 'java') with -d64 support.
--
-- WARNING:
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.
-- WARNING:
--
-- Detected 48 CPUs and 126 gigabytes of memory.
-- Detected Slurm with 'sinfo' binary in /usr/bin/sinfo.
-- Detected Slurm with task IDs up to 511 allowed.
-- 
-- Found   2 hosts with  24 cores and   22 GB memory under Slurm control.
-- Found  48 hosts with  48 cores and  124 GB memory under Slurm control.
--
--                         (tag)Threads
--                (tag)Memory         |
--        (tag)             |         |  algorithm
--        -------  ----------  --------  -----------------------------
-- Grid:  meryl     24.000 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       16.000 GB   24 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   22.000 GB   16 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    24.000 GB   16 CPUs  (overlap detection)
-- Grid:  utgovl    24.000 GB   16 CPUs  (overlap detection)
-- Grid:  cor       24.000 GB    4 CPUs  (read correction)
-- Grid:  ovb        4.000 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       32.000 GB    1 CPU   (overlap store sorting)
-- Grid:  red       41.000 GB    8 CPUs  (read error detection)
-- Grid:  oea        8.000 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat      124.000 GB   48 CPUs  (contig construction with bogart)
-- Grid:  cns        -.--- GB    8 CPUs  (consensus)
-- Grid:  gfa       64.000 GB   32 CPUs  (GFA alignment and processing)
--
-- In 'lculinaris.seqStore', found PacBio CLR reads:
--   PacBio CLR:               1
--
--   Raw:                      1
--
-- Generating assembly 'lculinaris' in '/mnt/stori/home/fk8jybr/output/canu_trim/lculinaris2':
--    - only correct raw reads.
--
-- Parameters:
--
--  genomeSize        4000000000
--
--  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.
--
-- OVERLAPPER (mhap) (correction) complete, not rewriting scripts.
--
--
-- Mhap overlap jobs failed, tried 2 times, giving up.
--   job correction/1-overlapper/results/000247.ovb FAILED.
--   job correction/1-overlapper/results/000304.ovb FAILED.
--   job correction/1-overlapper/results/000305.ovb FAILED.
--   job correction/1-overlapper/results/000307.ovb FAILED.
--   job correction/1-overlapper/results/000308.ovb FAILED.
--   job correction/1-overlapper/results/000322.ovb FAILED.
--   job correction/1-overlapper/results/000323.ovb FAILED.
--   job correction/1-overlapper/results/000325.ovb FAILED.
--   job correction/1-overlapper/results/000326.ovb FAILED.
--   job correction/1-overlapper/results/000327.ovb FAILED.
--   job correction/1-overlapper/results/000328.ovb FAILED.
--   job correction/1-overlapper/results/000329.ovb FAILED.
--   job correction/1-overlapper/results/000331.ovb FAILED.
--   job correction/1-overlapper/results/000332.ovb FAILED.
--   job correction/1-overlapper/results/000333.ovb FAILED.
--   job correction/1-overlapper/results/000334.ovb FAILED.
--   job correction/1-overlapper/results/000335.ovb FAILED.
--   job correction/1-overlapper/results/000336.ovb FAILED.
--   job correction/1-overlapper/results/000337.ovb FAILED.
--   job correction/1-overlapper/results/000338.ovb FAILED.
--   job correction/1-overlapper/results/000339.ovb FAILED.
--   job correction/1-overlapper/results/000340.ovb FAILED.
--   job correction/1-overlapper/results/000341.ovb FAILED.
--   job correction/1-overlapper/results/000342.ovb FAILED.
--   job correction/1-overlapper/results/000343.ovb FAILED.
--   job correction/1-overlapper/results/000344.ovb FAILED.
--   job correction/1-overlapper/results/000345.ovb FAILED.
--   job correction/1-overlapper/results/000346.ovb FAILED.
--   job correction/1-overlapper/results/000347.ovb FAILED.
--   job correction/1-overlapper/results/000348.ovb FAILED.
--   job correction/1-overlapper/results/000349.ovb FAILED.
--   job correction/1-overlapper/results/000350.ovb FAILED.
--   job correction/1-overlapper/results/000351.ovb FAILED.
--   job correction/1-overlapper/results/000353.ovb FAILED.
--   job correction/1-overlapper/results/000354.ovb FAILED.
--   job correction/1-overlapper/results/000355.ovb FAILED.
--   job correction/1-overlapper/results/000357.ovb FAILED.
--   job correction/1-overlapper/results/000358.ovb FAILED.
--

ABORT:
ABORT: Canu snapshot v2.0-development +375 changes (r9868 9492acc56ebe1ff0c7ee7b13ae1704a7db68dc5d)
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:

How can I resolve this issue?

skoren commented 4 years ago

Post one of the failing job logs, it's likely a JVM or grid issue.

I'll again reiterate that running the unreleased version is not recommended, it's not an appropriate test since you'll probably hit errors not present in the release. You don't need to wait to have a release installed. If you were able to download/compile the tip, you can also just download/compile the release tar instead or just use extract the pre-compiled binaries in your home directory.

hidvegin commented 4 years ago

I installed the canu v1.9 as you suggested. At the ovlB phase the cluster went down because there was an storage problem with the cluster. I re-run the canu with the same parameters. I got this error:

Found perl:
   /usr/bin/perl
   This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi

Found java:
   /mnt/stori/home/fk8jybr/.linuxbrew/bin/java
   openjdk version "1.8.0_242"

Found canu:
   /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/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 '1.8.0_242' (from 'java') with -d64 support.
--
-- WARNING:
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.
-- WARNING:
--
-- Detected 48 CPUs and 126 gigabytes of memory.
-- Detected Slurm with 'sinfo' binary in /usr/bin/sinfo.
-- Detected Slurm with task IDs up to 511 allowed.
-- 
-- Found   2 hosts with  24 cores and   22 GB memory under Slurm control.
-- Found  48 hosts with  48 cores and  124 GB memory under Slurm control.
--
--                     (tag)Threads
--            (tag)Memory         |
--        (tag)         |         |  algorithm
--        -------  ------  --------  -----------------------------
-- Grid:  meryl     24 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       16 GB   24 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   22 GB   16 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    24 GB   16 CPUs  (overlap detection)
-- Grid:  utgovl    24 GB   16 CPUs  (overlap detection)
-- Grid:  cor       24 GB    4 CPUs  (read correction)
-- Grid:  ovb        4 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       32 GB    1 CPU   (overlap store sorting)
-- Grid:  red       41 GB    8 CPUs  (read error detection)
-- Grid:  oea        8 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat      124 GB   48 CPUs  (contig construction with bogart)
-- Grid:  cns      --- GB    8 CPUs  (consensus)
-- Grid:  gfa       64 GB   32 CPUs  (GFA alignment and processing)
--
-- In 'lculinaris.seqStore', found PacBio reads:
--   Raw:        16602048
--   Corrected:  0
--   Trimmed:    0
--
-- Generating assembly 'lculinaris' in '/mnt/stori/home/fk8jybr/output/canu_corrected/lculinaris'
--
-- Parameters:
--
--  genomeSize        4000000000
--
--  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.
--
-- Creating overlap store correction/lculinaris.ovlStore using:
--    655 buckets
--    655 slices
--        using at most 29 GB memory each
--
-- Overlap store bucketizer jobs failed, tried 2 times, giving up.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0001 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0002 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0003 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0004 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0005 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0006 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0007 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0008 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0009 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0010 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0011 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0012 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0013 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0014 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0015 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0016 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0017 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0018 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0019 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0020 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0021 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0022 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0023 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0024 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0025 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0026 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0027 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0028 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0029 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0030 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0031 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0032 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0033 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0034 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0035 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0036 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0037 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0038 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0039 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0040 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0041 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0042 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0043 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0044 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0045 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0046 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0047 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0048 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0049 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0050 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0051 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0052 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0053 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0054 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0055 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0056 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0057 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0058 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0059 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0060 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0061 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0062 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0063 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0064 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0065 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0066 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0067 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0068 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0069 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0070 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0071 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0072 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0073 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0074 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0075 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0076 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0077 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0078 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0079 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0080 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0081 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0082 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0083 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0084 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0085 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0086 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0087 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0088 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0089 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0090 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0091 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0092 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0093 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0094 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0095 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0096 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0097 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0098 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0099 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0100 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0101 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0102 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0103 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0104 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0105 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0106 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0107 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0108 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0109 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0110 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0111 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0112 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0113 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0114 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0115 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0116 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0117 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0118 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0119 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0120 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0121 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0122 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0123 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0124 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0125 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0126 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0127 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0128 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0129 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0130 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0131 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0132 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0133 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0134 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0135 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0136 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0137 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0138 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0139 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0141 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0142 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0143 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0144 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0145 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0146 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0147 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0148 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0149 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0150 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0151 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0152 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0153 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0154 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0155 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0156 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0157 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0158 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0159 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0160 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0161 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0162 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0163 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0164 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0165 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0166 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0167 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0168 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0169 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0170 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0171 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0172 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0173 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0174 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0175 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0176 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0177 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0178 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0179 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0180 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0181 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0182 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0183 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0184 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0185 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0186 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0187 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0189 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0190 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0191 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0193 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0194 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0195 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0197 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0198 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0199 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0201 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0202 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0203 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0205 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0206 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0207 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0209 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0210 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0211 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0213 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0214 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0215 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0217 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0218 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0219 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0223 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0225 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0226 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0227 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0229 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0230 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0231 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0233 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0234 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0257 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0258 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0259 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0261 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0262 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0263 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0265 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0266 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0267 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0269 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0270 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0271 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0273 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0274 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0275 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0277 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0278 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0279 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0280 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0281 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0282 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0283 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0284 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0285 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0286 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0287 FAILED.
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--   job correction/lculinaris.ovlStore.BUILDING/bucket0641 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0642 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0643 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0644 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0645 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0646 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0647 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0648 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0649 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0650 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0651 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0652 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0653 FAILED.
--   job correction/lculinaris.ovlStore.BUILDING/bucket0654 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:

Should I delete the /correction/lculinaris.ovlStore.BUILDING/ folder and after that re-run the canu with the same parameter which I used for generate the 0-mercounts and 1-overlapper folders? When I re-run the canu I did not delete the lculinaris.ovlStore.BUILDING folder.

brianwalenz commented 4 years ago

On the suspicion that it was these jobs that killed your file server, instead of deleting the ovlStore directory and restarting canu, lets run these by hand with a slight modification to limit the number of jobs that run at the same time.

1) Remove all the bucket* directories in lculinaris.ovlStore.BUILDING. 2) Edit scripts/1-bucketize.jobSubmit-01.sh to change the -a option from something similar to -a 1-654 to -a 1-654%20. This will tell slurm to run only 20 jobs at the same time. I picked 20 for no particular reason. It's probably wildly conservative. 3) Still in directory lculinaris.ovlStore.BUILDING (that is, NOT in the scripts/ directory) submit the jobs to the grid with sh scripts/1-bucketize.jobSubmit-01.sh 4) Wait for them to finish and then restart canu.

Or you can delete the ovlStore directory entirely, restart canu, and see if you get a nasty email from your system managers. It depends on your mood, I guess....

hidvegin commented 4 years ago

Thank you for your answer. I deleted all of the bucket* folders. I changed the scripts/1-bucketize.jobSubmit-01.sh to this:

#!/bin/sh

sbatch \
  --cpus-per-task=1 --mem-per-cpu=5g --time=7-00:00:00 --partition=prod --account denolen -o logs/1-bucketize.%A_%a.out \
  -D `pwd` -J "ovB_lculinaris" \
  -a 1-654%20 \
  `pwd`/scripts/1-bucketize.sh 0 \
> ./scripts/1-bucketize.jobSubmit-01.out 2>&1

Should I change anything else? If I understand you, I should run this script with sh scripts/1-bucketize.jobSubmit-01.sh in lculinaris.ovlStore.BUILDING folder.

