Segmentation fault in TRINITY process when running from singularity image
bug
### Description of the bug
A segmentation fault error occurred in the `TRINITY` process during the `jellyfish` stage when it was run from the Singularity image.
It seems to be similar to [this reported issue](https://github.com/trinityrnaseq/trinityrnaseq/issues/927) and the authors recommend using their container (see their [response at the bottom of the thread](https://github.com/trinityrnaseq/trinityrnaseq/issues/927#issuecomment-2444014335)).
This should be corrected at the Trinity nf-core module.
### Command used and terminal output
```
$ nextflow run nf-core/denovotranscript -r 1.0.0 --input Mnova_samplesheet.csv --transrate_reference /home/ibar/adna/sandbox/OTE14085/GIU3625_Humpback_whale.transcript.fasta --outdir assembly_results --assemblers trinity -with-tower -profile apptainer,bunya -c /home/ibar/.nextflow/bunya.config
The exit status of the task that caused the workflow execution to fail was: 2
Error executing process > 'NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRINITY (pooled_reads)'
Caused by:
Process `NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRINITY (pooled_reads)` terminated with an error exit status (2)
Command executed:
# Note that Trinity needs the word 'trinity' in the outdir
Trinity \
--seqType fq \
--max_memory 160G \
--left input1/pooled_reads_1.merged.fastq.gz --right input2/pooled_reads_2.merged.fastq.gz \
--output pooled_reads_trinity \
--CPU 12 \
\
> >(tee pooled_reads.log)
gzip \
-cf \
pooled_reads_trinity.Trinity.fasta \
> pooled_reads.fa.gz
rm pooled_reads_trinity.Trinity.fasta
cat <<-END_VERSIONS > versions.yml
"NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRINITY":
trinity: $(Trinity --version | grep 'Trinity version:' | sed 's/Trinity version: Trinity-//')
END_VERSIONS
Command exit status:
2
Command output:
Sequence: CGCCCCGGGCCCCTCis smaller than 25 base pairs, skipping
Sequence: GGGGTGAACTCGGCGGGis smaller than 25 base pairs, skipping
Sequence: CTCCGTTTCCGACCTGGGCis smaller than 25 base pairs, skipping
Sequence: AGGACGCGGGGCCGGGCis smaller than 25 base pairs, skipping
Sequence: ACTCCCCTCGCCGGGGis smaller than 25 base pairs, skipping
Sequence: TCCGGGGGCGGGGAGCCGGGCis smaller than 25 base pairs, skipping
Sequence: CCGGGGGCGGGGAGCGGGGCGTGCis smaller than 25 base pairs, skipping
Sequence: TCCGGGGGCGGGGAGCCGGGCis smaller than 25 base pairs, skipping
Sequence: CGCCCCGGGCCCCTCis smaller than 25 base pairs, skipping
Sequence: TCCGGGGGCGGGGAGCCGGGCis smaller than 25 base pairs, skipping
Sequence: CCCTCCGTCGCCGGGis smaller than 25 base pairs, skipping
Sequence: GGGCGGGGAGCGGGCCGGGCis smaller than 25 base pairs, skipping
Sequence: GAAGAGGGGAGGGCGGGCCGGGCis smaller than 25 base pairs, skipping
Sequence: CCGGGATTCGGCGAGTGCTGCTGis smaller than 25 base pairs, skipping
Sequence: TCCCGCCGGCGGGAGCCCis smaller than 25 base pairs, skipping
Sequence: CGGGCAGGAGGATCGCTTGAGCCis smaller than 25 base pairs, skipping
Sequence: GTAACACTCGGGGCGis smaller than 25 base pairs, skipping
Sequence: CGCCCCGGGCCCCTCGis smaller than 25 base pairs, skipping
Sequence: TCCGGGGGCGGGGAGCGGGGis smaller than 25 base pairs, skipping
Sequence: AGGACGCGGGGCCGGGCGis smaller than 25 base pairs, skipping
Sequence: AGGACGCGGGGCCGGGCGis smaller than 25 base pairs, skipping
Sequence: CGCCCCGGGCCCCTCGis smaller than 25 base pairs, skipping
Sequence: TCCGGGGGCGGGGAGCCGGGCGis smaller than 25 base pairs, skipping
Sequence: TCCGGGGGCCGGGCGis smaller than 25 base pairs, skipping
STATS_GENERATION_TIME: 8147 seconds.
