The pipeline failed on the test_full profile option (segmentation fault, exit code 139)

[DarkoCucin]

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

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

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

[chriswyatt1]

See : nextflow-io/rnaseq-nf#7

I assume you are running from an M1 mac. There are a few potential fixes in the above link.