ERROR: Failed with exit code 134. (rc=34304)

[JuFengWang]

Hi,
I used the following commands:
canu -trim -p T_musculi -d canu maxThreads=20 genomeSize=30m minReadLength=200 minOverlapLength=100 -pacbio-corrected /data1/libq/WJF/pacbio/MNN1/r54295_20200223_075102/canu/T_musculi.correctedReads.fasta.gz

-- Starting command on Tue Mar 24 08:33:15 2020 with 345.909 GB free disk space

cd trimming/3-overlapbasedtrimming
/data1/libq/miniconda3/bin/splitReads \
-S ../../T_musculi.seqStore \
-O ../T_musculi.ovlStore \
-Ci ./T_musculi.1.trimReads.clear \
-Co ./T_musculi.2.splitReads.clear \
-e 0.045 \
-minlength 200 \
-o ./T_musculi.2.splitReads \
> ./T_musculi.2.splitReads.err 2>&1
sh: line 8: 17491 Aborted (core dumped) /data1/libq/miniconda3/bin/splitReads -S ../../T_musculi.seqStore -O ../T_musculi.ovlStore -Ci ./T_musculi.1.trimReads.clear -Co ./T_musculi.2.splitReads.clear -e 0.045 -minlength 200 -o ./T_musculi.2.splitReads > ./T_musculi.2.splitReads.err 2>&1

-- Finished on Tue Mar 24 08:36:43 2020 (208 seconds) with 345.907 GB free disk space
----------------------------------------

ERROR:
ERROR: Failed with exit code 134. (rc=34304)
ERROR:

CRASH:
CRASH: Canu 2.0
CRASH: Please panic, this is abnormal.
CRASH:
CRASH: splitReads failed.
CRASH:
CRASH: Failed at /data1/libq/miniconda3/bin/../lib/site_perl/canu/OverlapBasedTrimming.pm line 160.
CRASH: canu::OverlapBasedTrimming::splitReads("T_musculi") called at /data1/libq/miniconda3/bin/canu line 1031
CRASH:
CRASH: Last 50 lines of the relevant log file (trimming/3-overlapbasedtrimming/T_musculi.2.splitReads.err):
CRASH:
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: ZERO length suplied to intervalList::add(), ignoring interval.
CRASH: splitReads: overlapBasedTrimming/splitReads.C:368: int main(int, char**): Assertion w->clrBgn >= w->iniBgn' failed.`

CRASH:
CRASH: Failed with 'Aborted'; backtrace (libbacktrace):
CRASH: (null)::0 in (null)()
CRASH: (null)::0 in (null)()
CRASH: (null)::0 in (null)()
CRASH: (null)::0 in (null)()
CRASH: (null)::0 in (null)()
CRASH: (null)::0 in (null)()
CRASH: (null)::0 in (null)()
CRASH: (null)::0 in (null)()
CRASH: ../sysdeps/x86_64/elf/start.S::103 in (null)()
CRASH:

[skoren]

I am not sure you're really using v2.0, conda has a terrible install process that corrupts updates and we do not recommend using it. I updated the recipe a while back but not idea if it's what is being used. I suggest either completely removing the conda install and trying again or just download our binary from the release page which we know is built correctly.

If that still fails with the release download, are you able to share this dataset (see the FAQ for instructions to send it to us).

[JuFengWang]

It still failed with the release download，and I don't fnd the FAQ. Can you give me some tips?

[skoren]

I mean the FAQ on sending us data: https://canu.readthedocs.io/en/latest/faq.html#how-can-i-send-data-to-you

[skoren]

Are you able to share this data? Without that I'm going to close the issue since we've not seen this error locally.