Spare memory for samtools issue

bc2zb commented 4 months ago

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 commented 2 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!

paolo-kunderfranco commented 5 days ago

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

nf-core / rnasplice