search

ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
Other
763 stars 139 forks source link

Segmentation fault during Kmer counting for metaplasmidSPAdes: Only for a few samples #1368

Open Las02 opened 2 months ago

Las02 commented 2 months ago

Description of bug

When running metaplasmidSPAdes, the run terminates for a few of the runs (10 out of 49 samples) with a segmentation fault. They all terminate during the kmer counting step. 

  0:01:49.150     1M / 278M  INFO   K-mer Counting           (kmer_data.cpp             : 310)   Filtering singleton k-mers
  0:01:49.209   329M / 389M  INFO   K-mer Counting           (kmer_data.cpp             : 316)   Processing "/maps/projects/rasmussen/scratch/ptracker/ptracker/data/reads/circular_refs/Airways/simulation/2024.04.25_16.45.27_sample_7/reads/reads_noninterlaced/anonymous_reads_clean_1.fq.gz"
  0:15:29.216   329M / 419M  INFO   K-mer Counting           (kmer_data.cpp             : 325)   Processed 18498444 reads
  0:15:29.216   329M / 419M  INFO   K-mer Counting           (kmer_data.cpp             : 316)   Processing "/maps/projects/rasmussen/scratch/ptracker/ptracker/data/reads/circular_refs/Airways/simulation/2024.04.25_16.45.27_sample_7/reads/reads_noninterlaced/anonymous_reads_clean_2.fq.gz"
The program was terminated by segmentation fault
=== Stack Trace ===
/maps/projects/rasmussen/scratch/ptracker/run_mp_spades/bin/SPades-4/SPAdes-4.0.0-Linux/bin/spades-hammer() [0x41d5d9]
/maps/projects/rasmussen/scratch/ptracker/run_mp_spades/bin/SPades-4/SPAdes-4.0.0-Linux/bin/spades-hammer() [0x41dcef]
/lib64/libc.so.6(+0x4e5b0) [0x7ff5e059c5b0]
/maps/projects/rasmussen/scratch/ptracker/run_mp_spades/bin/SPades-4/SPAdes-4.0.0-Linux/bin/spades-hammer() [0x4998c0]
/maps/projects/rasmussen/scratch/ptracker/run_mp_spades/bin/SPades-4/SPAdes-4.0.0-Linux/bin/spades-hammer() [0x49b58d]
/maps/projects/rasmussen/scratch/ptracker/run_mp_spades/bin/SPades-4/SPAdes-4.0.0-Linux/bin/spades-hammer() [0x450d0a]
/maps/projects/rasmussen/scratch/ptracker/run_mp_spades/bin/SPades-4/SPAdes-4.0.0-Linux/bin/spades-hammer() [0x444576]
/lib64/libgomp.so.1(+0x1b4be) [0x7ff5e189a4be]
/lib64/libpthread.so.0(+0x81ca) [0x7ff5e16671ca]
/lib64/libc.so.6(clone+0x43) [0x7ff5e05878d3]

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes version: 4.0.0

Operating System

Red Hat Enterprise Linux 8.10 (Ootpa)

Python Version

python 3.9.0

Method of SPAdes installation

binaries

No errors reported in spades.log