So I do not have to use any other sbatch script to the SLURM. And if this script will be finished I can re-run the canu with the same paramaters which I used before.

skoren commented 4 years ago

Yes, that's right run the script from inside the BUILDING folder. You shouldn't have to run any other commands. Wait until all the jobs have completed (using SLURM to monitor the jobs). There will be log files output in the logs/1-bucket* files. You can check if they're reporting any errors or not. If they complete and you don't see any errors, then you can re-run the same canu command and parameters you used before.

hidvegin commented 4 years ago

I tried delete all of the BUILDING folder and rerun canu with the same parameters which I used before. Now since three days run the canu, but I get this error type:

Found perl:
   /usr/bin/perl
   This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi

Found java:
   /mnt/stori/home/fk8jybr/.linuxbrew/bin/java
   openjdk version "1.8.0_242"

Found canu:
   /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/bin/canu
   Canu 1.9

Running job 101 based on SLURM_ARRAY_TASK_ID=101 and offset=0.

Attempting to increase maximum allowed processes and open files.
  Max processes per user limited to 514718, no increase possible.
  Max open files limited to 131072, no increase possible.

Opened '../lculinaris.seqStore' with 16602048 reads.

Constructing slice 101 for store './lculinaris.ovlStore.BUILDING'.
 - Filtering overlaps over 1.0000 fraction error.

Bucketizing input    1 out of    1 - '1-overlapper/results/000101.ovb'
Success!
slurmstepd: error: Unable to send job complete message: Unable to contact slurm controller (connect failure)

All of the 654 process (slice) are running but I found several directories with bucketXXXX (XXXX=numbers). I think that several bucketizing jobs finished but canu can not send the complete message to the SLURM. How could I resolve this? How could I find which process is finished which not?

skoren commented 4 years ago

I wouldn't worry about it as the end of the job seems to indicate it finished, slurm just had an issue shutting the job down. Canu has tolerance for intermitted grid errors so it should find any jobs which did not finish for you and re-run them. I'd check your scheduler for remaining canu bucketizing jobs (if any) and the main canu job (to make sure the grid error didn't delete jobs in the queue).

skoren commented 4 years ago

Idle, seemed to be intermediate grid failure.

hidvegin commented 4 years ago

@brianwalenz and @skoren I tried run canu at bucketizing jobs. I have got 654 processes (slice) at this job. This 654 slices cause high IO at the HDD on the node and cause failure. The system managers asked me to reduce the process run on the same time. How could I reduce this slices on the same time?

I tried this script which @brianwalenz suggested to me:

#!/bin/sh

sbatch \
  --cpus-per-task=1 --mem-per-cpu=5g --time=7-00:00:00 --partition=prod --account denolen -o logs/1-bucketize.%A_%a.out \
  -D `pwd` -J "ovB_lculinaris" \
  -a 1-654%20 \
  `pwd`/scripts/1-bucketize.sh 0 \
> ./scripts/1-bucketize.jobSubmit-01.out 2>&1

But I get this error message in the 1-bucketize.jobSubmit-01.out file:

sbatch: error: Batch job submission failed: Invalid job array specification

This is the 1-bucketize.sh file:

#!/bin/sh

#  Path to Canu.

syst=`uname -s`
arch=`uname -m | sed s/x86_64/amd64/`

bin="/mnt/stori/home/fk8jybr/canu-1.9/$syst-$arch/bin"

if [ ! -d "$bin" ] ; then
  bin="/mnt/stori/home/fk8jybr/canu-1.9"
fi

#  Report paths.

echo ""
echo "Found perl:"
echo "  " `which perl`
echo "  " `perl --version | grep version`
echo ""
echo "Found java:"
echo "  " `which java`
echo "  " `java -showversion 2>&1 | head -n 1`
echo ""
echo "Found canu:"
echo "  " $bin/canu
echo "  " `$bin/canu -version`
echo ""

#  Environment for any object storage.

export CANU_OBJECT_STORE_CLIENT=
export CANU_OBJECT_STORE_CLIENT_UA=
export CANU_OBJECT_STORE_CLIENT_DA=
export CANU_OBJECT_STORE_NAMESPACE=
export CANU_OBJECT_STORE_PROJECT=

#  Discover the job ID to run, from either a grid environment variable and a
#  command line offset, or directly from the command line.
#
if [ x$SLURM_ARRAY_TASK_ID = x -o x$SLURM_ARRAY_TASK_ID = xundefined -o x$SLURM_ARRAY_TASK_ID = x0 ]; then
  baseid=$1
  offset=0
else
  baseid=$SLURM_ARRAY_TASK_ID
  offset=$1
fi
if [ x$offset = x ]; then
  offset=0
fi
if [ x$baseid = x ]; then
  echo Error: I need SLURM_ARRAY_TASK_ID set, or a job index on the command line.
  exit
fi
jobid=`expr -- $baseid + $offset`
if [ x$SLURM_ARRAY_TASK_ID = x ]; then
  echo Running job $jobid based on command line options.
else
  echo Running job $jobid based on SLURM_ARRAY_TASK_ID=$SLURM_ARRAY_TASK_ID and offset=$offset.
fi

echo ""
echo "Attempting to increase maximum allowed processes and open files."
max=`ulimit -Hu`
bef=`ulimit -Su`
if [ $bef -lt $max ] ; then
  ulimit -Su $max
  aft=`ulimit -Su`
  echo "  Changed max processes per user from $bef to $aft (max $max)."
else
  echo "  Max processes per user limited to $bef, no increase possible."
fi

max=`ulimit -Hn`
bef=`ulimit -Sn`
if [ $bef -lt $max ] ; then
  ulimit -Sn $max
  aft=`ulimit -Sn`
  echo "  Changed max open files from $bef to $aft (max $max)."
else
  echo "  Max open files limited to $bef, no increase possible."
fi

echo ""

#  This script should be executed from correction/lculinaris.ovlStore.BUILDING/, but the binary needs
#  to run from correction/ (all the paths in the config are relative to there).

cd ..

jobname=`printf %04d $jobid`

if [ -e ./lculinaris.ovlStore.BUILDING/bucket$jobname ] ; then
  echo "Bucketizing job finished; directory './lculinaris.ovlStore.BUILDING/bucket$jobname' exists."
  exit
fi

#
#  Bucketize!
#

$bin/ovStoreBucketizer \
  -O  ./lculinaris.ovlStore.BUILDING \
  -S ../lculinaris.seqStore \
  -C  ./lculinaris.ovlStore.config \
  -f \
  -b $jobid
skoren commented 4 years ago

The script looks correct as is the array specification (at least on our version of slurm). You should check with your admin group to help debug it. Is there a limit on the number of jobs in the array below 654? Is there another way to limit number of concurrent jobs?

hidvegin commented 4 years ago

@skoren Thank you for your answer. Yes, the SLURM has got a limitation of jobs in the array below 655 (exactly the maximum at 512). I checked I should use 655 slices. So, I have to make two different 1-bucketize.jobSubmit-01.sh and 1-bucketize.jobSubmit-02.sh

For 1-bucketize.jobSubmit-01.sh:

#!/bin/sh

sbatch \
  --cpus-per-task=1 --mem-per-cpu=5g --time=7-00:00:00 --partition=prod --account denolen -o logs/1-bucketize.%A_%a.out \
  -D `pwd` -J "ovB_lculinaris" \
  -a 1-511%20 \
  `pwd`/scripts/1-bucketize.sh 0 \
> ./scripts/1-bucketize.jobSubmit-01.out 2>&1

For 1-bucketize.jobSubmit-02.sh:

#!/bin/sh

sbatch \
  --cpus-per-task=1 --mem-per-cpu=5g --time=7-00:00:00 --partition=prod --account denolen -o logs/1-bucketize.%A_%a.out \
  -D `pwd` -J "ovB_lculinaris" \
  -a 1-142%20 \
  `pwd`/scripts/1-bucketize.sh 0 \
> ./scripts/1-bucketize.jobSubmit-01.out 2>&1

Should I change somehow the 0 at `pwd/scripts/1-bucketize.sh 0 ` ?

skoren commented 4 years ago

Yes, canu normally does this splitting for you. You should pass the offset to the second job, so something like:

#!/bin/sh

sbatch \
  --cpus-per-task=1 --mem-per-cpu=5g --time=7-00:00:00 --partition=prod --account denolen -o logs/1-bucketize.%A_%a.out \
  -D `pwd` -J "ovB_lculinaris" \
  -a 1-511%20 \
  `pwd`/scripts/1-bucketize.sh 0 \
> ./scripts/1-bucketize.jobSubmit-01.out 2>&1

and

#!/bin/sh

sbatch \
  --cpus-per-task=1 --mem-per-cpu=5g --time=7-00:00:00 --partition=prod --account denolen -o logs/1-bucketize.%A_%a.out \
  -D `pwd` -J "ovB_lculinaris" \
  -a 1-143%20 \
  `pwd`/scripts/1-bucketize.sh 511 \
> ./scripts/1-bucketize.jobSubmit-02.out 2>&1

So the second set of jobs will run jobs 511+1=512 to 511+143 = 654. If you have issues with I/O in this step, I expect you'll have issues in the next sorting step as well. You can make canu use this 20 job limit for all its array by using the parameter gridEngineArrayOption="-a ARRAY_JOBS%20" when you re-start.

hidvegin commented 4 years ago

So, If I change my canu parameters to this, canu will use only 20 job for all arrays:

canu -correct -p lculinaris -d $HOME/output/canu_corrected/lculinaris genomeSize=4.0g batMemory=124g batThreads=48 gridOptions="--time=3-00:00:00 --partition=prod --account denolen" gridEngineArrayOption="-a ARRAY_JOBS%20" -pacbio-raw $HOME/input/pacbio_raw/LC001pacbio.fastq.gz

skoren commented 4 years ago

Yep, it will always pass the %20.

hidvegin commented 4 years ago

I started re-run canu with gridEngineArrayOption="-a ARRAY_JOBS%20. I get this error in core.XXX file generating:

#
# There is insufficient memory for the Java Runtime Environment to continue.
# Native memory allocation (mmap) failed to map 1409286144 bytes for committing reserved memory.
# Possible reasons:
#   The system is out of physical RAM or swap space
#   The process is running with CompressedOops enabled, and the Java Heap may be blocking the growth of the native heap
# Possible solutions:
#   Reduce memory load on the system
#   Increase physical memory or swap space
#   Check if swap backing store is full
#   Decrease Java heap size (-Xmx/-Xms)
#   Decrease number of Java threads
#   Decrease Java thread stack sizes (-Xss)
#   Set larger code cache with -XX:ReservedCodeCacheSize=
# This output file may be truncated or incomplete.
#
#  Out of Memory Error (os_linux.cpp:2754), pid=642, tid=0x00007f6dc8434700
#
# JRE version:  (8.0_242-b08) (build )
# Java VM: OpenJDK 64-Bit Server VM (25.242-b08 mixed mode linux-amd64 compressed oops)
# Core dump written. Default location: /mnt/stori/home/fk8jybr/output/canu_corrected/lculinaris/correction/lculinaris.ovlStore.BUILDING/core or core.642
#

---------------  T H R E A D  ---------------

Current thread (0x00007f6dc000a000):  JavaThread "Unknown thread" [_thread_in_vm, id=656, stack(0x00007f6dc8335000,0x00007f6dc8435000)]