CMD finished (9881 seconds)
STATS_GENERATION_TIME: 9028 seconds.
CMD finished (11528 seconds)
CMD: touch left.fa.K25.stats.ok
CMD finished (0 seconds)
CMD: touch right.fa.K25.stats.ok
CMD finished (0 seconds)
-sorting each stats file by read name.
CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> left.fa.K25.stats.sort
CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> right.fa.K25.stats.sort
bash: line 1: 140302 Broken pipe tail -n +2 left.fa.K25.stats
140303 Segmentation fault (core dumped) | /usr/bin/sort -k1,1 -T . -S 80G >> left.fa.K25.stats.sort
Thread 5 terminated abnormally: Error, cmd: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> left.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
Error, thread exited with error Error, cmd: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> left.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
bash: line 1: 140304 Broken pipe tail -n +2 right.fa.K25.stats
140305 Segmentation fault (core dumped) | /usr/bin/sort -k1,1 -T . -S 80G >> right.fa.K25.stats.sort
Thread 6 terminated abnormally: Error, cmd: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> right.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
Error, thread exited with error Error, cmd: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> right.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
Error, 2 threads errored out at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 1011.
Error, cmd: /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl --seqType fq --JM 160G --max_cov 200 --min_cov 1 --CPU 12 --output pooled_reads_trinity/insilico_read_normalization --max_CV 10000 --left input1/pooled_reads_1.merged.fastq.gz --right input2/pooled_reads_2.merged.fastq.gz --pairs_together --PARALLEL_STATS died with ret 7424 at /usr/local/bin/Trinity line 2919.
main::process_cmd("/usr/local/opt/trinity-2.15.1/util/insilico_read_normalizatio"...) called at /usr/local/bin/Trinity line 3472
main::normalize("/scratch/project_mnt/S0016/sandbox/OTE14085/Mnova_denovotrans"..., 200, ARRAY(0x55940f599a48), ARRAY(0x55940f5fa830)) called at /usr/local/bin/Trinity line 3412
main::run_normalization(200, ARRAY(0x55940f599a48), ARRAY(0x55940f5fa830)) called at /usr/local/bin/Trinity line 1450
Command wrapper:
Sequence: CGCCCCGGGCCCCTCis smaller than 25 base pairs, skipping
Sequence: GGGGTGAACTCGGCGGGis smaller than 25 base pairs, skipping
Sequence: CTCCGTTTCCGACCTGGGCis smaller than 25 base pairs, skipping
Sequence: AGGACGCGGGGCCGGGCis smaller than 25 base pairs, skipping
Sequence: ACTCCCCTCGCCGGGGis smaller than 25 base pairs, skipping
Sequence: TCCGGGGGCGGGGAGCCGGGCis smaller than 25 base pairs, skipping
Sequence: CCGGGGGCGGGGAGCGGGGCGTGCis smaller than 25 base pairs, skipping
Sequence: TCCGGGGGCGGGGAGCCGGGCis smaller than 25 base pairs, skipping
Sequence: CGCCCCGGGCCCCTCis smaller than 25 base pairs, skipping
Sequence: TCCGGGGGCGGGGAGCCGGGCis smaller than 25 base pairs, skipping
Sequence: CCCTCCGTCGCCGGGis smaller than 25 base pairs, skipping
Sequence: GGGCGGGGAGCGGGCCGGGCis smaller than 25 base pairs, skipping
Sequence: GAAGAGGGGAGGGCGGGCCGGGCis smaller than 25 base pairs, skipping
Sequence: CCGGGATTCGGCGAGTGCTGCTGis smaller than 25 base pairs, skipping
Sequence: TCCCGCCGGCGGGAGCCCis smaller than 25 base pairs, skipping
Sequence: CGGGCAGGAGGATCGCTTGAGCCis smaller than 25 base pairs, skipping
Sequence: GTAACACTCGGGGCGis smaller than 25 base pairs, skipping
Sequence: CGCCCCGGGCCCCTCGis smaller than 25 base pairs, skipping
Sequence: TCCGGGGGCGGGGAGCGGGGis smaller than 25 base pairs, skipping
Sequence: AGGACGCGGGGCCGGGCGis smaller than 25 base pairs, skipping
Sequence: AGGACGCGGGGCCGGGCGis smaller than 25 base pairs, skipping
Sequence: CGCCCCGGGCCCCTCGis smaller than 25 base pairs, skipping
Sequence: TCCGGGGGCGGGGAGCCGGGCGis smaller than 25 base pairs, skipping
Sequence: TCCGGGGGCCGGGCGis smaller than 25 base pairs, skipping
STATS_GENERATION_TIME: 8147 seconds.
