Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2 (NCIH2126_tumor_0pct_rep1_vs_NCIH2126_baseline_rep2)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2 (NCIH2126_tumor_0pct_rep1_vs_NCIH2126_baseline_rep2)` terminated with an error exit status (1)


Command executed:

  sentieon driver \
      -t 36 \
      -r Homo_sapiens_assembly38.fasta \
      --interval_padding 100 \
      -i dna_s1462.recalibrated.bam -i dna_s1456.recalibrated.bam \
      --interval wgs_calling_regions_noseconds.hg38.bed \
      --algo TNhaplotyper2 \
      --tumor_sample NCIH2126_tumor_0pct_rep1 --normal_sample NCIH2126_baseline_rep2 \
      --call_germline_sites \
      --germline_vcf af-only-gnomad.hg38.vcf.gz \
      --pon aih_blood_normal_36_pon.vcf.gz \
      NCIH2126_tumor_0pct_rep1_vs_NCIH2126_baseline_rep2.tnseq.vcf.gz \
      --algo OrientationBias --tumor_sample NCIH2126_tumor_0pct_rep1 NCIH2126_tumor_0pct_rep1_vs_NCIH2126_baseline_rep2.tnseq.orientation_data.tsv \
      --algo ContaminationModel --tumor_sample NCIH2126_tumor_0pct_rep1 --normal_sample NCIH2126_baseline_rep2 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments NCIH2126_tumor_0pct_rep1_vs_NCIH2126_baseline_rep2.tnseq.segments NCIH2126_tumor_0pct_rep1_vs_NCIH2126_baseline_rep2.tnseq.contamination_data.tsv
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2":
      sentieon: $(echo $(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 36 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i dna_s1462.recalibrated.bam -i dna_s1456.recalibrated.bam --interval wgs_calling_regions_noseconds.hg38.bed --algo TNhaplotyper2 --tumor_sample NCIH2126_tumor_0pct_rep1 --normal_sample NCIH2126_baseline_rep2 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon aih_blood_normal_36_pon.vcf.gz NCIH2126_tumor_0pct_rep1_vs_NCIH2126_baseline_rep2.tnseq.vcf.gz --algo OrientationBias --tumor_sample NCIH2126_tumor_0pct_rep1 NCIH2126_tumor_0pct_rep1_vs_NCIH2126_baseline_rep2.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample NCIH2126_tumor_0pct_rep1 --normal_sample NCIH2126_baseline_rep2 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments NCIH2126_tumor_0pct_rep1_vs_NCIH2126_baseline_rep2.tnseq.segments NCIH2126_tumor_0pct_rep1_vs_NCIH2126_baseline_rep2.tnseq.contamination_data.tsv
  This software is licensed to bgold@natera.com by Sentieon Inc.
  TNhaplotyper2: tumor sample SM tag "NCIH2126_tumor_0pct_rep1" is not present in the bam file

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/f937c5d2e9babbc5c3c9c372e7e1f4

Container:
  292967571998.dkr.ecr.us-west-2.amazonaws.com/community.wave.seqera.io/library/sentieon:202308.03--b599c8ad694846bd

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