Stack: [0x00007f6dc8335000,0x00007f6dc8435000],  sp=0x00007f6dc8433420,  free space=1017k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
V  [libjvm.so+0x9fb5cd]  VMError::report_and_die()+0x15d
V  [libjvm.so+0x4c217a]  report_vm_out_of_memory(char const*, int, unsigned long, VMErrorType, char const*)+0x8a
V  [libjvm.so+0x861ca8]  os::pd_commit_memory(char*, unsigned long, unsigned long, bool)+0xd8
V  [libjvm.so+0x85957f]  os::commit_memory(char*, unsigned long, unsigned long, bool)+0x1f
V  [libjvm.so+0x9f8314]  VirtualSpace::expand_by(unsigned long, bool)+0x1b4
V  [libjvm.so+0x5abd0d]  CardGeneration::CardGeneration(ReservedSpace, unsigned long, int, GenRemSet*)+0xed
V  [libjvm.so+0x99f355]  TenuredGeneration::TenuredGeneration(ReservedSpace, unsigned long, int, GenRemSet*)+0x65
V  [libjvm.so+0x5ac951]  GenerationSpec::init(ReservedSpace, int, GenRemSet*)+0x101
V  [libjvm.so+0x59e5f8]  GenCollectedHeap::initialize()+0x1d8
V  [libjvm.so+0x9c6c19]  Universe::initialize_heap()+0x189
V  [libjvm.so+0x9c6e13]  universe_init()+0x33
V  [libjvm.so+0x5ea1e5]  init_globals()+0x55
V  [libjvm.so+0x9aa454]  Threads::create_vm(JavaVMInitArgs*, bool*)+0x284
V  [libjvm.so+0x658191]  JNI_CreateJavaVM+0x51
C  [libjli.so+0x7998]  JavaMain+0x88
C  [libpthread.so.0+0x7e65]  start_thread+0xc5

---------------  P R O C E S S  ---------------

Java Threads: ( => current thread )

Other Threads:

=>0x00007f6dc000a000 (exited) JavaThread "Unknown thread" [_thread_in_vm, id=656, stack(0x00007f6dc8335000,0x00007f6dc8435000)]

VM state:not at safepoint (not fully initialized)

VM Mutex/Monitor currently owned by a thread: None

heap address: 0x0000000080200000, size: 30718 MB, Compressed Oops mode: Non-zero based:0x00000000801ff000, Oop shift amount: 3
Narrow klass base: 0x0000000000000000, Narrow klass shift: 0

GC Heap History (0 events):
No events

Deoptimization events (0 events):
No events

Classes redefined (0 events):
No events

Internal exceptions (0 events):
No events

Events (0 events):
No events
skoren commented 4 years ago

That's not a Canu error and certainly has nothing to do with %20 but an issue with the grid system. The node JVM on your node failed which means your node was overloaded and not reserving memory properly. The only reason JVM is open during store building is to check the version and it was only trying to use 1gb memory whereas the bucketizing jobs had asked for 5gb. This means the cluster isn't properly reserving memory for jobs or at least wasn't for this job. I'd suggest checking with your IT why that is the case but nothing we can do in canu to fix that.

hidvegin commented 4 years ago

I will try use the node default openjdk because until now I used openjdk from homebrew. Which files should I delete from the process directory? I would like to restrat canu from the latest finished job.

skoren commented 4 years ago

You don't need to delete any files, it should restart correctly itself.

hidvegin commented 4 years ago

I restarted canu and I get this error:

ERROR:  mhap overlapper requires java version at least 1.8.0; you have unknown (from 'java').
ERROR:  'java -Xmx1g -showversion' reports:

But If I use java -Xmx1g -showversion:

java -Xmx1g -showversion
openjdk version "11.0.6" 2020-01-14 LTS
OpenJDK Runtime Environment 18.9 (build 11.0.6+10-LTS)
OpenJDK 64-Bit Server VM 18.9 (build 11.0.6+10-LTS, mixed mode)
Usage: java [options] <mainclass> [args...]
           (to execute a class)
   or  java [options] -jar <jarfile> [args...]
           (to execute a jar file)
   or  java [options] -m <module>[/<mainclass>] [args...]
       java [options] --module <module>[/<mainclass>] [args...]
           (to execute the main class in a module)
   or  java [options] <sourcefile> [args]
           (to execute a single source-file program)

 Arguments following the main class, source file, -jar <jarfile>,
 -m or --module <module>/<mainclass> are passed as the arguments to
 main class.

 where options include:

    -cp <class search path of directories and zip/jar files>
    -classpath <class search path of directories and zip/jar files>
    --class-path <class search path of directories and zip/jar files>
                  A : separated list of directories, JAR archives,
                  and ZIP archives to search for class files.
    -p <module path>
    --module-path <module path>...
                  A : separated list of directories, each directory
                  is a directory of modules.
    --upgrade-module-path <module path>...
                  A : separated list of directories, each directory
                  is a directory of modules that replace upgradeable
                  modules in the runtime image
    --add-modules <module name>[,<module name>...]
                  root modules to resolve in addition to the initial module.
                  <module name> can also be ALL-DEFAULT, ALL-SYSTEM,
                  ALL-MODULE-PATH.
    --list-modules
                  list observable modules and exit
    -d <module name>
    --describe-module <module name>
                  describe a module and exit
    --dry-run     create VM and load main class but do not execute main method.
                  The --dry-run option may be useful for validating the
                  command-line options such as the module system configuration.
    --validate-modules
                  validate all modules and exit
                  The --validate-modules option may be useful for finding
                  conflicts and other errors with modules on the module path.
    -D<name>=<value>
                  set a system property
    -verbose:[class|module|gc|jni]
                  enable verbose output
    -version      print product version to the error stream and exit
    --version     print product version to the output stream and exit
    -showversion  print product version to the error stream and continue
    --show-version
                  print product version to the output stream and continue
    --show-module-resolution
                  show module resolution output during startup
    -? -h -help
                  print this help message to the error stream
    --help        print this help message to the output stream
    -X            print help on extra options to the error stream
    --help-extra  print help on extra options to the output stream
    -ea[:<packagename>...|:<classname>]
    -enableassertions[:<packagename>...|:<classname>]
                  enable assertions with specified granularity
    -da[:<packagename>...|:<classname>]
    -disableassertions[:<packagename>...|:<classname>]
                  disable assertions with specified granularity
    -esa | -enablesystemassertions
                  enable system assertions
    -dsa | -disablesystemassertions
                  disable system assertions
    -agentlib:<libname>[=<options>]
                  load native agent library <libname>, e.g. -agentlib:jdwp
                  see also -agentlib:jdwp=help
    -agentpath:<pathname>[=<options>]
                  load native agent library by full pathname
    -javaagent:<jarpath>[=<options>]
                  load Java programming language agent, see java.lang.instrument
    -splash:<imagepath>
                  show splash screen with specified image
                  HiDPI scaled images are automatically supported and used
                  if available. The unscaled image filename, e.g. image.ext,
                  should always be passed as the argument to the -splash option.
                  The most appropriate scaled image provided will be picked up
                  automatically.
                  See the SplashScreen API documentation for more information
    @argument files
                  one or more argument files containing options
    -disable-@files
                  prevent further argument file expansion
    --enable-preview
                  allow classes to depend on preview features of this release
To specify an argument for a long option, you can use --<name>=<value> or
--<name> <value>.

It seems to me there are java on the node but maybe canu cannot detect it. Somehow could I solve this?

skoren commented 4 years ago

How did you get this far if Java wasn't working properly, you're already past the steps that use java?

Canu just runs the command java so if it's not working it's because that java isn't available in the path on the compute nodes. You should provide the full path to whatever java you want to use using the java="/full/path/to/java/bin" parameter.

However, I doubt the JVM is the source of the issue. The original error was an out of memory issue on the node when you were using 1/5 reserved GB. That implies the node was not properly holding the memory you asked for. I'd go back and try to find out how much memory that job was using/how much it had reserved/requested/and why it was unable to run. You might need to get help from your IT for that.

hidvegin commented 4 years ago

I used java from homebrew and this worked very well until that error with memory. But I think that the error caused that I did not used the default java on the node. But it seems the error is different. I will ask some help from the IT to solve this issue.

skoren commented 4 years ago

The default java on the node is not set so I'm not sure you can avoid using home-brew (or you wouldn't have gotten that error about versions). You can use a non-homebrew java (assuming which java is indeed not a homebrew version) if you give a full path to its binary, as long as it is also available on the compute nodes.

hidvegin commented 4 years ago

canu would like to run this script:

#!/bin/sh

sbatch \
  --cpus-per-task=1 --mem-per-cpu=39680m --time=7-00:00:00 --partition=prod --account denolen -o logs/2-sort.%A_%a.out \
  -D `pwd` -J "ovS_lculinaris" \
  -a 1-20%20 \
  `pwd`/scripts/2-sort.sh 0 \
> ./scripts/2-sort.jobSubmit-01.out 2>&1

I think the error will be that the node which I use it is 48 CPU and 148 GB ram. canu would like 39.6 GB ram and 1 CPU/process. SLURM run somehow the 20 process run in the same time on the same node and 20x39.6GB is not available from the maximum 148GB ram/node. I wrote an email to the IT, I hope they will be resolve this error with the SLURM.

skoren commented 4 years ago

That's consistent with my initial guess when you first hit the error with %20 that your cluster isn't checking the memory request. This is also the source of the JVM error and may actually be why you hit the I/O issues too, it over-scheduled the jobs before too causing higher I/O load.

You can work around this by setting gridOptionsOVS="--cpus-per-task=16 --mem-per-cpu=2500m which should reserve 16 cores and limit you to three jobs. In general, any job using more than 3gb/core (so bucketizing, sorting) would run into this issue on your cluster.

hidvegin commented 4 years ago

I put this parameter in canu command and restarted. Now I see that canu made core.XXXX files and 2-correction, lculinaris.corStore.WORKING new directory. 

Found perl:
   /usr/bin/perl
   This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi

Found java:
   /mnt/stori/home/fk8jybr/.linuxbrew/bin/java
   openjdk version "1.8.0_242"

Found canu:
   /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/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 '1.8.0_242' (from 'java') with -d64 support.
--
-- WARNING:
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.
-- WARNING:
--
-- Detected 48 CPUs and 126 gigabytes of memory.
-- Detected Slurm with 'sinfo' binary in /usr/bin/sinfo.
-- Detected Slurm with task IDs up to 511 allowed.
-- 
-- Found   2 hosts with  24 cores and   22 GB memory under Slurm control.
-- Found  48 hosts with  48 cores and  124 GB memory under Slurm control.
--
--                     (tag)Threads
--            (tag)Memory         |
--        (tag)         |         |  algorithm
--        -------  ------  --------  -----------------------------
-- Grid:  meryl     24 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       16 GB   24 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   22 GB   16 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    24 GB   16 CPUs  (overlap detection)
-- Grid:  utgovl    24 GB   16 CPUs  (overlap detection)
-- Grid:  cor       24 GB    4 CPUs  (read correction)
-- Grid:  ovb        4 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       32 GB    1 CPU   (overlap store sorting)
-- Grid:  red       41 GB    8 CPUs  (read error detection)
-- Grid:  oea        8 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat      124 GB   48 CPUs  (contig construction with bogart)
-- Grid:  cns      --- GB    8 CPUs  (consensus)
-- Grid:  gfa       64 GB   32 CPUs  (GFA alignment and processing)
--
-- In 'lculinaris.seqStore', found PacBio reads:
--   Raw:        16602048
--   Corrected:  0
--   Trimmed:    0
--
-- Generating assembly 'lculinaris' in '/mnt/stori/home/fk8jybr/output/canu_corrected/lculinaris'
--
-- Parameters:
--
--  genomeSize        4000000000
--
--  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.
--
-- Creating overlap store correction/lculinaris.ovlStore using:
--    655 buckets
--    655 slices
--        using at most 29 GB memory each
-- Overlap store sorter finished.
-- No change in report.
-- Finished stage 'cor-overlapStoreSorterCheck', reset canuIteration.
----------------------------------------
-- Starting command on Mon May 25 12:36:14 2020 with 178218.65 GB free disk space

    cd correction
    /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/bin/ovStoreIndexer \
      -O  ./lculinaris.ovlStore.BUILDING \
      -S ../lculinaris.seqStore \
      -C  ./lculinaris.ovlStore.config \
      -delete \
    > ./lculinaris.ovlStore.BUILDING.index.err 2>&1

-- Finished on Mon May 25 13:10:56 2020 (2082 seconds) with 178631.055 GB free disk space
----------------------------------------
-- Checking store.
----------------------------------------
-- Starting command on Mon May 25 13:10:56 2020 with 178631.055 GB free disk space

    cd correction
    /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/bin/ovStoreDump \
     -S ../lculinaris.seqStore \
     -O  ./lculinaris.ovlStore \
     -counts \
     > ./lculinaris.ovlStore/counts.dat 2> ./lculinaris.ovlStore/counts.err

-- Finished on Mon May 25 13:11:05 2020 (9 seconds) with 178630.841 GB free disk space
----------------------------------------
--
-- Overlap store 'correction/lculinaris.ovlStore' successfully constructed.
-- Found 811016098412 overlaps for 16585800 reads; 16248 reads have no overlaps.
--
--
-- Purged 7900.121 GB in 1674 overlap output files.
-- No change in report.
-- Finished stage 'cor-createOverlapStore', reset canuIteration.
-- Set corMinCoverage=4 based on read coverage of 32.
-- Global filter scores will be estimated.
-- Computing correction layouts.
----------------------------------------
-- Starting command on Mon May 25 13:17:00 2020 with 186531.187 GB free disk space

    cd correction
    /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/bin/generateCorrectionLayouts \
      -S ../lculinaris.seqStore \
      -O  ./lculinaris.ovlStore \
      -C  ./lculinaris.corStore.WORKING \
      -eC 80 \
    > ./lculinaris.corStore.err 2>&1

This was the last output report. I think that canu is at "read correction" stage where it should use 4 CPU core and 48 GB ram. But now canu use only 1 CPU and run only one process on one node. This is normal?

