Error executing process > 'DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:TIH_HRD_CALLING (positive_somatic_control_1)'

Caused by:
  Process `DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:TIH_HRD_CALLING (positive_somatic_control_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 "positive_somatic_control_1" \
      --output_dir "." \
      --facets_pileup_file "positive_somatic_control_1.pileup.csv.gz" \
      --somatic_vcf_file "positive_somatic_control_1.vcf.gz" \
      --coverage_profiles_file "dbsnp_baseline_altera.260120.tsv.gz" \
      --vendor altera --config_file hrd_score_altera_config.260508.json --cnv_signatures_file cnv_signatures_signatera.251008.tsv --ridge_model_file ridge_model.260505.tsv --facets_lib_path env
  
  cat <<-END_VERSIONS > versions.yml
  "DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:TIH_HRD_CALLING":
      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:
  x86_64-conda-linux-gnu-cc -shared -L/opt/conda/envs/env_tih_hrd_running_env/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/envs/env_tih_hrd_running_env/lib -Wl,-rpath-link,/opt/conda/envs/env_tih_hrd_running_env/lib -L/opt/conda/envs/env_tih_hrd_running_env/lib -o HRDscoreAlteraBam.so 000.init.o cbs2rank.o rshared.o scansnp-random.o -lgfortran -lm -lquadmath -L/opt/conda/envs/env_tih_hrd_running_env/lib/R/lib -lR
  No man pages found in package  'HRDscoreAlteraBam' 
   Tumor bam =  
   Normal bam =  
   FACETS pileup = positive_somatic_control_1.pileup.csv.gz 
   Bypass segments =  
   Bypass ploidy =  
   Somatic vcf = positive_somatic_control_1.vcf.gz 
   Starting from:  pileup 

Command error:
  
  The following object is masked from 'package:GenomicRanges':
  
      shift
  
  The following object is masked from 'package:IRanges':
  
      shift
  
  The following objects are masked from 'package:S4Vectors':
  
      first, second
  
  The following objects are masked from 'package:dplyr':
  
      between, first, last
  
  Loading required package: gridExtra
  
  Attaching package: 'gridExtra'
  
  The following object is masked from 'package:Biobase':
  
      combine
  
  The following object is masked from 'package:BiocGenerics':
  
      combine
  
  The following object is masked from 'package:dplyr':
  
      combine
  
  
  Attaching package: 'purrr'
  
  The following object is masked from 'package:data.table':
  
      transpose
  
  The following object is masked from 'package:GenomicRanges':
  
      reduce
  
  The following object is masked from 'package:IRanges':
  
      reduce
  
  Error: Configuration file not found. Identified path: 
  Execution halted

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/7377f5dd385518c1992c59cc3fa8f5

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

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