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.
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
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
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
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" doneOut 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