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marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
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Abnormal error #2322

Open ewoutcrombez opened 1 week ago

ewoutcrombez commented 1 week ago

Hello,

I tried running Canu using the command canu -p Canu -d ../results/Canu genomeSize=158m corOutCoverage=200 correctedErrorRate=0.15 -nanopore reads.fastq.gz on a slurm grid cluster, but got this "abnormal" error:

ERROR:
ERROR:  Failed with exit code 139.  (rc=35584)
ERROR:

CRASH:
CRASH: canu 2.2
CRASH: Please panic, this is abnormal.
CRASH:
CRASH:   splitReads failed.
CRASH:
CRASH: Failed at /shared/clssoft/apps/x86_64/canu/2.2/bin/../lib/site_perl/canu/OverlapBasedTrimming.pm line 140.
CRASH:  canu::OverlapBasedTrimming::splitReads("SP0407_Canu") called at /software/shared/apps/x86_64/canu/2.2/bin/canu line 1106
CRASH: 
CRASH: Last 50 lines of the relevant log file (trimming/3-overlapbasedtrimming/SP0407_Canu.2.splitReads.err):
CRASH:
CRASH: Processing from ID 1 to 3024626 out of 3024626 reads, using errorRate = 0.15
CRASH: splitReads: stores/sqStore.H:403: uint32 sqStore::sqStore_getReadLength(uint32, sqRead_which): Assertion `id > 0' failed.
CRASH: 
CRASH: Failed with 'Aborted'; backtrace (libbacktrace):
CRASH: 
CRASH: Failed with 'Segmentation fault'; backtrace (libbacktrace):
CRASH:

I have no idea what is the cause of this error. Could you help me resolve this? Many thanks!