When I tried to run nf-core/viralintegration pipeline on test_full profile option I encountered an issue. An issue is related to segmentation fault (exit code 139) in the process that I will list below.
I saw that exit code 139 is related to receiving SIGSEGV signal. And that error can be related to the access system memory that either doesn’t exist or that the process lacks permission to access. I run this task with RAM and CPUs requirements that are higher and the task failed with the same error.
When I run with test profile option the pipeline executed successfully.
Command used and terminal output
nextflow run main.nf -profile 'test_full,docker' --max_cpus 7 --max_memory '14.GB' --outdir test_full_profile
ERROR ~ Error executing process > 'NFCORE_VIRALINTEGRATION:VIRALINTEGRATION:STAR_ALIGN_HOST (sample1_T1)'
Caused by:
Process `NFCORE_VIRALINTEGRATION:VIRALINTEGRATION:STAR_ALIGN_HOST (sample1_T1)` terminated with an error exit status (139)
Command executed:
STAR \
--genomeDir star \
--readFilesIn sample1_R1.fastq.gz sample1_R2.fastq.gz \
--runThreadN 7 \
--outFileNamePrefix sample1_T1.host. \
\
--sjdbGTFfile genes.gtf \
--outSAMattrRGline ID:sample1_T1.host 'SM:sample1_T1.host' 'PL:illumina' \
--readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMunmapped Within --twopassMode Basic --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSplicedMateMapLminOverLmate 0 --alignSplicedMateMapLmin 30 --outReadsUnmapped Fastx
if [ -f sample1_T1.host.Unmapped.out.mate1 ]; then
mv sample1_T1.host.Unmapped.out.mate1 sample1_T1.host.unmapped_1.fastq
gzip sample1_T1.host.unmapped_1.fastq
fi
if [ -f sample1_T1.host.Unmapped.out.mate2 ]; then
mv sample1_T1.host.Unmapped.out.mate2 sample1_T1.host.unmapped_2.fastq
gzip sample1_T1.host.unmapped_2.fastq
fi
cat <<-END_VERSIONS > versions.yml
"NFCORE_VIRALINTEGRATION:VIRALINTEGRATION:STAR_ALIGN_HOST":
star: $(STAR --version | sed -e "s/STAR_//g")
END_VERSIONS
Command exit status:
139
Command output:
STAR --genomeDir star --readFilesIn sample1_R1.fastq.gz sample1_R2.fastq.gz --runThreadN 7 --outFileNamePrefix sample1_T1.host. --sjdbGTFfile genes.gtf --outSAMattrRGline ID:sample1_T1.host SM:sample1_T1.host PL:illumina --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMunmapped Within --twopassMode Basic --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSplicedMateMapLminOverLmate 0 --alignSplicedMateMapLmin 30 --outReadsUnmapped Fastx
STAR version: 2.7.9a compiled: 2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
Feb 26 17:03:44 ..... started STAR run
Feb 26 17:03:44 ..... loading genome
Feb 26 17:03:45 ..... processing annotations GTF
Feb 26 17:03:46 ..... inserting junctions into the genome indices
Feb 26 17:03:47 ..... started 1st pass mapping
Command error:
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
STAR --genomeDir star --readFilesIn sample1_R1.fastq.gz sample1_R2.fastq.gz --runThreadN 7 --outFileNamePrefix sample1_T1.host. --sjdbGTFfile genes.gtf --outSAMattrRGline ID:sample1_T1.host SM:sample1_T1.host PL:illumina --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMunmapped Within --twopassMode Basic --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSplicedMateMapLminOverLmate 0 --alignSplicedMateMapLmin 30 --outReadsUnmapped Fastx
STAR version: 2.7.9a compiled: 2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
Feb 26 17:03:44 ..... started STAR run
Feb 26 17:03:44 ..... loading genome
Feb 26 17:03:45 ..... processing annotations GTF
Feb 26 17:03:46 ..... inserting junctions into the genome indices
Feb 26 17:03:47 ..... started 1st pass mapping
qemu: uncaught target signal 11 (Segmentation fault) - core dumped
Description of the bug
When I tried to run nf-core/viralintegration pipeline on
test_full
profile option I encountered an issue. An issue is related to segmentation fault (exit code 139) in the process that I will list below.I saw that exit code 139 is related to receiving SIGSEGV signal. And that error can be related to the access system memory that either doesn’t exist or that the process lacks permission to access. I run this task with RAM and CPUs requirements that are higher and the task failed with the same error.
When I run with
test
profile option the pipeline executed successfully.Command used and terminal output
Relevant files
nextflow_viralintegration.log
System information
Nextflow version - 23.10.1 Executor - local Container engine - Docker OS - masOs Version of nf-core/hlatyping - 0.11.1