This is the last script which canu run on the SLURM.

#!/bin/sh

#  Path to Canu.

syst=`uname -s`
arch=`uname -m | sed s/x86_64/amd64/`

bin="/mnt/stori/home/fk8jybr/canu-1.9/$syst-$arch/bin"

if [ ! -d "$bin" ] ; then
  bin="/mnt/stori/home/fk8jybr/canu-1.9"
fi

#  Report paths.

echo ""
echo "Found perl:"
echo "  " `which perl`
echo "  " `perl --version | grep version`
echo ""
echo "Found java:"
echo "  " `which java`
echo "  " `java -showversion 2>&1 | head -n 1`
echo ""
echo "Found canu:"
echo "  " $bin/canu
echo "  " `$bin/canu -version`
echo ""

#  Environment for any object storage.

export CANU_OBJECT_STORE_CLIENT=
export CANU_OBJECT_STORE_CLIENT_UA=
export CANU_OBJECT_STORE_CLIENT_DA=
export CANU_OBJECT_STORE_NAMESPACE=
export CANU_OBJECT_STORE_PROJECT=

rm -f canu.out
ln -s canu-scripts/canu.26.out canu.out

/usr/bin/env perl \
$bin/canu -correct -p 'lculinaris' 'genomeSize=4.0g' 'batMemory=124g' 'batThreads=48' 'gridOptions=--time=7-00:00:00 --partition=prod --account denolen' 'gridEngineArrayOption=-a ARRAY_JOBS%20' 'gridOptionsOVS=--cpus-per-task=16 --mem-per-cpu=2500m' -pacbio-raw '/mnt/stori/home/fk8jybr/input/pacbio_raw/LC001pacbio.fastq.gz' canuIteration=1
skoren commented 4 years ago

Yep, that's correct, it's not always going to use all cores, some steps are single-threaded.

hidvegin commented 4 years ago

canu finished the correction process.

This is the final report file:

Found perl:
   /usr/bin/perl
   This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi

Found java:
   /mnt/stori/home/fk8jybr/.linuxbrew/bin/java
   openjdk version "1.8.0_242"

Found canu:
   /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/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 '1.8.0_242' (from 'java') with -d64 support.
--
-- WARNING:
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.
-- WARNING:
--
-- Detected 48 CPUs and 126 gigabytes of memory.
-- Detected Slurm with 'sinfo' binary in /usr/bin/sinfo.
-- Detected Slurm with task IDs up to 511 allowed.
-- 
-- Found   2 hosts with  24 cores and   22 GB memory under Slurm control.
-- Found  48 hosts with  48 cores and  124 GB memory under Slurm control.
--
--                     (tag)Threads
--            (tag)Memory         |
--        (tag)         |         |  algorithm
--        -------  ------  --------  -----------------------------
-- Grid:  meryl     24 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       16 GB   24 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   22 GB   16 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    24 GB   16 CPUs  (overlap detection)
-- Grid:  utgovl    24 GB   16 CPUs  (overlap detection)
-- Grid:  cor       24 GB    4 CPUs  (read correction)
-- Grid:  ovb        4 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       32 GB    1 CPU   (overlap store sorting)
-- Grid:  red       41 GB    8 CPUs  (read error detection)
-- Grid:  oea        8 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat      124 GB   48 CPUs  (contig construction with bogart)
-- Grid:  cns      --- GB    8 CPUs  (consensus)
-- Grid:  gfa       64 GB   32 CPUs  (GFA alignment and processing)
--
-- In 'lculinaris.seqStore', found PacBio reads:
--   Raw:        16602048
--   Corrected:  0
--   Trimmed:    0
--
-- Generating assembly 'lculinaris' in '/mnt/stori/home/fk8jybr/output/canu_corrected/lculinaris'
--
-- Parameters:
--
--  genomeSize        4000000000
--
--  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 32.
-- Found 256 read correction output files.
-- No change in report.
-- Finished stage 'cor-generateCorrectedReadsCheck', reset canuIteration.
-- Found 256 read correction output files.
-- No change in report.
-- Finished stage 'cor-generateCorrectedReadsCheck', reset canuIteration.
-- Found 256 read correction output files.
-- No change in report.
-- Finished stage 'cor-generateCorrectedReadsCheck', reset canuIteration.
--
-- Loading corrected reads into corStore and seqStore.
----------------------------------------
-- Starting command on Sat May 30 19:52:24 2020 with 186184.395 GB free disk space

    cd correction
    /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/bin/loadCorrectedReads \
      -S ../lculinaris.seqStore \
      -C ./lculinaris.corStore \
      -L ./2-correction/corjob.files \
    >  ./lculinaris.loadCorrectedReads.log \
    2> ./lculinaris.loadCorrectedReads.err

-- Finished on Sat May 30 20:24:49 2020 (1945 seconds) with 186131.596 GB free disk space
----------------------------------------
--
-- WARNING: gnuplot failed.
--
----------------------------------------
--
-- In sequence store './lculinaris.seqStore':
--   Found 13537706 reads.
--   Found 102118358098 bases (25.52 times coverage).
--
--   Read length histogram (one '*' equals 122729.3 reads):
--        0   4999 2684392 *********************
--     5000   9999 8591051 **********************************************************************
--    10000  14999 1824672 **************
--    15000  19999 332581 **
--    20000  24999  74856 
--    25000  29999  17240 
--    30000  34999   4962 
--    35000  39999   1935 
--    40000  44999   1088 
--    45000  49999    847 
--    50000  54999    706 
--    55000  59999    522 
--    60000  64999    397 
--    65000  69999    406 
--    70000  74999    360 
--    75000  79999    328 
--    80000  84999    267 
--    85000  89999    245 
--    90000  94999    186 
--    95000  99999    148 
--   100000 104999    142 
--   105000 109999    100 
--   110000 114999     71 
--   115000 119999     62 
--   120000 124999     44 
--   125000 129999     29 
--   130000 134999     18 
--   135000 139999     10 
--   140000 144999      8 
--   145000 149999      8 
--   150000 154999      5 
--   155000 159999      3 
--   160000 164999      5 
--   165000 169999      3 
--   170000 174999      2 
--   175000 179999      3 
--   180000 184999      2 
--   185000 189999      0 
--   190000 194999      0 
--   195000 199999      0 
--   200000 204999      2 
--
-- Purging correctReads output after loading into stores.
-- Purged 256 .cns outputs.
-- Purged 256 .out job log outputs.
--
-- Purging overlaps used for correction.
-- Report changed.
-- Finished stage 'cor-loadCorrectedReads', reset canuIteration.
----------------------------------------
-- Starting command on Sat May 30 20:36:36 2020 with 201466.761 GB free disk space

    cd .
    /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/bin/sqStoreDumpFASTQ \
      -corrected \
      -S ./lculinaris.seqStore \
      -o ./lculinaris.correctedReads.gz \
      -fasta \
      -nolibname \
    > lculinaris.correctedReads.fasta.err 2>&1

-- Finished on Sat May 30 22:02:36 2020 (5160 seconds) with 201435.818 GB free disk space
----------------------------------------
--
-- Corrected reads saved in 'lculinaris.correctedReads.fasta.gz'.
-- No change in report.
-- Finished stage 'cor-dumpCorrectedReads', reset canuIteration.
--
-- Bye.

Now I would like to start the trim process in canu. This is the planned parameters which I would like to use in canu:

canu -trim -p lculinaris -d $HOME/output/canu_trim/lculinaris genomeSize=4.0g batMemory=124g batThreads=48 gridOptions="--time=7-00:00:00 --partition=prod --account XXXX" gridEngineArrayOption="-a ARRAY_JOBS%20" gridOptionsOVS="--cpus-per-task=16 --mem-per-cpu=2500m" -pacbio-corrected $HOME/output/canu_corrected/lculinaris/lculinaris.correctedReads.fasta.gz

Is this parameters good for canu? Should I use ARRAY_JOBS%20" gridOptionsOVS="--cpus-per-task=16 --mem-per-cpu=2500m?

hidvegin commented 4 years ago

@skoren

I run canu -trim with this parameters:

canu -trim -p lculinaris -d $HOME/output/canu_trim/lculinaris genomeSize=4.0g batMemory=124g batThreads=48 gridOptions="--time=7-00:00:00 --partition=prod --account XXXX" gridEngineArrayOption="-a ARRAY_JOBS%20" gridOptionsOVS="--cpus-per-task=16 --mem-per-cpu=2500m" -pacbio-corrected $HOME/output/canu_corrected/lculinaris/lculinaris.correctedReads.fasta.gz

I get this error message from canu:

Found perl:
   /usr/bin/perl
   This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi

Found java:
   /mnt/stori/home/fk8jybr/.linuxbrew/bin/java
   openjdk version "1.8.0_242"

Found canu:
   /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/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 '1.8.0_242' (from 'java') with -d64 support.
--
-- WARNING:
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.
-- WARNING:
--
-- Detected 48 CPUs and 126 gigabytes of memory.
-- Detected Slurm with 'sinfo' binary in /usr/bin/sinfo.
-- Detected Slurm with task IDs up to 511 allowed.
-- 
-- Found   2 hosts with  24 cores and   22 GB memory under Slurm control.
-- Found  48 hosts with  48 cores and  124 GB memory under Slurm control.
--
--                     (tag)Threads
--            (tag)Memory         |
--        (tag)         |         |  algorithm
--        -------  ------  --------  -----------------------------
-- Grid:  meryl     24 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       16 GB   24 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   22 GB   16 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    24 GB   16 CPUs  (overlap detection)
-- Grid:  utgovl    24 GB   16 CPUs  (overlap detection)
-- Grid:  cor       24 GB    4 CPUs  (read correction)
-- Grid:  ovb        4 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       32 GB    1 CPU   (overlap store sorting)
-- Grid:  red       41 GB    8 CPUs  (read error detection)
-- Grid:  oea        8 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat      124 GB   48 CPUs  (contig construction with bogart)
-- Grid:  cns      --- GB    8 CPUs  (consensus)
-- Grid:  gfa       64 GB   32 CPUs  (GFA alignment and processing)
--
-- In 'lculinaris.seqStore', found PacBio reads:
--   Raw:        0
--   Corrected:  13239306
--   Trimmed:    0
--
-- Generating assembly 'lculinaris' in '/mnt/stori/home/fk8jybr/output/canu_trim/lculinaris'
--
-- Parameters:
--
--  genomeSize        4000000000
--
--  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 TRIMMING
--
-- No change in report.
--
-- Creating overlap store trimming/lculinaris.ovlStore using:
--    140 buckets
--    140 slices
--        using at most 29 GB memory each
-- Overlap store sorter finished.
-- No change in report.
-- Finished stage 'obt-overlapStoreSorterCheck', reset canuIteration.
----------------------------------------
-- Starting command on Fri Jun  5 12:00:34 2020 with 196332.982 GB free disk space

    cd trimming
    /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/bin/ovStoreIndexer \
      -O  ./lculinaris.ovlStore.BUILDING \
      -S ../lculinaris.seqStore \
      -C  ./lculinaris.ovlStore.config \
      -delete \
    > ./lculinaris.ovlStore.BUILDING.index.err 2>&1

