search

ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
Other
713 stars 131 forks source link

Error: spades-hammer, OS return value: 1 #1313

Open osvatic opened 3 weeks ago

osvatic commented 3 weeks ago

Description of bug

Spades-hammer is terminating because of a segmentation fault while kmer-counting and reports an "OS return value: 1".

Command line:

/lisc/scratch/jmf/internal/Analyses_Jay/JMF_2108_11/.snakemake/conda/0ae2b4a3475f1b8ec4109c90dec7e0d2_/bin/spades.py      -t      48      -m      1000    -k      21,31,41,51,61,71,81,91,101,111,121     --meta  --pe-12 1       /lisc/scratch/jmf/internal/Analyses_Jay/JMF_2108_11/data/interleave_DNA/JMF-2108-11-0010C.interleave.fastq.gz   -o      /lisc/scratch/jmf/internal/Analyses_Jay/JMF_2108_11/results/JMF-2108-11-0010C_spades

Details from spades.log: Analyses_Jay/JMF_2108_11/results/JMF-2108-11-0010C_spades/split_input/JMF-2108-11-0010C.interleave_1.fastq 0:01:18.914 329M / 897M INFO K-mer Counting (kmer_data.cpp : 324) Processed 1201470 reads 0:01:18.915 329M / 897M INFO K-mer Counting (kmer_data.cpp : 315) Processing /lisc/scratch/jmf/internal/Analyses_Jay/JMF_2108_11/results/JMF-2108-11-0010C_spades/split_input/JMF-2108-11-0010C.interleave_2.fastq The program was terminated by segmentation fault === Stack Trace === /lisc/scratch/jmf/internal/Analyses_Jay/JMF_210811/.snakemake/conda/0ae2b4a3475f1b8ec4109c90dec7e0d2/bin/spades-hammer(+0x1b3d7) [0x55bce55dd3d7] /lisc/scratch/jmf/internal/Analyses_Jay/JMF_210811/.snakemake/conda/0ae2b4a3475f1b8ec4109c90dec7e0d2/bin/spades-hammer(+0x1bf06) [0x55bce55ddf06] /lib64/libc.so.6(+0x3e6f0) [0x7fbbc903e6f0] /lisc/scratch/jmf/internal/Analyses_Jay/JMF_210811/.snakemake/conda/0ae2b4a3475f1b8ec4109c90dec7e0d2/bin/spades-hammer(+0x8e83f) [0x55bce565083f] /lisc/scratch/jmf/internal/Analyses_Jay/JMF_210811/.snakemake/conda/0ae2b4a3475f1b8ec4109c90dec7e0d2/bin/spades-hammer(+0x908f3) [0x55bce56528f3] /lisc/scratch/jmf/internal/Analyses_Jay/JMF_210811/.snakemake/conda/0ae2b4a3475f1b8ec4109c90dec7e0d2/bin/spades-hammer(+0x4a1f6) [0x55bce560c1f6] /lisc/scratch/jmf/internal/Analyses_Jay/JMF_210811/.snakemake/conda/0ae2b4a3475f1b8ec4109c90dec7e0d2/bin/spades-hammer(+0x4a3d6) [0x55bce560c3d6] /lisc/scratch/jmf/internal/Analyses_Jay/JMF_210811/.snakemake/conda/0ae2b4a3475f1b8ec4109c90dec7e0d2/bin/../lib/libgomp.so.1(+0x186d9) [0x7fbbc932f6d9] /lib64/libc.so.6(+0x89c12) [0x7fbbc9089c12] /lib64/libc.so.6(+0x10ecc0) [0x7fbbc910ecc0]

== Error == system call for: "['/lisc/scratch/jmf/internal/Analyses_Jay/JMF_210811/.snakemake/conda/0ae2b4a3475f1b8ec4109c90dec7e0d2/bin/spades-hammer', '/lisc/scratch/jmf/internal/Analyses_Jay/JMF_2108_11/results/JMF-2108-11-0010C_spades/corrected/configs/config.info']" finished abnormally, OS return value: 1 None

This seems to be specific to a certain dataset as I have no problems running SPAdes on others within this project.

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes 3.15.5

Operating System

Linux-5.14.0-362.24.1.0.1.el9_3.x86_64-x86_64-with-glibc2.34

Python Version

version: 3.12.3

Method of SPAdes installation

unkown

No errors reported in spades.log

asl commented 3 weeks ago

Does the problem reproduce with the latest SPAdes 4.0?

osvatic commented 3 weeks ago

Yes, this is reproducible in SPAdes 4.0. The OS return value is the same and it looks like it gets stuck at the same place.

params.txt spades.log