CMD finished (9881 seconds)
STATS_GENERATION_TIME: 9028 seconds.
CMD finished (11528 seconds)
CMD: touch left.fa.K25.stats.ok
CMD finished (0 seconds)
CMD: touch right.fa.K25.stats.ok
CMD finished (0 seconds)
-sorting each stats file by read name.
CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> left.fa.K25.stats.sort
CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> right.fa.K25.stats.sort
bash: line 1: 140302 Broken pipe tail -n +2 left.fa.K25.stats
140303 Segmentation fault (core dumped) | /usr/bin/sort -k1,1 -T . -S 80G >> left.fa.K25.stats.sort
Thread 5 terminated abnormally: Error, cmd: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> left.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
Error, thread exited with error Error, cmd: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> left.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
bash: line 1: 140304 Broken pipe tail -n +2 right.fa.K25.stats
140305 Segmentation fault (core dumped) | /usr/bin/sort -k1,1 -T . -S 80G >> right.fa.K25.stats.sort
Thread 6 terminated abnormally: Error, cmd: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> right.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
Error, thread exited with error Error, cmd: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort -k1,1 -T . -S 80G >> right.fa.K25.stats.sort died with ret 35584 at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 807.
Error, 2 threads errored out at /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 1011.
Error, cmd: /usr/local/opt/trinity-2.15.1/util/insilico_read_normalization.pl --seqType fq --JM 160G --max_cov 200 --min_cov 1 --CPU 12 --output pooled_reads_trinity/insilico_read_normalization --max_CV 10000 --left input1/pooled_reads_1.merged.fastq.gz --right input2/pooled_reads_2.merged.fastq.gz --pairs_together --PARALLEL_STATS died with ret 7424 at /usr/local/bin/Trinity line 2919.
main::process_cmd("/usr/local/opt/trinity-2.15.1/util/insilico_read_normalizatio"...) called at /usr/local/bin/Trinity line 3472
main::normalize("/scratch/project_mnt/S0016/sandbox/OTE14085/Mnova_denovotrans"..., 200, ARRAY(0x55940f599a48), ARRAY(0x55940f5fa830)) called at /usr/local/bin/Trinity line 3412
main::run_normalization(200, ARRAY(0x55940f599a48), ARRAY(0x55940f5fa830)) called at /usr/local/bin/Trinity line 1450
Work dir:
/scratch/project_mnt/S0016/sandbox/OTE14085/Mnova_denovotranscript_assembly/work/fc/c26cbe596b01b63a68ee82ae92682d
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
```
### Relevant files
_No response_
### System information
- Nextflow version (eg. 24.04.4)
- Hardware: HPC
- Executor: slurm
- Container engine: Apptainer
- OS: Rocky Linux release 8.10 (Green Obsidian)
- Version of nf-core/denovotranscript: 1.0.0
关闭于 2024-11-29 3 条评论