Error executing process > 'SOMATIC_CNV_REF_BUILDER:SOMA_CNV_PROBE_COUNTS (Sig_18_Blood)'

Caused by:
  Process `SOMATIC_CNV_REF_BUILDER:SOMA_CNV_PROBE_COUNTS (Sig_18_Blood)` terminated with an error exit status (1)


Command executed:

  SHARD1="chr1,chr4,chr15,chr19,chr22,chrY"
  SHARD2="chr2,chr8,chr9,chr17,chr18,chr20"
  SHARD3="chr3,chr5,chr10,chr11,chr13,chr14"
  SHARD4="chr6,chr7,chr12,chr16,chr21,chrX"
  
  probe_counts -m frac -t 1 -r "$SHARD1" Sig_18_Blood.recalibrated.bam xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_chr21.bed \
      "sample_id=Sig_18_Blood" "specimen_id=custom_Sig_18_tumor_normal" \
      "flowcell=unknown" "sample_type=normal" > counts_s1.tsv &
  probe_counts -m frac -t 1 -r "$SHARD2" Sig_18_Blood.recalibrated.bam xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_chr21.bed \
      "sample_id=Sig_18_Blood" "specimen_id=custom_Sig_18_tumor_normal" \
      "flowcell=unknown" "sample_type=normal" > counts_s2.tsv &
  probe_counts -m frac -t 1 -r "$SHARD3" Sig_18_Blood.recalibrated.bam xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_chr21.bed \
      "sample_id=Sig_18_Blood" "specimen_id=custom_Sig_18_tumor_normal" \
      "flowcell=unknown" "sample_type=normal" > counts_s3.tsv &
  probe_counts -m frac -t 1 -r "$SHARD4" Sig_18_Blood.recalibrated.bam xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_chr21.bed \
      "sample_id=Sig_18_Blood" "specimen_id=custom_Sig_18_tumor_normal" \
      "flowcell=unknown" "sample_type=normal" > counts_s4.tsv &
  wait
  
  { head -1 counts_s1.tsv | cut -f2-;
    for f in counts_s*.tsv; do tail -n +2 "$f"; done | sort -t'	' -k1,1n | cut -f2-;
  } | gzip > Sig_18_Blood_probes.tsv.gz
  
  cat <<-END_VERSIONS > versions.yml
  "SOMATIC_CNV_REF_BUILDER:SOMA_CNV_PROBE_COUNTS":
      soma-cnv: 20260603-050173b
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/4c0e9cbd859a7304f5d463c8f793de

Container:
  292967571998.dkr.ecr.us-west-2.amazonaws.com/soma-cnv:20260603-050173b

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`