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Stack trace - The program was terminated by segmentation fault #1291

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emilyn16 opened this issue May 13, 2024 · 0 comments
Open
1 task done

Stack trace - The program was terminated by segmentation fault #1291

emilyn16 opened this issue May 13, 2024 · 0 comments

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@emilyn16
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Description of bug

I am using metaspades.py to assemble my sequences using this command:
for i in *.outfile1.fastq do metaspades.py -o ~/Projects/Moss2024/analysis/bacteria/fastq/metaspades/${i%%.outfile1.fastq}"" -1 ~/Projects/Moss2024/analysis/bacteria/fastq/$i -2 ~/Projects/Moss2024/analysis/bacteria/fastq/${i%%.outfile1.fastq}".outfile2.fastq" -t 32 echo "${i}: Has been completed" done
Out of all of my samples, only two gave me the error message stated in the title. I'm wondering what could be causing this error message if all of my other samples worked.

spades.log

Command line: /home/eneff/miniconda3/envs/spades/bin/metaspades.py -o /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/metaspades/J_H2 -1 /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/J_H2.outfile1.fastq -2 /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/J_H2.outfile2.fastq -t 32

System information:
SPAdes version: 3.15.5
Python version: 3.11.0
OS: Linux-5.4.0-176-generic-x86_64-with-glibc2.31

Output dir: /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/metaspades/J_H2
Mode: read error correction and assembling
Debug mode is turned OFF

Dataset parameters:
Metagenomic mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/J_H2.outfile1.fastq']
right reads: ['/home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/J_H2.outfile2.fastq']
interlaced reads: not specified
single reads: not specified
merged reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed
Assembly parameters:
k: [21, 33, 55]
Repeat resolution is enabled
Mismatch careful mode is turned OFF
MismatchCorrector will be SKIPPED
Coverage cutoff is turned OFF
Other parameters:
Dir for temp files: /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/metaspades/J_H2/tmp
Threads: 32
Memory limit (in Gb): 250

======= SPAdes pipeline started. Log can be found here: /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/metaspades/J_H2/spades.log

/home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/J_H2.outfile1.fastq: max reads length: 150
/home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/J_H2.outfile2.fastq: max reads length: 150

Reads length: 150

===== Before start started.

===== Read error correction started.

===== Read error correction started.

== Running: /home/eneff/miniconda3/envs/spades/bin/spades-hammer /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/metaspades/J_H2/corrected/configs/config.info