-- Finished on Fri Jun  5 12:00:37 2020 (3 seconds) with 196332.982 GB free disk space
----------------------------------------

ERROR:
ERROR:  Failed with exit code 1.  (rc=256)
ERROR:

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:
ABORT:   failed to build index for overlap store.
ABORT:
ABORT: Disk space available:  196332.982 GB
ABORT:
ABORT: Last 50 lines of the relevant log file (trimming/lculinaris.ovlStore.BUILDING.index.err):
ABORT:
ABORT:    -    96   9022347   9117031 13239306 1238038855
ABORT:    -    97   9117032   9213921 13239306 1238028613
ABORT:    -    98   9213922   9312559 13239306 1238022755
ABORT:    -    99   9312560   9410058 13239306 1238040868
ABORT:    -   100   9410059   9505434 13239306 1238003136
ABORT:    -   101   9505435   9602855 13239306 1238033880
ABORT:    -   102   9602856   9701542 13239306 1238034193
ABORT:    -   103   9701543   9798790 13239306 1238038333
ABORT:    -   104   9798791   9897882 13239306 1238041623
ABORT:    -   105   9897883   9995235 13239306 1238039975
ABORT:    -   106   9995236  10090533 13239306 1238043784
ABORT:    -   107  10090534  10185681 13239306 1238016973
ABORT:    -   108  10185682  10284408 13239306 1238040236
ABORT:    -   109  10284409  10383953 13239306 1238043761
ABORT:    -   110  10383954  10483605 13239306 1238011557
ABORT:    -   111  10483606  10580623 13239306 1238038894
ABORT:    -   112  10580624  10680239 13239306 1238037228
ABORT:    -   113  10680240  10775880 13239306 1238008865
ABORT:    -   114  10775881  10862941 13239306 1238033983
ABORT:    -   115  10862942  10951310 13239306 1238028646
ABORT:    -   116  10951311  11037978 13239306 1238032078
ABORT:    -   117  11037979  11125930 13239306 1238012796
ABORT:    -   118  11125931  11211879 13239306 1238042048
ABORT:    -   119  11211880  11301488 13239306 1237993580
ABORT:    -   120  11301489  11389528 13239306 1237999527
ABORT:    -   121  11389529  11479453 13239306 1238020347
ABORT:    -   122  11479454  11569927 13239306 1238021084
ABORT:    -   123  11569928  11658469 13239306 1238025566
ABORT:    -   124  11658470  11749014 13239306 1238015219
ABORT:    -   125  11749015  11838420 13239306 1238042162
ABORT:    -   126  11838421  11930016 13239306 1238043721
ABORT:    -   127  11930017  12023443 13239306 1238009956
ABORT:    -   128  12023444  12121824 13239306 1238027058
ABORT:    -   129  12121825  12219155 13239306 1238020453
ABORT:    -   130  12219156  12317534 13239306 1238017301
ABORT:    -   131  12317535  12415718 13239306 1238035668
ABORT:    -   132  12415719  12513002 13239306 1238019383
ABORT:    -   133  12513003  12609640 13239306 1238019439
ABORT:    -   134  12609641  12709310 13239306 1238035664
ABORT:    -   135  12709311  12809528 13239306 1238031891
ABORT:    -   136  12809529  12908112 13239306 1237970502
ABORT:    -   137  12908113  13006608 13239306 1238041020
ABORT:    -   138  13006609  13104672 13239306 1238039725
ABORT:    -   139  13104673  13204611 13239306 1238038743
ABORT:    -   140  13204612  13239306 13239306  443463959
ABORT:    - ----- --------- --------- -------- ----------
ABORT:    -
ABORT:    - Merging indexes.
ABORT:    -
ABORT:   AS_UTL_loadFile()-- File './lculinaris.ovlStore.BUILDING/0004.index' contains 9611946 objects, but asked to load 13239307.
ABORT:

How could I resolve this error?

skoren commented 4 years ago

This is again an I/O error, it looks like there are truncated files in your run. You can try removing the BUILDING folder and restarting Canu limiting the concurrency even more.

hidvegin commented 4 years ago

Thank @skoren for your answer and help. I deleted the BUILDING folder and restarted with gridEngineArrayOption="-a ARRAY_JOBS%5" parameter. I hope this will resolve the problem.

hidvegin commented 4 years ago

Dear @skoren ! canu -trim is finished succesfully. This is the report:

Found perl:
   /usr/bin/perl
   This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi

Found java:
   /mnt/stori/home/fk8jybr/.linuxbrew/bin/java
   openjdk version "1.8.0_242"

Found canu:
   /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/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 '1.8.0_242' (from 'java') with -d64 support.
--
-- WARNING:
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.
-- WARNING:
--
-- Detected 48 CPUs and 126 gigabytes of memory.
-- Detected Slurm with 'sinfo' binary in /usr/bin/sinfo.
-- Detected Slurm with task IDs up to 511 allowed.
-- 
-- Found   2 hosts with  24 cores and   22 GB memory under Slurm control.
-- Found  48 hosts with  48 cores and  124 GB memory under Slurm control.
--
--                     (tag)Threads
--            (tag)Memory         |
--        (tag)         |         |  algorithm
--        -------  ------  --------  -----------------------------
-- Grid:  meryl     24 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       16 GB   24 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   22 GB   16 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    24 GB   16 CPUs  (overlap detection)
-- Grid:  utgovl    24 GB   16 CPUs  (overlap detection)
-- Grid:  cor       24 GB    4 CPUs  (read correction)
-- Grid:  ovb        4 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       32 GB    1 CPU   (overlap store sorting)
-- Grid:  red       41 GB    8 CPUs  (read error detection)
-- Grid:  oea        8 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat      124 GB   48 CPUs  (contig construction with bogart)
-- Grid:  cns      --- GB    8 CPUs  (consensus)
-- Grid:  gfa       64 GB   32 CPUs  (GFA alignment and processing)
--
-- In 'lculinaris.seqStore', found PacBio reads:
--   Raw:        0
--   Corrected:  13239306
--   Trimmed:    0
--
-- Generating assembly 'lculinaris' in '/mnt/stori/home/fk8jybr/output/canu_trim/lculinaris'
--
-- Parameters:
--
--  genomeSize        4000000000
--
--  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 TRIMMING
--
-- No change in report.
--
-- Creating overlap store trimming/lculinaris.ovlStore using:
--    140 buckets
--    140 slices
--        using at most 29 GB memory each
-- Overlap store sorter finished.
-- No change in report.
-- Finished stage 'obt-overlapStoreSorterCheck', reset canuIteration.
----------------------------------------
-- Starting command on Sat Jun  6 16:26:40 2020 with 196331.682 GB free disk space

    cd trimming
    /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/bin/ovStoreIndexer \
      -O  ./lculinaris.ovlStore.BUILDING \
      -S ../lculinaris.seqStore \
      -C  ./lculinaris.ovlStore.config \
      -delete \
    > ./lculinaris.ovlStore.BUILDING.index.err 2>&1

-- Finished on Sat Jun  6 16:29:20 2020 (160 seconds) with 196379.079 GB free disk space
----------------------------------------
-- Checking store.
----------------------------------------
-- Starting command on Sat Jun  6 16:29:20 2020 with 196379.079 GB free disk space

    cd trimming
    /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/bin/ovStoreDump \
     -S ../lculinaris.seqStore \
     -O  ./lculinaris.ovlStore \
     -counts \
     > ./lculinaris.ovlStore/counts.dat 2> ./lculinaris.ovlStore/counts.err

-- Finished on Sat Jun  6 16:29:26 2020 (6 seconds) with 196378.918 GB free disk space
----------------------------------------
--
-- Overlap store 'trimming/lculinaris.ovlStore' successfully constructed.
-- Found 172528613832 overlaps for 13194326 reads; 44980 reads have no overlaps.
--
--
-- Purged 1601.381 GB in 1479 overlap output files.
-- No change in report.
-- Finished stage 'obt-createOverlapStore', reset canuIteration.
----------------------------------------
-- Starting command on Sat Jun  6 16:30:17 2020 with 197980.467 GB free disk space

    cd trimming/3-overlapbasedtrimming
    /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/bin/trimReads \
      -S  ../../lculinaris.seqStore \
      -O  ../lculinaris.ovlStore \
      -Co ./lculinaris.1.trimReads.clear \
      -e  0.045 \
      -minlength 1000 \
      -ol 500 \
      -oc 2 \
      -o  ./lculinaris.1.trimReads \
    >     ./lculinaris.1.trimReads.err 2>&1

-- Finished on Sun Jun  7 10:24:53 2020 (64476 seconds, like watching paint dry) with 197979.398 GB free disk space
----------------------------------------
--  PARAMETERS:
--  ----------
--     1000    (reads trimmed below this many bases are deleted)
--   0.0450    (use overlaps at or below this fraction error)
--      500    (break region if overlap is less than this long, for 'largest covered' algorithm)
--        2    (break region if overlap coverage is less than this many reads, for 'largest covered' algorithm)
--  
--  INPUT READS:
--  -----------
--  13239306 reads 101922713657 bases (reads processed)
--       0 reads            0 bases (reads not processed, previously deleted)
--       0 reads            0 bases (reads not processed, in a library where trimming isn't allowed)
--  
--  OUTPUT READS:
--  ------------
--  8675204 reads  64449313446 bases (trimmed reads output)
--  4391617 reads  34400198870 bases (reads with no change, kept as is)
--   44980 reads    202296459 bases (reads with no overlaps, deleted)
--  127505 reads    239054913 bases (reads with short trimmed length, deleted)
--  
--  TRIMMING DETAILS:
--  ----------------
--  5468905 reads   1357056015 bases (bases trimmed from the 5' end of a read)
--  6167745 reads   1274793954 bases (bases trimmed from the 3' end of a read)
-- Report changed.
-- Finished stage 'obt-trimReads', reset canuIteration.
----------------------------------------
-- Starting command on Sun Jun  7 10:24:53 2020 with 197979.398 GB free disk space

    cd trimming/3-overlapbasedtrimming
    /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/bin/splitReads \
      -S  ../../lculinaris.seqStore \
      -O  ../lculinaris.ovlStore \
      -Ci ./lculinaris.1.trimReads.clear \
      -Co ./lculinaris.2.splitReads.clear \
      -e  0.045 \
      -minlength 1000 \
      -o  ./lculinaris.2.splitReads \
    >     ./lculinaris.2.splitReads.err 2>&1

-- Finished on Wed Jun 10 04:49:14 2020 (239061 seconds, at least I didn't crash) with 197978.779 GB free disk space
----------------------------------------
--  PARAMETERS:
--  ----------
--     1000    (reads trimmed below this many bases are deleted)
--   0.0450    (use overlaps at or below this fraction error)
--  INPUT READS:
--  -----------
--  13066821 reads 101481362285 bases (reads processed)
--  172485 reads    441351372 bases (reads not processed, previously deleted)
--       0 reads            0 bases (reads not processed, in a library where trimming isn't allowed)
--  
--  PROCESSED:
--  --------
--       0 reads            0 bases (no overlaps)
--     411 reads      1116341 bases (no coverage after adjusting for trimming done already)
--       0 reads            0 bases (processed for chimera)
--       0 reads            0 bases (processed for spur)
--  13066410 reads 101480245944 bases (processed for subreads)
--  
--  READS WITH SIGNALS:
--  ------------------
--       0 reads            0 signals (number of 5' spur signal)
--       0 reads            0 signals (number of 3' spur signal)
--       0 reads            0 signals (number of chimera signal)
--  111435 reads       111996 signals (number of subread signal)
--  
--  SIGNALS:
--  -------
--       0 reads            0 bases (size of 5' spur signal)
--       0 reads            0 bases (size of 3' spur signal)
--       0 reads            0 bases (size of chimera signal)
--  111996 reads     43559760 bases (size of subread signal)
--  
--  TRIMMING:
--  --------
--   60001 reads    437016237 bases (trimmed from the 5' end of the read)
--   51465 reads    373583750 bases (trimmed from the 3' end of the read)
-- Report changed.
-- Finished stage 'obt-splitReads', reset canuIteration.
----------------------------------------
-- Starting command on Wed Jun 10 04:49:14 2020 with 197978.779 GB free disk space

    cd trimming/3-overlapbasedtrimming
    /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/bin/loadTrimmedReads \
      -S ../../lculinaris.seqStore \
      -c ./lculinaris.2.splitReads.clear \
    > ./lculinaris.loadtrimmedReads.err 2>&1

