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:
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 spacecd 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>&1sh: 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 2.0CRASH: 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 1031CRASH: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**): Assertionw->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: