Running assembly :1 overlap correction jobs failed with buffer overflow detected error

lpryszcz commented 6 years ago

Hi, my run failed duringRunning assembly. I've tried to rerun it, but got exactly the same error. Any hints? Bests,

----------------------------------------START CONCURRENT Tue Mar 20 16:57:51 2018
/home/lpryszcz/cluster/hybrids/mbizzarri/masurca/ATCC42981/CA.mr.41.15.15.0.02/3-overlapcorrection/ovlcorr.sh 1 > /home/lpryszcz/cluster/hybrids/mbizzarri/masurca/ATCC42981/CA.mr.41.15.15.0.02/3-overlapcorrection/0001.err 2>&1
----------------------------------------END CONCURRENT Tue Mar 20 16:57:58 2018 (7 seconds)
Overlap correction job 1 (/home/lpryszcz/cluster/hybrids/mbizzarri/masurca/ATCC42981/CA.mr.41.15.15.0.02/3-overlapcorrection/0001) failed.
================================================================================

runCA failed.

----------------------------------------
Stack trace:

 at /home/lpryszcz/src/MaSuRCA-3.2.4/bin/../CA8/Linux-amd64/bin/runCA line 1613.
        main::caFailure('1 overlap correction jobs failed; remove /home/lpryszcz/clust...', undef) called at /home/lpryszcz/src/MaSuRCA-3.2.4/bin/../CA8/Linux-amd64/bin/runCA line 4514
        main::overlapCorrection() called at /home/lpryszcz/src/MaSuRCA-3.2.4/bin/../CA8/Linux-amd64/bin/runCA line 6526

----------------------------------------
Failure message:

1 overlap correction jobs failed; remove /home/lpryszcz/cluster/hybrids/mbizzarri/masurca/ATCC42981/CA.mr.41.15.15.0.02/3-overlapcorrection/ovlcorr.sh (or run by hand) to try again

Overlap correction job 1 (/home/lpryszcz/cluster/hybrids/mbizzarri/masurca/ATCC42981/CA.mr.41.15.15.0.02/3-overlapcorrection/0001) failed.
================================================================================

runCA failed.

----------------------------------------
Stack trace:

 at /home/lpryszcz/src/MaSuRCA-3.2.4/bin/../CA8/Linux-amd64/bin/runCA line 1613.
        main::caFailure('1 overlap correction jobs failed; remove /home/lpryszcz/clust...', undef) called at /home/lpryszcz/src/MaSuRCA-3.2.4/bin/../CA8/Linux-amd64/bin/runCA line 4514
        main::overlapCorrection() called at /home/lpryszcz/src/MaSuRCA-3.2.4/bin/../CA8/Linux-amd64/bin/runCA line 6526

----------------------------------------
Failure message:

1 overlap correction jobs failed; remove /home/lpryszcz/cluster/hybrids/mbizzarri/masurca/ATCC42981/CA.mr.41.15.15.0.02/3-overlapcorrection/ovlcorr.sh (or run by hand) to try again

lpryszcz commented 6 years ago

crossposted also on SF: https://sourceforge.net/p/wgs-assembler/bugs/261/

lpryszcz commented 6 years ago

Sadly, I've encountered similar problem with another genome...

lpryszcz commented 6 years ago

As Sergey pointed out, adding doFragmentCorrection=0 to runCA will do the job. You can execute below from withing MaSuRCA src:

sed -i.bck 's/cnsReuseUnitigs=1" > runCA.spec/cnsReuseUnitigs=1\ndoFragmentCorrection=0" > runCA.spec/' bin/mega_reads_assemble_*.sh

and then restart your run rm CA*/3-overlapcorrection/ovlcorr.sh; ~/src/masurca/bin/masurca configuration.txt; time ./assemble.sh

alekseyzimin / masurca

Running assembly :1 overlap correction jobs failed with buffer overflow detected error #8