Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2 (1029_BGFD-T1-TDNA-1_vs_1029_BGFD-N1-BDNA-1)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2 (1029_BGFD-T1-TDNA-1_vs_1029_BGFD-N1-BDNA-1)` terminated with an error exit status (1)


Command executed:

  sentieon driver \
      -t 36 \
      -r Homo_sapiens_assembly38.fasta \
       \
      -i 1029_BGFD-N1-BDNA-1.recal.bam -i 1029_BGFD-T1-TDNA-1.recal.bam \
      --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38.bed \
      --algo TNhaplotyper2 \
      --tumor_sample 1029_BGFD_1029_BGFD-T1-TDNA-1 --normal_sample 1029_BGFD_1029_BGFD-N1-BDNA-1 \
      --call_germline_sites \
      --germline_vcf af-only-gnomad.hg38.vcf.gz \
      --pon aih_blood_normal_36_pon.vcf.gz \
      1029_BGFD-T1-TDNA-1_vs_1029_BGFD-N1-BDNA-1.tnseq.vcf.gz \
      --algo OrientationBias --tumor_sample 1029_BGFD_1029_BGFD-T1-TDNA-1 1029_BGFD-T1-TDNA-1_vs_1029_BGFD-N1-BDNA-1.tnseq.orientation_data.tsv \
      --algo ContaminationModel --tumor_sample 1029_BGFD_1029_BGFD-T1-TDNA-1 --normal_sample 1029_BGFD_1029_BGFD-N1-BDNA-1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 1029_BGFD-T1-TDNA-1_vs_1029_BGFD-N1-BDNA-1.tnseq.segments 1029_BGFD-T1-TDNA-1_vs_1029_BGFD-N1-BDNA-1.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 -i 1029_BGFD-N1-BDNA-1.recal.bam -i 1029_BGFD-T1-TDNA-1.recal.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38.bed --algo TNhaplotyper2 --tumor_sample 1029_BGFD_1029_BGFD-T1-TDNA-1 --normal_sample 1029_BGFD_1029_BGFD-N1-BDNA-1 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon aih_blood_normal_36_pon.vcf.gz 1029_BGFD-T1-TDNA-1_vs_1029_BGFD-N1-BDNA-1.tnseq.vcf.gz --algo OrientationBias --tumor_sample 1029_BGFD_1029_BGFD-T1-TDNA-1 1029_BGFD-T1-TDNA-1_vs_1029_BGFD-N1-BDNA-1.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample 1029_BGFD_1029_BGFD-T1-TDNA-1 --normal_sample 1029_BGFD_1029_BGFD-N1-BDNA-1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 1029_BGFD-T1-TDNA-1_vs_1029_BGFD-N1-BDNA-1.tnseq.segments 1029_BGFD-T1-TDNA-1_vs_1029_BGFD-N1-BDNA-1.tnseq.contamination_data.tsv
  This software is licensed to bgold@natera.com by Sentieon Inc.
  TNhaplotyper2: tumor sample SM tag "1029_BGFD_1029_BGFD-T1-TDNA-1" is not present in the bam file

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/87fc62a9b6c57521f5643fb8530ee4

Container:
  community.wave.seqera.io/library/sentieon:202308.03--b599c8ad694846bd

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