-- Finished on Wed Jun 10 04:49:18 2020 (4 seconds) with 197978.286 GB free disk space
----------------------------------------
--
-- WARNING: gnuplot failed.
--
----------------------------------------
--
-- In sequence store './lculinaris.seqStore':
--   Found 13066705 reads.
--   Found 98038813470 bases (24.5 times coverage).
--
--   Read length histogram (one '*' equals 122186.22 reads):
--        0   4999 2468173 ********************
--     5000   9999 8553036 **********************************************************************
--    10000  14999 1717798 **************
--    15000  19999 260729 **
--    20000  24999  51869 
--    25000  29999  10731 
--    30000  34999   2004 
--    35000  39999    659 
--    40000  44999    380 
--    45000  49999    268 
--    50000  54999    225 
--    55000  59999    187 
--    60000  64999    140 
--    65000  69999    132 
--    70000  74999     88 
--    75000  79999     77 
--    80000  84999     69 
--    85000  89999     40 
--    90000  94999     31 
--    95000  99999     11 
--   100000 104999     22 
--   105000 109999     13 
--   110000 114999      8 
--   115000 119999      6 
--   120000 124999      3 
--   125000 129999      2 
--   130000 134999      2 
--   135000 139999      0 
--   140000 144999      1 
--   145000 149999      0 
--   150000 154999      0 
--   155000 159999      0 
--   160000 164999      0 
--   165000 169999      0 
--   170000 174999      0 
--   175000 179999      1 
--
-- Purging overlaps used for trimming.
-- Report changed.
-- Finished stage 'obt-dumpReads', reset canuIteration.
----------------------------------------
-- Starting command on Wed Jun 10 04:54:46 2020 with 201192.927 GB free disk space

    cd .
    /mnt/stori/home/fk8jybr/canu-1.9/Linux-amd64/bin/sqStoreDumpFASTQ \
      -trimmed \
      -S ./lculinaris.seqStore \
      -o ./lculinaris.trimmedReads.gz \
      -fasta \
      -nolibname \
    > ./lculinaris.trimmedReads.fasta.err 2>&1

-- Finished on Wed Jun 10 06:05:21 2020 (4236 seconds) with 201163.05 GB free disk space
----------------------------------------
--
-- Trimmed reads saved in 'lculinaris.trimmedReads.fasta.gz'.
-- No change in report.
-- Finished stage 'cor-dumpTrimmedReads', reset canuIteration.
--
-- Bye.

I would like to continue with the assemble porcess. This is the planned parameters:

canu -assemble -p lculinaris -d lculinaris genomeSize=4g batMemory=124g batThreads=48 gridOptions="--time=7-00:00:00 --partition=prod --account XXXX" gridEngineArrayOption="-a ARRAY_JOBS%5" gridOptionsOVS="--cpus-per-task=16 --mem-per-cpu=2500m" correctedErrorRate=0.085 corMhapFilterThreshold=0.0000000002 corMhapOptions="--threshold 0.80 --num-hashes 512 --num-min-matches 3 --ordered-sketch-size 1000 --ordered-kmer-size 14 --min-olap-length 2000 --repeat-idf-scale 50" mhapMemory=60g mhapBlockSize=500 ovlMerDistinct=0.975 -pacbio-corrected lculinaris.trimmedReads.fasta.gz

This parameters are good or enough for the canu assembly? Should I change something in the parameters?

skoren commented 4 years ago

The parameters look OK, all the options related to mhap are unnecessary as they are not used for the trimming/unitigging steps. I'd also suggest updating to v2.0 if you can and just run the same command with the trimmed reads since there have been a bunch of fixes and improvements from version 1.9 to 2.0.

hidvegin commented 4 years ago

Thank you for your answer. I updated canu v1.9 to v2.0 and deleted the mhap related options.

hidvegin commented 4 years ago

Dear @skoren

I get an error at contig construction with bogart.

This was the error message:

-- Canu 2.0
--
-- Detected Java(TM) Runtime Environment '1.8.0_242' (from 'java') with -d64 support.
--
-- WARNING:
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.
-- WARNING:
--
-- Detected 48 CPUs and 126 gigabytes of memory.
-- Detected Slurm with 'sinfo' binary in /usr/bin/sinfo.
-- Detected Slurm with task IDs up to 511 allowed.
-- 
-- Found   2 hosts with  24 cores and   22 GB memory under Slurm control.
-- Found  48 hosts with  48 cores and  124 GB memory under Slurm control.
--
--                         (tag)Threads
--                (tag)Memory         |
--        (tag)             |         |  algorithm
--        -------  ----------  --------  -----------------------------
-- Grid:  meryl     24.000 GB    8 CPUs  (k-mer counting)
-- Grid:  hap       16.000 GB   24 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap   22.000 GB   16 CPUs  (overlap detection with mhap)
-- Grid:  obtovl    24.000 GB   16 CPUs  (overlap detection)
-- Grid:  utgovl    24.000 GB   16 CPUs  (overlap detection)
-- Grid:  cor       24.000 GB    4 CPUs  (read correction)
-- Grid:  ovb        4.000 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs       32.000 GB    1 CPU   (overlap store sorting)
-- Grid:  red       41.000 GB    8 CPUs  (read error detection)
-- Grid:  oea        8.000 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat      120.000 GB   48 CPUs  (contig construction with bogart)
-- Grid:  cns        -.--- GB    8 CPUs  (consensus)
-- Grid:  gfa       64.000 GB   32 CPUs  (GFA alignment and processing)
--
-- In 'lculinaris.seqStore', found PacBio CLR reads:
--   PacBio CLR:               1
--
--   Corrected:                1
--   Corrected and Trimmed:    1
--
-- Generating assembly 'lculinaris' in '/mnt/stori/home/fk8jybr/output/canu_assemble/lculinaris':
--    - assemble corrected and trimmed reads.
--
-- Parameters:
--
--  genomeSize        4000000000
--
--  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 ASSEMBLY
--
-- No change in report.
-- No change in report.
--
-- Bogart failed, retry
--
-- No change in report.
--
-- Running jobs.  Second attempt out of 2.
--
-- Failed to submit compute jobs.  Delay 10 seconds and try again.

CRASH:
CRASH: Canu 2.0
CRASH: Please panic, this is abnormal.
CRASH:
CRASH:   Failed to submit compute jobs.
CRASH:
CRASH: Failed at /mnt/stori/home/fk8jybr/canu-2.0/Linux-amd64/bin/../lib/site_perl/canu/Execution.pm line 1275.
CRASH:  canu::Execution::submitOrRunParallelJob('lculinaris', 'bat', 'unitigging/4-unitigger', 'unitigger', 1) called at /mnt/stori/home/fk8jybr/canu-2.0/Linux-amd64/bin/../lib/site_perl/canu/Unitig.pm line 350
CRASH:  canu::Unitig::unitigCheck('lculinaris') called at /mnt/stori/home/fk8jybr/canu-2.0/Linux-amd64/bin/canu line 1069
CRASH: 
CRASH: Last 50 lines of the relevant log file (unitigging/4-unitigger/unitigger.jobSubmit-01.out):
CRASH:
CRASH: sbatch: error: Batch job submission failed: Requested node configuration is not available
CRASH:

I checked the sh file:

#!/bin/sh

sbatch \
  --cpus-per-task=48 --mem-per-cpu=3200m --time=7-00:00:00 --partition=prod --account denolen -o unitigger.%A_%a.out \
  -D `pwd` -J "bat_lculinaris" \
  -a 1-1%5 \
  `pwd`/unitigger.sh 0 \
> ./unitigger.jobSubmit-01.out 2>&1

canu try allocate 48 CPU and 3200 MB memory/CPU. This HPC which I can use, only allow allocate maximum 2600 MB memory/CPU and one node has got maximum 48 CPU, so tha maximum memory is 124800 MB/node. How could I add a paramater to canu for allocate maximum 2600 MB memory/CPU and maximum 48 CPU/node?

skoren commented 4 years ago

The memory isn't an issue here, the error is that before you had:

-- Bogart failed, retry
--
-- No change in report.
--
-- Running jobs.  Second attempt out of 2.

so it already failed once, post the log from the failed run (*.err and *.out in unitigging/4-unitigger folder).

hidvegin commented 4 years ago

Thank @skoren for your answer.

This is the *.out file:

Found perl:
   /usr/bin/perl
   This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi

Found java:
   /mnt/stori/home/fk8jybr/.linuxbrew/bin/java
   openjdk version "1.8.0_242"

Found canu:
   /mnt/stori/home/fk8jybr/canu-2.0/Linux-amd64/bin/canu
   Canu 2.0

Running job 1 based on SLURM_ARRAY_TASK_ID=1 and offset=0.
/var/spool/slurmd/job423491/slurm_script: line 128:  4444 Killed                  $bin/bogart -S ../../lculinaris.seqStore -O ../lculinaris.ovlStore -o ./lculinaris -gs 4000000000 -eg 0.085 -eM 0.085 -mo 500 -covgapolap 500 -lopsided nobest 50 -minolappercent 0.0 -dg 12 -db 12 -dr 6 -ca 2100 -cp 200 -threads 48 -M 120 -unassembled 2 0 1.0 0.5 3 > ./unitigger.err 2>&1
bogart appears to have failed. No lculinaris.ctgStore or lculinaris.utgStore found.

This is the *.err file:

COVGAPOLAP 500
LOPSIDED NOBEST 50
MINOLAPPERCENT 0.000000

==> PARAMETERS.

Resources:
  Memory                120 GB
  Compute Threads       48 (command line)

Lengths:
  Minimum read          0 bases
  Minimum overlap       500 bases

Overlap Error Rates:
  Graph                 0.085 (8.500%)
  Max                   0.085 (8.500%)

Deviations:
  Graph                 12.000
  Bubble                12.000
  Repeat                6.000

Similarity Thresholds:
  Graph                 0.000
  Bubble                0.100
  Repeat                0.100

Edge Confusion:
  Absolute              2100
  Percent               200.0000

Unitig Construction:
  Minimum intersection  500 bases
  Maxiumum placements   2 positions

Debugging Enabled:
  (none)

==> LOADING AND FILTERING OVERLAPS.

sqStore_loadMetadata()-- Using 'corrected-trimmed' 0x10 reads.
ReadInfo()-- Using 13066705 reads, no minimum read length used.

OverlapCache()-- limited to 122880MB memory (user supplied).

