Open bc2zb opened 4 months ago
Hi Brian,
Sorry for the delayed response! I just merged a pull request into the dev branch that updates the bam_stats_samtools subworkflow, along with all the samtools modules. When you have a moment, could you give it a try and see if it resolves your memory issue?
Thanks!
Dear All, I am facing the same error with samtools sort,
Command:
nextflow run nf-core/rnasplice --input $wd/samplesheet.csv --contrasts $wd/contrast.csv --outdir splicing_results --genome GRCm38 --aligner star_salmon --dexseq_exon true --edger_exon false --rmats false --dexseq_dtu true --dtu_txi scaledTPM --suppa false --suppa_per_local_event false --suppa_per_isoform false --save_reference false --sashimi_plot false -config $wd/new.config -profile HPC -r dev -resume
error:
`ERROR ~ Error executing process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (adult_ko_4)
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (adult_ko_4)` terminated with an error exit status (137)
Command executed:
samtools sort \
\
-@ 12 \
-m 6144M \
-o adult_ko_4_sorted.bam \
-T adult_ko_4_sorted \
adult_ko_4.Aligned.out.bam
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT":
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS
Command exit status:
137
Command output:
(empty)
Command error:
.command.sh: line 8: 44 Killed samtools sort -@ 12 -m 6144M -o adult_ko_4_sorted.bam -T adult_ko_4_sorted adult_ko_4.Aligned.out.bam
/var/lib/slurmd/job764301/slurm_script: line 334: 33010 Killed env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} SINGULARITYENV_NXF_DEBUG="${NXF_DEBUG:=0}" singularity exec --no-home --pid -B /home/pkf /home/pkf/pkunderfranco/singularity/quay.io-biocontainers-samtools-1.17--h00cdaf9_0.img /bin/bash -c "cd $NXF_TASK_WORKDIR; eval $(nxf_container_env); /bin/bash .command.run nxf_trace"
more .command.log
/home/pkf/gendata2/bioinformatica/progetti/Greco/P125/qki/nfcore/work/5f/8b36bdc193d59166e3a01bc5fc8cfc/.command.sh: line 8: 44 Killed sam
tools sort -@ 12 -m 6144M -o adult_ko_5_sorted.bam -T adult_ko_5_sorted adult_ko_5.Aligned.out.bam
/var/lib/slurmd/job764356/slurm_script: line 334: 13548 Killed env - PATH="$PATH" ${TMP:+SINGULARITYENV_TMP="$TMP"} ${TMPDIR:+SINGULARITYENV_
TMPDIR="$TMPDIR"} ${NXF_TASK_WORKDIR:+SINGULARITYENV_NXF_TASK_WORKDIR="$NXF_TASK_WORKDIR"} SINGULARITYENV_NXF_DEBUG="${NXF_DEBUG:=0}" singularity exec --no-ho
me --pid -B /home/pkf /home/pkf/pkunderfranco/singularity/quay.io-biocontainers-samtools-1.17--h00cdaf9_0.img /bin/bash -c "cd $NXF_TASK_WORKDIR; eval $(nxf_c
ontainer_env); /bin/bash /home/pkf/gendata2/bioinformatica/progetti/Greco/P125/qki/nfcore/work/5f/8b36bdc193d59166e3a01bc5fc8cfc/.command.run nxf_trace"
slurmstepd-node6: error: Detected 1 oom-kill event(s) in step 764356.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory han
dler.
Could you please assist me? Many Thanks Paolo
Description of the bug
Experiencing 137 on samtools sort, after talking with slack community and seqeria, seems to be related to this
Command used and terminal output
Relevant files
.nextflow.log
System information
No response