Error in STAR_ALIGN: Segmentation fault with STAR v2.7.9a

Open jonbra opened this issue 1 year ago • 0 comments

Description of the bug

Hi, I'm getting a segmentation fault with STAR_ALIGN v2.7.9a. I also tried to increase the allocated RAM for the process to 200GB (and 16 cpus), but still get this message:

ERROR ~ Error executing process > 'NFCORE_VIRALINTEGRATION:VIRALINTEGRATION:STAR_ALIGN_HOST (CONTROL_REP1_T1)'

Caused by:
  Process `NFCORE_VIRALINTEGRATION:VIRALINTEGRATION:STAR_ALIGN_HOST (CONTROL_REP1_T1)` terminated with an error exit status (139)


Command executed:

  STAR \
      --genomeDir star \
      --readFilesIn C4_S19_L001_R1_001.fastq.gz C4_S19_L001_R2_001.fastq.gz  \
      --runThreadN 16 \
      --outFileNamePrefix CONTROL_REP1_T1.host. \
       \
      --sjdbGTFfile genes.gtf \
      --outSAMattrRGline ID:CONTROL_REP1_T1.host 'SM:CONTROL_REP1_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 CONTROL_REP1_T1.host.Unmapped.out.mate1 ]; then
      mv CONTROL_REP1_T1.host.Unmapped.out.mate1 CONTROL_REP1_T1.host.unmapped_1.fastq
      gzip CONTROL_REP1_T1.host.unmapped_1.fastq
  fi
  if [ -f CONTROL_REP1_T1.host.Unmapped.out.mate2 ]; then
      mv CONTROL_REP1_T1.host.Unmapped.out.mate2 CONTROL_REP1_T1.host.unmapped_2.fastq
      gzip CONTROL_REP1_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 C4_S19_L001_R1_001.fastq.gz C4_S19_L001_R2_001.fastq.gz --runThreadN 16 --outFileNamePrefix CONTROL_REP1_T1.host. --sjdbGTFfile genes.gtf --outSAMattrRGline ID:CONTROL_REP1_T1.host SM:CONTROL_REP1_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
  Nov 07 13:13:53 ..... started STAR run
  Nov 07 13:13:53 ..... loading genome
  Nov 07 13:14:11 ..... processing annotations GTF
  Nov 07 13:14:21 ..... inserting junctions into the genome indices
  Nov 07 13:15:20 ..... started 1st pass mapping

Command error:
        STAR --genomeDir star --readFilesIn C4_S19_L001_R1_001.fastq.gz C4_S19_L001_R2_001.fastq.gz --runThreadN 16 --outFileNamePrefix CONTROL_REP1_T1.host. --sjdbGTFfile genes.gtf --outSAMattrRGline ID:CONTROL_REP1_T1.host SM:CONTROL_REP1_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
  Nov 07 13:13:53 ..... started STAR run
  Nov 07 13:13:53 ..... loading genome
  Nov 07 13:14:11 ..... processing annotations GTF
  Nov 07 13:14:21 ..... inserting junctions into the genome indices
  Nov 07 13:15:20 ..... started 1st pass mapping
  .command.sh: line 10:    33 Segmentation fault      (core dumped) STAR --genomeDir star --readFilesIn C4_S19_L001_R1_001.fastq.gz C4_S19_L001_R2_001.fastq.gz --runThreadN 16 --outFileNamePrefix CONTROL_REP1_T1.host. --sjdbGTFfile genes.gtf --outSAMattrRGline ID:CONTROL_REP1_T1.host 'SM:CONTROL_REP1_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

Work dir:
  /mnt/tempdata/work/fc/60ae601f5a32187a05983790ab9a46

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details

I created a Wave container of STAR v 2.7.11b and put that in the process together with 16 cpu and 200 GB RAM and then STAR seem to finish but I got this error:

ERROR ~ Error executing process > 'NFCORE_VIRALINTEGRATION:VIRALINTEGRATION:STAR_ALIGN_HOST (CONTROL_REP1_T1)'

Caused by:
  /mnt/tempdata/work/f6/ea323a77925b4cbfdbb1d0d4404f04/CONTROL_REP1_T1.host._STARgenome



 -- Check '.nextflow.log' file for details

Here's the output of .command.out:

cat /mnt/tempdata/work/f6/ea323a77925b4cbfdbb1d0d4404f04/.command.out
        /opt/conda/bin/STAR-avx2 --genomeDir star --readFilesIn C4_S19_L001_R1_001.fastq.gz C4_S19_L001_R2_001.fastq.gz --runThreadN 12 --outFileNamePrefix CONTROL_REP1_T1.host. --sjdbGTFfile genes.gtf --outSAMattrRGline ID:CONTROL_REP1_T1.host SM:CONTROL_REP1_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: 2.7.11b   compiled: 2024-07-03T14:39:20+0000 :/opt/conda/conda-bld/star_1720017372352/work/source
Nov 07 13:45:00 ..... started STAR run
Nov 07 13:45:00 ..... loading genome
Nov 07 13:45:18 ..... processing annotations GTF
Nov 07 13:45:27 ..... inserting junctions into the genome indices
Nov 07 13:46:18 ..... started 1st pass mapping
Nov 07 13:50:01 ..... finished 1st pass mapping
Nov 07 13:50:01 ..... inserting junctions into the genome indices
Nov 07 13:50:54 ..... started mapping
Nov 07 13:54:43 ..... finished mapping
Nov 07 13:54:46 ..... started sorting BAM
Nov 07 13:55:03 ..... finished successfully

Command used and terminal output

Relevant files

No response

System information

No response

Nov 13 '24 19:11 jonbra