Error executing process > 'SOMATIC_CNV_CALLING:SOMA_CNV_PROBE_COUNTS (1029_0I-N1-BDNA-1_B23KGCJLT4_1)'

Caused by:
  Process `SOMATIC_CNV_CALLING:SOMA_CNV_PROBE_COUNTS (1029_0I-N1-BDNA-1_B23KGCJLT4_1)` 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 "$SHARD1" 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed \
      "sample_id=1029_0I-N1-BDNA-1_B23KGCJLT4_1" "specimen_id=1029_0I" \
      "flowcell=A23KCGYLT4" "sample_type=normal" > counts_s1.tsv &
  probe_counts -m frac -t 1 -r "$SHARD2" 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed \
      "sample_id=1029_0I-N1-BDNA-1_B23KGCJLT4_1" "specimen_id=1029_0I" \
      "flowcell=A23KCGYLT4" "sample_type=normal" > counts_s2.tsv &
  probe_counts -m frac -t 1 -r "$SHARD3" 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed \
      "sample_id=1029_0I-N1-BDNA-1_B23KGCJLT4_1" "specimen_id=1029_0I" \
      "flowcell=A23KCGYLT4" "sample_type=normal" > counts_s3.tsv &
  probe_counts -m frac -t 1 -r "$SHARD4" 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed \
      "sample_id=1029_0I-N1-BDNA-1_B23KGCJLT4_1" "specimen_id=1029_0I" \
      "flowcell=A23KCGYLT4" "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 > 1029_0I-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz

Command exit status:
  1

Command output:
  (empty)

Command error:
  Command 'ps' required by nextflow to collect task metrics cannot be found

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/7eedc54e51000d16be99500b35147d

Container:
  292967571998.dkr.ecr.us-west-2.amazonaws.com/soma-cnv:latest

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`