OverlapCache()--      99MB for read data.
OverlapCache()--     398MB for best edges.
OverlapCache()--    1295MB for tigs.
OverlapCache()--     348MB for tigs - read layouts.
OverlapCache()--     498MB for tigs - error profiles.
OverlapCache()--   30720MB for tigs - error profile overlaps.
OverlapCache()--   12890MB for other processes.
OverlapCache()-- ---------
OverlapCache()--   46501MB for data structures (sum of above).
OverlapCache()-- ---------
OverlapCache()--     249MB for overlap store structure.
OverlapCache()--   76129MB for overlap data.
OverlapCache()-- ---------
OverlapCache()--  122880MB allowed.
OverlapCache()--
OverlapCache()-- Retain at least 49 overlaps/read, based on 24.51x coverage.
OverlapCache()-- Initial guess at 381 overlaps/read.
OverlapCache()--
OverlapCache()-- Adjusting for sparse overlaps.
OverlapCache()--
OverlapCache()--               reads loading olaps          olaps               memory
OverlapCache()--   olaps/read       all      some          loaded                 free
OverlapCache()--   ----------   -------   -------     ----------- -------     --------
OverlapCache()--          381   8912732   4153973      2670750356  46.69%      35377 MB
OverlapCache()--          939   11202944   1863761      4240043400  74.13%      11431 MB
OverlapCache()--         1340   11938878   1127827       531789490  84.39%       2479 MB
OverlapCache()--         1484   12122076    944629       680706689  86.99%        206 MB
OverlapCache()--         1498   12138239    928466       693826470  87.22%          6 MB
OverlapCache()--
OverlapCache()-- Loading overlaps.
OverlapCache()--
OverlapCache()--          read from store           saved in cache
OverlapCache()--   ------------ ---------   ------------ ---------
OverlapCache()--       41560581 (000.73%)       36134880 (000.63%)
OverlapCache()--       84746468 (001.48%)       73716353 (001.29%)
OverlapCache()--      127774283 (002.23%)      111211142 (001.94%)
OverlapCache()--      172287456 (003.01%)      149696721 (002.62%)
OverlapCache()--      215650520 (003.77%)      187260435 (003.27%)
OverlapCache()--      259225282 (004.53%)      225024430 (003.93%)
OverlapCache()--      302505057 (005.29%)      262812507 (004.59%)
OverlapCache()--      345795227 (006.05%)      300504962 (005.25%)
OverlapCache()--      388416681 (006.79%)      337708756 (005.90%)
OverlapCache()--      432216937 (007.56%)      375819289 (006.57%)
OverlapCache()--      475081984 (008.31%)      413229209 (007.22%)
OverlapCache()--      517225067 (009.04%)      450221646 (007.87%)
OverlapCache()--      560817149 (009.80%)      488095206 (008.53%)
OverlapCache()--      604144073 (010.56%)      525712799 (009.19%)
OverlapCache()--      648880791 (011.34%)      564146579 (009.86%)
OverlapCache()--      693161699 (012.12%)      602523558 (010.53%)
OverlapCache()--      736505407 (012.88%)      640161810 (011.19%)
OverlapCache()--      780028764 (013.64%)      678035570 (011.85%)
OverlapCache()--      824364505 (014.41%)      716058311 (012.52%)
OverlapCache()--      868324876 (015.18%)      754319430 (013.19%)
OverlapCache()--      913155225 (015.96%)      792916397 (013.86%)
OverlapCache()--      957366036 (016.74%)      830986947 (014.53%)
OverlapCache()--     1001508335 (017.51%)      869036571 (015.19%)
OverlapCache()--     1045342918 (018.28%)      906881301 (015.86%)
OverlapCache()--     1090489707 (019.07%)      945749441 (016.53%)
OverlapCache()--     1136258113 (019.87%)      984959862 (017.22%)
OverlapCache()--     1182699675 (020.68%)     1024242493 (017.91%)
OverlapCache()--     1228618963 (021.48%)     1063741566 (018.60%)
OverlapCache()--     1274196514 (022.28%)     1102818505 (019.28%)
OverlapCache()--     1319504765 (023.07%)     1141659308 (019.96%)
OverlapCache()--     1365511550 (023.87%)     1181179331 (020.65%)
OverlapCache()--     1409886806 (024.65%)     1219876700 (021.33%)
OverlapCache()--     1453940821 (025.42%)     1258065288 (021.99%)
OverlapCache()--     1498885214 (026.21%)     1296739011 (022.67%)
OverlapCache()--     1545005558 (027.01%)     1335890534 (023.36%)
OverlapCache()--     1592267632 (027.84%)     1375722299 (024.05%)
OverlapCache()--     1640105989 (028.67%)     1415986296 (024.76%)
OverlapCache()--     1687227767 (029.50%)     1456011685 (025.46%)
OverlapCache()--     1734200184 (030.32%)     1495999165 (026.15%)
OverlapCache()--     1780692947 (031.13%)     1535425417 (026.84%)
OverlapCache()--     1828421800 (031.97%)     1576007846 (027.55%)
OverlapCache()--     1875641445 (032.79%)     1615832102 (028.25%)
OverlapCache()--     1923741692 (033.63%)     1656256798 (028.96%)
OverlapCache()--     1970765986 (034.46%)     1695982769 (029.65%)
OverlapCache()--     2018596202 (035.29%)     1736558000 (030.36%)
OverlapCache()--     2064790309 (036.10%)     1775995194 (031.05%)
OverlapCache()--     2111885099 (036.92%)     1816430628 (031.76%)
OverlapCache()--     2158187752 (037.73%)     1856012555 (032.45%)
OverlapCache()--     2205198946 (038.55%)     1895875819 (033.15%)
OverlapCache()--     2251542255 (039.36%)     1935248375 (033.83%)
OverlapCache()--     2297888547 (040.17%)     1974947300 (034.53%)
OverlapCache()--     2343751932 (040.98%)     2014098665 (035.21%)
OverlapCache()--     2389476737 (041.78%)     2053296140 (035.90%)
OverlapCache()--     2435402940 (042.58%)     2092594905 (036.59%)
OverlapCache()--     2477732730 (043.32%)     2129352009 (037.23%)
OverlapCache()--     2519035704 (044.04%)     2165025002 (037.85%)
OverlapCache()--     2560670900 (044.77%)     2201140257 (038.48%)
OverlapCache()--     2602530726 (045.50%)     2237415328 (039.12%)
OverlapCache()--     2644584349 (046.24%)     2273648723 (039.75%)
OverlapCache()--     2685246575 (046.95%)     2308921955 (040.37%)
OverlapCache()--     2725700779 (047.65%)     2344206941 (040.98%)
OverlapCache()--     2766148348 (048.36%)     2379547339 (041.60%)
OverlapCache()--     2808536295 (049.10%)     2416226438 (042.24%)
OverlapCache()--     2849916908 (049.83%)     2452332228 (042.87%)
OverlapCache()--     2891383432 (050.55%)     2488443266 (043.51%)
OverlapCache()--     2932537066 (051.27%)     2524195437 (044.13%)
OverlapCache()--     2974858267 (052.01%)     2560972053 (044.77%)
OverlapCache()--     3017021510 (052.75%)     2597624874 (045.41%)
OverlapCache()--     3059036141 (053.48%)     2634073367 (046.05%)
OverlapCache()--     3100100522 (054.20%)     2669992594 (046.68%)
OverlapCache()--     3141445493 (054.92%)     2706011442 (047.31%)
OverlapCache()--     3182508874 (055.64%)     2741976352 (047.94%)
OverlapCache()--     3225074510 (056.38%)     2779241589 (048.59%)
OverlapCache()--     3265627474 (057.09%)     2814608899 (049.21%)
OverlapCache()--     3307125397 (057.82%)     2851058887 (049.85%)
OverlapCache()--     3348103643 (058.54%)     2887009832 (050.47%)
OverlapCache()--     3390423922 (059.28%)     2923857740 (051.12%)
OverlapCache()--     3431051641 (059.99%)     2959239805 (051.74%)
OverlapCache()--     3471661363 (060.70%)     2995079935 (052.36%)
OverlapCache()--     3513191833 (061.42%)     3031296704 (053.00%)
OverlapCache()--     3556697233 (062.18%)     3068293456 (053.64%)
OverlapCache()--     3600446488 (062.95%)     3105397008 (054.29%)
OverlapCache()--     3644309938 (063.71%)     3142767849 (054.95%)
OverlapCache()--     3687531415 (064.47%)     3180015455 (055.60%)
OverlapCache()--     3730397011 (065.22%)     3216834662 (056.24%)
OverlapCache()--     3772634260 (065.96%)     3253196420 (056.88%)
OverlapCache()--     3815993510 (066.72%)     3290454756 (057.53%)
OverlapCache()--     3858946617 (067.47%)     3327351154 (058.17%)
OverlapCache()--     3901626333 (068.21%)     3364086913 (058.81%)
OverlapCache()--     3944106556 (068.96%)     3401052818 (059.46%)
OverlapCache()--     3987094530 (069.71%)     3438060084 (060.11%)
OverlapCache()--     4030044269 (070.46%)     3475030769 (060.75%)
OverlapCache()--     4073718821 (071.22%)     3512455826 (061.41%)
OverlapCache()--     4117572983 (071.99%)     3549933498 (062.06%)
OverlapCache()--     4160318597 (072.74%)     3586654518 (062.71%)
OverlapCache()--     4202319875 (073.47%)     3622928580 (063.34%)
OverlapCache()--     4244883484 (074.21%)     3659660763 (063.98%)
OverlapCache()--     4286916222 (074.95%)     3695887922 (064.62%)
OverlapCache()--     4330329382 (075.71%)     3732961076 (065.26%)
OverlapCache()--     4372887035 (076.45%)     3769503073 (065.90%)
OverlapCache()--     4415194389 (077.19%)     3806048601 (066.54%)
OverlapCache()--     4456906915 (077.92%)     3842048940 (067.17%)
OverlapCache()--     4499095835 (078.66%)     3878567325 (067.81%)
OverlapCache()--     4541731564 (079.40%)     3914989771 (068.45%)
OverlapCache()--     4584198592 (080.15%)     3951437841 (069.08%)
OverlapCache()--     4626932006 (080.89%)     3988284516 (069.73%)
OverlapCache()--     4673905864 (081.71%)     4028914091 (070.44%)
OverlapCache()--     4722596235 (082.57%)     4070780002 (071.17%)
OverlapCache()--     4771348483 (083.42%)     4112737659 (071.90%)
OverlapCache()--     4819171112 (084.25%)     4153934829 (072.62%)
OverlapCache()--     4867060444 (085.09%)     4195306914 (073.35%)
OverlapCache()--     4914571551 (085.92%)     4236061358 (074.06%)
OverlapCache()--     4962805245 (086.77%)     4277292200 (074.78%)
OverlapCache()--     5010102003 (087.59%)     4317818812 (075.49%)
OverlapCache()--     5056471788 (088.40%)     4357973871 (076.19%)
OverlapCache()--     5104352836 (089.24%)     4398878603 (076.91%)
OverlapCache()--     5151500553 (090.06%)     4439533843 (077.62%)
OverlapCache()--     5198409878 (090.88%)     4479681652 (078.32%)
OverlapCache()--     5241007390 (091.63%)     4516926238 (078.97%)
OverlapCache()--     5281753691 (092.34%)     4552726601 (079.60%)
OverlapCache()--     5322765484 (093.06%)     4588644189 (080.22%)
OverlapCache()--     5363616272 (093.77%)     4624487726 (080.85%)
OverlapCache()--     5404859761 (094.49%)     4660362312 (081.48%)
OverlapCache()--     5446434830 (095.22%)     4696593664 (082.11%)
OverlapCache()--     5487615260 (095.94%)     4732607281 (082.74%)
OverlapCache()--     5528115091 (096.65%)     4768290049 (083.36%)
OverlapCache()--     5568470276 (097.35%)     4803596134 (083.98%)
OverlapCache()--     5609992229 (098.08%)     4840048648 (084.62%)
OverlapCache()--     5651065168 (098.80%)     4876019781 (085.25%)
OverlapCache()--     5692250844 (099.52%)     4911985563 (085.88%)
OverlapCache()--   ------------ ---------   ------------ ---------
OverlapCache()--     5719799114 (100.00%)     4936065994 (086.30%)
OverlapCache()--
OverlapCache()-- Ignored 61466148 duplicate overlaps.
OverlapCache()--
OverlapCache()-- Symmetrizing overlaps.
OverlapCache()--   Finding missing twins.
OverlapCache()--   Found 679159097 overlaps with non-symmetric error rates.
OverlapCache()--   Found 560905114 missing twins in 4936065994 overlaps, 747716 are strong.
OverlapCache()--   Dropping weak non-twin overlaps; allocated 0 MB scratch space.
OverlapCache()--   Dropped 139413811 overlaps; scratch space released.
OverlapCache()--   Adding 421491303 missing twin overlaps.
OverlapCache()--   Finished.