0:00:00.000 1M / 24M INFO General (main.cpp : 75) Starting BayesHammer, built from N/A, git revision N/A
0:00:00.024 1M / 24M INFO General (main.cpp : 76) Loading config from /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/metaspades/J_H2/corrected/configs/config.info
0:00:00.038 1M / 24M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 32
0:00:00.044 1M / 24M INFO General (memory_limit.cpp : 54) Memory limit set to 250 Gb
0:00:00.044 1M / 24M INFO General (main.cpp : 86) Trying to determine PHRED offset
0:00:00.053 1M / 24M INFO General (main.cpp : 92) Determined value is 33
0:00:00.053 1M / 24M INFO General (hammer_tools.cpp : 38) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
0:00:00.053 1M / 24M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes
=== ITERATION 0 begins ===
0:00:00.053 1M / 24M INFO K-mer Counting (kmer_data.cpp : 283) Estimating k-mer count
0:00:00.197 513M / 519M INFO K-mer Counting (kmer_data.cpp : 288) Processing /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/J_H2.outfile1.fastq
0:00:02.454 513M / 519M INFO K-mer Counting (kmer_data.cpp : 297) Processed 921697 reads
0:00:02.454 513M / 519M INFO K-mer Counting (kmer_data.cpp : 288) Processing /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/J_H2.outfile2.fastq
0:00:04.765 513M / 519M INFO K-mer Counting (kmer_data.cpp : 297) Processed 1843394 reads
0:00:04.766 513M / 519M INFO K-mer Counting (kmer_data.cpp : 302) Total 1843394 reads processed
0:00:05.276 513M / 519M INFO K-mer Counting (kmer_data.cpp : 305) Estimated 65924449 distinct kmers
0:00:05.277 1M / 519M INFO K-mer Counting (kmer_data.cpp : 309) Filtering singleton k-mers
0:00:05.289 165M / 519M INFO K-mer Counting (kmer_data.cpp : 315) Processing /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/J_H2.outfile1.fastq
0:00:30.397 165M / 519M INFO K-mer Counting (kmer_data.cpp : 324) Processed 921697 reads
0:00:30.397 165M / 519M INFO K-mer Counting (kmer_data.cpp : 315) Processing /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/J_H2.outfile2.fastq
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation faultThe program was terminated by segmentation fault
=== Stack Trace ===
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
The program was terminated by segmentation fault
=== Stack Trace ===
/home/eneff/miniconda3/envs/spades/bin/spades-hammer(+0x1ddbc) [0x556827bb2dbc]
/home/eneff/miniconda3/envs/spades/bin/spades-hammer(+0x1e2bc) [0x556827bb32bc]
/lib/x86_64-linux-gnu/libc.so.6(+0x43090) [0x7f2b8a609090]
/home/eneff/miniconda3/envs/spades/bin/spades-hammer(+0x99bbb) [0x556827c2ebbb]
/home/eneff/miniconda3/envs/spades/bin/spades-hammer(+0x51f78) [0x556827be6f78]
/home/eneff/miniconda3/envs/spades/bin/spades-hammer(+0x5217e) [0x556827be717e]
/home/eneff/miniconda3/envs/spades/bin/../lib/libgomp.so.1(+0x177f0) [0x7f2b8a80d7f0]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x8609) [0x7f2b8a7c0609]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x43) [0x7f2b8a6e5353]
/home/eneff/miniconda3/envs/spades/bin/spades-hammer(+0x1ddbc) [0x556827bb2dbc]
/home/eneff/miniconda3/envs/spades/bin/spades-hammer(+0x1e2bc) [0x556827bb32bc]
/lib/x86_64-linux-gnu/libc.so.6(+0x43090) [0x7f2b8a609090]
/home/eneff/miniconda3/envs/spades/bin/spades-hammer(+0x99bbb) [0x556827c2ebbb]
/home/eneff/miniconda3/envs/spades/bin/spades-hammer(+0x5203b) [0x556827be703b]
/home/eneff/miniconda3/envs/spades/bin/spades-hammer(+0x5217e) [0x556827be717e]
/home/eneff/miniconda3/envs/spades/bin/../lib/libgomp.so.1(+0x177f0) [0x7f2b8a80d7f0]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x8609) [0x7f2b8a7c0609]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x43) [0x7f2b8a6e5353]

== Error == system call for: "['/home/eneff/miniconda3/envs/spades/bin/spades-hammer', '/home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/metaspades/J_H2/corrected/configs/config.info']" finished abnormally, OS return value: 1
None

In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.

SPAdes log can be found here: /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/metaspades/J_H2/spades.log

Thank you for using SPAdes!

params.txt

Command line: /home/eneff/miniconda3/envs/spades/bin/metaspades.py -o /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/metaspades/J_H2 -1 /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/J_H2.outfile1.fastq -2 /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/J_H2.outfile2.fastq -t 32

System information:
SPAdes version: 3.15.5
Python version: 3.11.0
OS: Linux-5.4.0-176-generic-x86_64-with-glibc2.31

Output dir: /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/metaspades/J_H2
Mode: read error correction and assembling
Debug mode is turned OFF

Dataset parameters:
Metagenomic mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/J_H2.outfile1.fastq']
right reads: ['/home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/J_H2.outfile2.fastq']
interlaced reads: not specified
single reads: not specified
merged reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed
Assembly parameters:
k: [21, 33, 55]
Repeat resolution is enabled
Mismatch careful mode is turned OFF
MismatchCorrector will be SKIPPED
Coverage cutoff is turned OFF
Other parameters:
Dir for temp files: /home/eneff/Projects/PhJ2022/analysis/bacteria/fastq/new_fastq_files/metaspades/J_H2/tmp
Threads: 32
Memory limit (in Gb): 250

SPAdes version

SPAdes v3.15.5

Operating System

linux

Python Version

Python v3.11.0

Method of SPAdes installation

conda

No errors reported in spades.log

  • Yes
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@emilyn16