Error executing process > 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP (NA12878_c_0002_gDNA_0005_B23KYWJLT4_1;SNP_GRCh38_hg38_wChr)'

Caused by:
  Process `NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP (NA12878_c_0002_gDNA_0005_B23KYWJLT4_1;SNP_GRCh38_hg38_wChr)` terminated with an error exit status (1)


Command executed:

  echo "NA12878_c_0002_gDNA_0005_B23KYWJLT4_1" > sample_name.list
  
  bcftools \
      mpileup \
      --fasta-ref Homo_sapiens_assembly38.fasta \
       \
      NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.bam \
      -T SNP_GRCh38_hg38_wChr.bed \
       \
      | bcftools call --output-type v --no-version --ploidy 1 -c \
      | bcftools reheader --samples sample_name.list \
      | bcftools view --output-file NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.ngscheckmate.vcf.gz --output-type z --no-version
  
  
  
  tabix -p vcf -f NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.ngscheckmate.vcf.gz
  
  bcftools stats NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.ngscheckmate.vcf.gz > NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.ngscheckmate.bcftools_stats.txt
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP":
      bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/22249524483517c21f096c942aafba

Container:
  292967571998.dkr.ecr.us-west-2.amazonaws.com/quay/biocontainers/bcftools:1.20--h8b25389_0

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