Error executing process > 'NFCORE_SAREK:SAREK:CRAM_HLATYPING_ALL:CRAM_FILTER_HLA (1029_BBCQ-N1-BDNA-1_2375WFLT3_s21)'

Caused by:
  Process `NFCORE_SAREK:SAREK:CRAM_HLATYPING_ALL:CRAM_FILTER_HLA (1029_BBCQ-N1-BDNA-1_2375WFLT3_s21)` terminated with an error exit status (2)


Command executed:

  # Detect input type and set up appropriate pipeline
  # CRAM requires samtools conversion first; BAM can be read directly by sambamba
  if [[ "1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.recalibrated.bam" == *.cram ]]; then
      INPUT_CMD="samtools view -h -b --reference Homo_sapiens_assembly38.fasta 1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.recalibrated.bam"
  else
      INPUT_CMD="cat 1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.recalibrated.bam"
  fi
  
  MAX_READS=10000
  
  # Filter reads and sort by name
  eval $INPUT_CMD | \
  sambamba view \
      -f bam -h \
      -t 18 \
      -F "unmapped or mate_is_unmapped or (ref_name == 'chr6' and position > 29844528 and position < 33100696) or ref_name =~ /^HLA|chr6.*alt/" \
      /dev/stdin | \
  sambamba sort \
      -n \
      -t 18 \
      -o filtered.bam \
      /dev/stdin
  
  # Count read pairs and optionally subsample
  TOTAL_READS=$(samtools view -c filtered.bam)
  TOTAL_PAIRS=$((TOTAL_READS / 2))
  echo "HLA filter: $TOTAL_PAIRS read pairs extracted"
  
  if [[ $MAX_READS -gt 0 && $TOTAL_PAIRS -gt $MAX_READS ]]; then
      # Calculate subsample fraction (add 5% buffer to account for sampling variance)
      FRAC=$(awk "BEGIN {printf "%.4f", ($MAX_READS * 1.05) / $TOTAL_PAIRS}")
      echo "Subsampling to ~$MAX_READS pairs (fraction: $FRAC)"
      samtools view -s 42.$FRAC -b filtered.bam | \
      samtools fastq \
          -@ 18 \
          -1 1029_BBCQ-N1-BDNA-1_2375WFLT3_s21_R1.fq.gz \
          -2 1029_BBCQ-N1-BDNA-1_2375WFLT3_s21_R2.fq.gz \
          -0 /dev/null \
          -s /dev/null \
          -
  else
      # No subsampling needed
      samtools fastq \
          -@ 18 \
          -1 1029_BBCQ-N1-BDNA-1_2375WFLT3_s21_R1.fq.gz \
          -2 1029_BBCQ-N1-BDNA-1_2375WFLT3_s21_R2.fq.gz \
          -0 /dev/null \
          -s /dev/null \
          filtered.bam
  fi
  
  rm -f filtered.bam
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:CRAM_HLATYPING_ALL:CRAM_FILTER_HLA":
      sambamba: $(sambamba --version 2>&1 | head -1 | awk '{print $2}')
      samtools: $(samtools --version | head -1 | awk '{print $2}')
  END_VERSIONS

Command exit status:
  2

Command output:
  HLA filter: 1278131 read pairs extracted

Command error:
  
  sambamba 1.0.1
   by Artem Tarasov and Pjotr Prins (C) 2012-2023
      LDC 1.39.0 / DMD v2.109.1 / LLVM17.0.6 / bootstrap LDC - the LLVM D compiler (1.39.0)
  
  
  sambamba 1.0.1
   by Artem Tarasov and Pjotr Prins (C) 2012-2023
      LDC 1.39.0 / DMD v2.109.1 / LLVM17.0.6 / bootstrap LDC - the LLVM D compiler (1.39.0)
  
  awk: line 1: syntax error at or near %

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/03b184e6f0e77b703ed3815225de95

Container:
  community.wave.seqera.io/library/sambamba_samtools:0966924e22545fbe

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line