Error executing process > 'MUTECT2_TUMOR_ONLY (LS0882)'

Caused by:
  Process `MUTECT2_TUMOR_ONLY (LS0882)` terminated with an error exit status (1)


Command executed:

  set -euo pipefail
  
  gatk --java-options '-Xmx14g' Mutect2 \
      -R 'hg38.fa' \
      -I 'LS0882_tumor.bam' \
      --tumor-sample 'LS0882' \
      -L 'TST500C_manifest.bed' \
      -O 'LS0882.mutect2.raw.vcf.gz' \
      --native-pair-hmm-threads 4 \
      --max-mnp-distance 0 \
      --germline-resource 'af-only-gnomad.hg38.vcf.gz'
  
  gatk --java-options '-Xmx14g' FilterMutectCalls \
      -R 'hg38.fa' \
      -V 'LS0882.mutect2.raw.vcf.gz' \
      --stats 'LS0882.mutect2.raw.vcf.gz.stats' \
      -O 'LS0882.mutect2.filtered.vcf.gz'
  
  gatk --java-options '-Xmx14g' SelectVariants \
      -R 'hg38.fa' \
      -V 'LS0882.mutect2.filtered.vcf.gz' \
      --exclude-filtered true \
      -O 'LS0882.mutect2.pass.vcf.gz'

Command exit status:
  1

Command output:
  (empty)

Work dir:
  s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/77/8ef1aa1e5026c17ec3d44aaad278c7

Container:
  broadinstitute/gatk:4.5.0.0

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