BestOverlapGraph()-- Computing Best Overlap Graph.
BestOverlapGraph()-- Allocating best edges (398MB).
BestOverlapGraph()-- Filtering high error edges.
BestOverlapGraph()--   Ignore overlaps with more than 6.423634% error.
BestOverlapGraph()-- Filtering reads with a gap in overlap coverage.
BestOverlapGraph()--   14474 reads removed.
BestOverlapGraph()-- Filtering reads with lopsided best edges (more than 50% different).
BestOverlapGraph()--   173783 reads have lopsided edges.
BestOverlapGraph()-- Filtering spur reads.
BestOverlapGraph()--   After initial scan, found:
BestOverlapGraph()--     412016 spur reads.
BestOverlapGraph()--     485911 5' spur paths.
BestOverlapGraph()--     466758 3' spur paths.
BestOverlapGraph()--   After iteration 1, found:
BestOverlapGraph()--     412016 spur reads.
BestOverlapGraph()--     478074 5' spur paths;  49196 5' edges changed to avoid a spur path.
BestOverlapGraph()--     457159 3' spur paths;  60860 5' edges changed to avoid a spur path.
BestOverlapGraph()--   After iteration 2, found:
BestOverlapGraph()--     412016 spur reads.
BestOverlapGraph()--     474273 5' spur paths;   3392 5' edges changed to avoid a spur path.
BestOverlapGraph()--     450834 3' spur paths;   3449 5' edges changed to avoid a spur path.
BestOverlapGraph()--   After iteration 3, found:
BestOverlapGraph()--     412016 spur reads.
BestOverlapGraph()--     473922 5' spur paths;    339 5' edges changed to avoid a spur path.
BestOverlapGraph()--     450501 3' spur paths;    371 5' edges changed to avoid a spur path.
BestOverlapGraph()--   After iteration 4, found:
BestOverlapGraph()--     412016 spur reads.
BestOverlapGraph()--     473900 5' spur paths;     22 5' edges changed to avoid a spur path.
BestOverlapGraph()--     450491 3' spur paths;     44 5' edges changed to avoid a spur path.
BestOverlapGraph()--   After iteration 5, found:
BestOverlapGraph()--     412016 spur reads.
BestOverlapGraph()--     473899 5' spur paths;      1 5' edges changed to avoid a spur path.
BestOverlapGraph()--     450490 3' spur paths;      0 5' edges changed to avoid a spur path.
BestOverlapGraph()--   After iteration 6, found:
BestOverlapGraph()--     412016 spur reads.
BestOverlapGraph()--     473899 5' spur paths;      0 5' edges changed to avoid a spur path.
BestOverlapGraph()--     450489 3' spur paths;      2 5' edges changed to avoid a spur path.
Cleared 0 5' and 0 3' best edges on contained reads.

==> BUILDING GREEDY TIGS.

breakSingletonTigs()-- Removed 372723 singleton tigs; reads are now unplaced.
optimizePositions()-- Optimizing read positions for 13066706 reads in 525613 tigs, with 48 threads.
optimizePositions()--   Allocating scratch space for 13066706 reads (408334 KB).
optimizePositions()--   Initializing positions with 48 threads.
optimizePositions()--   Recomputing positions, iteration 1, with 48 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 12983611 reads
optimizePositions()--     changed:    83095 reads
optimizePositions()--   Recomputing positions, iteration 2, with 48 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 13026055 reads
optimizePositions()--     changed:    40651 reads
optimizePositions()--   Recomputing positions, iteration 3, with 48 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 13061761 reads
optimizePositions()--     changed:     4945 reads
optimizePositions()--   Recomputing positions, iteration 4, with 48 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 13064625 reads
optimizePositions()--     changed:     2081 reads
optimizePositions()--   Recomputing positions, iteration 5, with 48 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 13065287 reads
optimizePositions()--     changed:     1419 reads
optimizePositions()--   Expanding short reads with 48 threads.
optimizePositions()--   Updating positions.
optimizePositions()--   Finished.
splitDiscontinuous()-- Tested 152923 tigs, split 19 tigs into 38 new tigs.
detectSpur() done.
tested         37043
nEdges      5' 25055   3' 26146
nPotential     3686      3878
nVerified       122       118

==> PLACE CONTAINED READS.

computeErrorProfiles()-- Computing error profiles for 525651 tigs, with 48 threads.
computeErrorProfiles()-- Finished.

placeContains()-- placing 11391637 contained and 387197 unplaced reads, with 48 threads.
placeContains()-- Placed 10584191 contained reads and 81121 unplaced reads.
placeContains()-- Failed to place 807446 contained reads (too high error suspected) and 306076 unplaced reads (lack of overlaps suspected).
optimizePositions()-- Optimizing read positions for 13066706 reads in 525651 tigs, with 48 threads.
optimizePositions()--   Allocating scratch space for 13066706 reads (408334 KB).
optimizePositions()--   Initializing positions with 48 threads.
optimizePositions()--   Recomputing positions, iteration 1, with 48 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 10358262 reads
optimizePositions()--     changed:   2708444 reads
optimizePositions()--   Recomputing positions, iteration 2, with 48 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 12519596 reads
optimizePositions()--     changed:   547110 reads
optimizePositions()--   Recomputing positions, iteration 3, with 48 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 12832763 reads
optimizePositions()--     changed:   233943 reads
optimizePositions()--   Recomputing positions, iteration 4, with 48 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 12936543 reads
optimizePositions()--     changed:   130163 reads
optimizePositions()--   Recomputing positions, iteration 5, with 48 threads.
optimizePositions()--     Reset zero.
optimizePositions()--     Checking convergence.
optimizePositions()--     converged: 12969447 reads
optimizePositions()--     changed:    97259 reads
optimizePositions()--   Expanding short reads with 48 threads.
optimizePositions()--   Updating positions.
optimizePositions()--   Finished.
splitDiscontinuous()-- Tested 153013 tigs, split 55 tigs into 112 new tigs.

==> MERGE ORPHANS.

computeErrorProfiles()-- Computing error profiles for 525763 tigs, with 48 threads.
computeErrorProfiles()-- Finished.

findPotentialOrphans()-- working on 525763 tigs.
findPotentialOrphans()-- found 57408 potential orphans.
mergeOrphans()-- flagged   31165        bubble tigs with 1230257 reads
mergeOrphans()-- placed      210 unique orphan tigs with 453 reads
mergeOrphans()-- shattered   486 repeat orphan tigs with 1006 reads
mergeOrphans()-- ignored       0               tigs with 0 reads; failed to place
mergeOrphans()--

----------------------------------------
Building new graph after removing 10666748 placed reads and 1230257 bubble reads.

BestOverlapGraph()-- Computing Best Overlap Graph.
BestOverlapGraph()-- Allocating best edges (398MB).
BestOverlapGraph()-- Filtering high error edges.
BestOverlapGraph()--   Ignore overlaps with more than 6.315305% error.
BestOverlapGraph()-- Filtering reads with a gap in overlap coverage.
BestOverlapGraph()--   72540 reads removed.
BestOverlapGraph()-- Filtering reads with lopsided best edges (more than 50% different).
BestOverlapGraph()--   297165 reads have lopsided edges.
BestOverlapGraph()-- Filtering spur reads.
BestOverlapGraph()--   After initial scan, found:
BestOverlapGraph()--     565499 spur reads.
BestOverlapGraph()--     660489 5' spur paths.
BestOverlapGraph()--     637847 3' spur paths.
BestOverlapGraph()--   After iteration 1, found:
BestOverlapGraph()--     565499 spur reads.
BestOverlapGraph()--     652162 5' spur paths;  53522 5' edges changed to avoid a spur path.
BestOverlapGraph()--     628229 3' spur paths;  62199 5' edges changed to avoid a spur path.
BestOverlapGraph()--   After iteration 2, found:
BestOverlapGraph()--     565499 spur reads.
BestOverlapGraph()--     647701 5' spur paths;   4104 5' edges changed to avoid a spur path.
BestOverlapGraph()--     621990 3' spur paths;   4159 5' edges changed to avoid a spur path.
BestOverlapGraph()--   After iteration 3, found:
BestOverlapGraph()--     565499 spur reads.
BestOverlapGraph()--     647210 5' spur paths;    521 5' edges changed to avoid a spur path.
BestOverlapGraph()--     621510 3' spur paths;    513 5' edges changed to avoid a spur path.
BestOverlapGraph()--   After iteration 4, found:
BestOverlapGraph()--     565499 spur reads.
BestOverlapGraph()--     647192 5' spur paths;     17 5' edges changed to avoid a spur path.
BestOverlapGraph()--     621499 3' spur paths;     32 5' edges changed to avoid a spur path.
BestOverlapGraph()--   After iteration 5, found:
BestOverlapGraph()--     565499 spur reads.
BestOverlapGraph()--     647192 5' spur paths;      0 5' edges changed to avoid a spur path.
BestOverlapGraph()--     621499 3' spur paths;      0 5' edges changed to avoid a spur path.
Cleared 0 5' and 0 3' best edges on contained reads.
classifyAsUnassembled()--      7 tigs       26659 bases -- singleton
classifyAsUnassembled()--      0 tigs           0 bases -- too few reads        (< 2 reads)
classifyAsUnassembled()--      0 tigs           0 bases -- too short            (< 0 bp)
classifyAsUnassembled()--      0 tigs           0 bases -- single spanning read (> 1.000000 tig length)
classifyAsUnassembled()--   2266 tigs    32382999 bases -- low coverage         (> 0.500000 tig length at < 3 coverage)
classifyAsUnassembled()-- 151170 tigs  3868425641 bases -- acceptable contigs

==> GENERATING ASSEMBLY GRAPH.

computeErrorProfiles()-- Computing error profiles for 525763 tigs, with 48 threads.
computeErrorProfiles()-- Finished.

AssemblyGraph()-- allocating vectors for placements, 598.146MB
AssemblyGraph()-- finding edges for 11953183 reads (10584191 contained), ignoring 1113522 unplaced reads, with 48 threads.
skoren commented 4 years ago

There's no Bogart error in your posted log, the only message is:

/var/spool/slurmd/job423491/slurm_script: line 128:  4444 Killed                  $bin/bogart -S ../../lculinaris.seqStore -O ../lculinaris.ovlStore -o ./lculinaris -gs 4000000000 -eg 0.085 -eM 0.085 -mo 500 -covgapolap 500 -lopsided nobest 50 -minolappercent 0.0 -dg 12 -db 12 -dr 6 -ca 2100 -cp 200 -threads 48 -M 120 -unassembled 2 0 1.0 0.5 3 > ./unitigger.err 2>&1

so I presume your cluster killed the Bogart run due to memory or a timeout. Check your cluster job history to see why the job failed (did it use too much memory, did it hit a timeout). You can probably edit the command to lower the memory further to -M 100 or even -M 60 without issue. Run the unitigging.sh script by hand once you figure out the issue again and then you can resume Canu.

hidvegin commented 4 years ago

Thank @skoren for your answer. I tried run the unitigging.sh but I get this error:

Found perl:
   /usr/bin/perl
   This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi

Found java:
   /mnt/stori/home/fk8jybr/.linuxbrew/bin/java
   openjdk version "1.8.0_242"

Found canu:
   /mnt/stori/home/fk8jybr/canu-2.0/Linux-amd64/bin/canu
   Canu 2.0

Error: I need SLURM_ARRAY_TASK_ID set, or a job index on the command line.
skoren commented 4 years ago

You need to provide a job number to unitigging.sh so run it as unitigging.sh.sh 1

hidvegin commented 4 years ago

I tried what you suggested. I increased the CPU and memory to 30 CPU and 60 GB ram in the unitigging.sh. But I did not change the CPU and memory in batch script. So, I allocated 48 CPU and 124 GB ram in the batch script but I used only 30 CPU and 60 GB ram in the unitigging.sh script. With this solution the script is successfully finished and after this I rerun canu.