Spare memory for samtools issue

[bc2zb]

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

nextflow run nf-core/rnasplice \
-resume \
--input 'sample-input.csv' \
--contrasts 'contrasts.csv' \
-profile biowulf \
--gtf /data/capaldobj/Homo_sapiens.GRCh38.108.gtf \
--fasta /data/capaldobj/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa \
--outdir 'human-samples-grch38-rna-seq-splice-results' \
--suppa false

Relevant files

.nextflow.log

System information

No response

[jma1991]

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!

[paolo-kunderfranco]

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