Overlap-jobs failed: canu-1.8

[marcoeml]

Dear all I am using canu-1.8, I guess the most updated version of canu. After a few hours of running, I got the error message bellow. I used this command line:

/home/vinatzerlab/Software/canu-1.8/Linux-amd64/bin/canu -p BAV2934_WT -d Canu_Assembly genomeSize=4.8m -nanopore-raw BAV2934_MinION_reads.fastq stopOnReadQuality=false

I will really appreciate your help. Best

-- Running jobs.  First attempt out of 2.
----------------------------------------
-- Starting 'utgovl' concurrent execution on Fri Apr  5 15:26:04 2019 with 1179.55 GB free disk space (8 processes; 2 concurrently)

    cd unitigging/1-overlapper
    ./overlap.sh 1 > ./overlap.000001.out 2>&1
    ./overlap.sh 2 > ./overlap.000002.out 2>&1
    ./overlap.sh 3 > ./overlap.000003.out 2>&1
    ./overlap.sh 4 > ./overlap.000004.out 2>&1
    ./overlap.sh 5 > ./overlap.000005.out 2>&1
    ./overlap.sh 6 > ./overlap.000006.out 2>&1
    ./overlap.sh 7 > ./overlap.000007.out 2>&1
    ./overlap.sh 8 > ./overlap.000008.out 2>&1

-- Finished on Fri Apr  5 16:01:32 2019 (2128 seconds) with 1178.918 GB free disk space
----------------------------------------
--
-- Overlap jobs failed, retry.
--   job unitigging/1-overlapper/001/000004.ovb FAILED.
--   job unitigging/1-overlapper/001/000005.ovb FAILED.
--   job unitigging/1-overlapper/001/000006.ovb FAILED.
--   job unitigging/1-overlapper/001/000007.ovb FAILED.
--   job unitigging/1-overlapper/001/000008.ovb FAILED.
--
--
-- Running jobs.  Second attempt out of 2.
----------------------------------------
-- Starting 'utgovl' concurrent execution on Fri Apr  5 16:01:32 2019 with 1178.918 GB free disk space (5 processes; 2 concurrently)

    cd unitigging/1-overlapper
    ./overlap.sh 4 > ./overlap.000004.out 2>&1
    ./overlap.sh 5 > ./overlap.000005.out 2>&1
    ./overlap.sh 6 > ./overlap.000006.out 2>&1
    ./overlap.sh 7 > ./overlap.000007.out 2>&1
    ./overlap.sh 8 > ./overlap.000008.out 2>&1

-- Finished on Fri Apr  5 16:01:33 2019 (one second) with 1178.918 GB free disk space
----------------------------------------
--
-- Overlap jobs failed, tried 2 times, giving up.
--   job unitigging/1-overlapper/001/000004.ovb FAILED.
--   job unitigging/1-overlapper/001/000005.ovb FAILED.
--   job unitigging/1-overlapper/001/000006.ovb FAILED.
--   job unitigging/1-overlapper/001/000007.ovb FAILED.
--   job unitigging/1-overlapper/001/000008.ovb FAILED.
--

ABORT:
ABORT: Canu 1.8
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:

[skoren]

One of the logs of the failed jobs should have more details, can you post it (e.g. unitigging/1-overlapper/*4*.out? You can also post the full canu log as it will have more info on your machine and the resources it is trying to use.

[marcoeml]

Hi Sergey

This is overlap.000004.out:

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: /home/vinatzerlab/miniconda3/bin/java openjdk version "11.0.1" 2018-10-16 LTS

Found canu: /home/vinatzerlab/Software/canu-1.8/Linux-amd64/bin/canu readline() on closed filehandle F at /home/vinatzerlab/Software/canu-1.8/Linux-amd64/bin/../lib/site_perl/canu/Defaults.pm line 1079.

Running job 4 based on command line options. ./overlap.sh: /home/vinatzerlab/Software/canu-1.8/Linux-amd64/bin/overlapInCore: /home/vinatzerlab/.linuxbrew/lib/ld.so: bad ELF interpreter: No such file or directory

For the full canu log, do you mean files in the canu-logs folder?

Thank you very much for your help!

[marcoeml]

This is what I saw on the screen after I ran my commands.

Canu_fail.txt

[skoren]

Ah this is an issue with your system:

./overlap.sh: /home/vinatzerlab/Software/canu-1.8/Linux-amd64/bin/overlapInCore: /home/vinatzerlab/.linuxbrew/lib/ld.so: bad ELF interpreter: No such file or directory

seems something in the installation of brew changed between the time you launched canu and now so it is now missing a critical system library. The fact that it run to this point implies that something changed around Friday, April 5th after 4pm. Based on this brew issue, it seems like you may have to re-install brew from scratch: https://github.com/Linuxbrew/legacy-linuxbrew/issues/677

[marcoeml]

Thank you very much Sergey!

It worked. My run is done now! Best