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

Caused by:
  Process `SOMATIC_CNV_CALLING:SOMA_CNV_ALLELE_COUNTS (1029_0I-N1-BDNA-1_B23KGCJLT4_1)` terminated with an error exit status (1)


Command executed:

  SHARD1="chr1,chr4,chr15,chr19,chr22,chrY,chr2,chr8,chr9,chr17,chr18,chr20"
  SHARD2="chr3,chr5,chr10,chr11,chr13,chr14,chr6,chr7,chr12,chr16,chr21,chrX"
  
  allele_counts -t 2 -r "$SHARD1" 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam dbsnp138.snps.hg38.tsv.gz \
      "sample_id=1029_0I-N1-BDNA-1_B23KGCJLT4_1" "specimen_id=1029_0I" \
      "flowcell=A23KCGYLT4" "sample_type=normal" > allele_s1.tsv &
  allele_counts -t 2 -r "$SHARD2" 1029_0I-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam dbsnp138.snps.hg38.tsv.gz \
      "sample_id=1029_0I-N1-BDNA-1_B23KGCJLT4_1" "specimen_id=1029_0I" \
      "flowcell=A23KCGYLT4" "sample_type=normal" > allele_s2.tsv &
  wait
  
  { head -1 allele_s1.tsv | cut -f2-;
    for f in allele_s*.tsv; do tail -n +2 "$f"; done | sort -t'	' -k1,1n | cut -f2-;
  } | gzip > 1029_0I-N1-BDNA-1_B23KGCJLT4_1_alleles.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/bb/0d41195a580270ff32a3e99b8c97b5

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

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