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Error: spades-hammer, OS return value: 1 #1313
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Does the problem reproduce with the latest SPAdes 4.0? |
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. |
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Description of bug
Spades-hammer is terminating because of a segmentation fault while kmer-counting and reports an "OS return value: 1".
Command line:
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_2108_11/.snakemake/conda/0ae2b4a3475f1b8ec4109c90dec7e0d2_/bin/spades-hammer(+0x1b3d7) [0x55bce55dd3d7]
/lisc/scratch/jmf/internal/Analyses_Jay/JMF_2108_11/.snakemake/conda/0ae2b4a3475f1b8ec4109c90dec7e0d2_/bin/spades-hammer(+0x1bf06) [0x55bce55ddf06]
/lib64/libc.so.6(+0x3e6f0) [0x7fbbc903e6f0]
/lisc/scratch/jmf/internal/Analyses_Jay/JMF_2108_11/.snakemake/conda/0ae2b4a3475f1b8ec4109c90dec7e0d2_/bin/spades-hammer(+0x8e83f) [0x55bce565083f]
/lisc/scratch/jmf/internal/Analyses_Jay/JMF_2108_11/.snakemake/conda/0ae2b4a3475f1b8ec4109c90dec7e0d2_/bin/spades-hammer(+0x908f3) [0x55bce56528f3]
/lisc/scratch/jmf/internal/Analyses_Jay/JMF_2108_11/.snakemake/conda/0ae2b4a3475f1b8ec4109c90dec7e0d2_/bin/spades-hammer(+0x4a1f6) [0x55bce560c1f6]
/lisc/scratch/jmf/internal/Analyses_Jay/JMF_2108_11/.snakemake/conda/0ae2b4a3475f1b8ec4109c90dec7e0d2_/bin/spades-hammer(+0x4a3d6) [0x55bce560c3d6]
/lisc/scratch/jmf/internal/Analyses_Jay/JMF_2108_11/.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_2108_11/.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
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