Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_PLTF (869_BU7-T1-TDNA-1_A23MJ3TLT4_1_vs_869_BU7-N1-BDNA-1_B23H3TCLT3_1)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_PLTF (869_BU7-T1-TDNA-1_A23MJ3TLT4_1_vs_869_BU7-N1-BDNA-1_B23H3TCLT3_1)` terminated with an error exit status (1)


Command executed:

  # Install the TiH-HRD package to a local library
  mkdir -p R_libs
  R CMD INSTALL --library=R_libs hrd_score_altera_bam
  export R_LIBS_USER=${PWD}/R_libs
  
  # Identify the path to the HRD-Altera script
  SCRIPT_PATH=$(Rscript -e "system.file('exec', 'hrd_altera_bam.R', package = 'HRDscoreAlteraBam')" | cut -f 2 -d ' ' | sed 's/"//g')
  
  # Run the HRD-Altera script
  Rscript ${SCRIPT_PATH} \
      --sample_id "869_BU7-T1-TDNA-1_A23MJ3TLT4_1_vs_869_BU7-N1-BDNA-1_B23H3TCLT3_1" \
      --output_dir "." \
      --bypass_segments "869_BU7-T1-TDNA-1_A23MJ3TLT4_1_vs_869_BU7-N1-BDNA-1_B23H3TCLT3_1.segments.csv" \
      --bypass_ploidy "869_BU7-T1-TDNA-1_A23MJ3TLT4_1_vs_869_BU7-N1-BDNA-1_B23H3TCLT3_1.purity_ploidy.csv" \
      --somatic_vcf_file "869_BU7-T1-TDNA-1_A23MJ3TLT4_1_vs_869_BU7-N1-BDNA-1_B23H3TCLT3_1.vcf.gz" \
      --vendor altera --config_file hrd_score_altera_config.260123.json --cnv_signatures_file cnv_signatures_signatera.251008.tsv --ridge_model_file ridge_models.260126.tsv --facets_lib_path env
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:TIH_HRD_PLTF":
      hrd_calling: $(Rscript -e 'packageVersion("HRDscoreAlteraBam")' 2>/dev/null | cut -f2 -d  ' ' | iconv -f utf-8 -t ascii//translit || echo "unknown")
      r-base: $(Rscript -e 'cat(as.character(getRversion()))' 2>/dev/null || echo "4.3.3")
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/88dcd07ff159cd55ebdf366b81e922

Container:
  901094524821.dkr.ecr.us-west-2.amazonaws.com/cgp-hrd_caller:v0.2

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