Error executing process > 'NFCORE_SAREK:SAREK:CRAM_HLATYPING_ALL:FASTQ_HLATYPING_OPTITYPE:OPTITYPE (1029_BICA-N1-BDNA-1_2375WFLT3_s32)'

Caused by:
  K8s Job nf-9a53b49279325ee668c05521c668234d-4afb3 execution failed: Job has reached the specified backoff limit


Command executed:

  # Create a config for OptiType on a per sample basis with task.ext.args2
  echo "[mapping]" > config.ini
  echo "razers3=razers3" >> config.ini
  echo "threads=12" >> config.ini
  echo "[ilp]" >> config.ini
  echo "solver=glpk" >> config.ini
  echo "threads=12" >> config.ini
  echo "[behavior]" >> config.ini
  echo "deletebam=true" >> config.ini
  echo "unpaired_weight=0" >> config.ini
  echo "use_discordant=false" >> config.ini
  
  # Custom reference is automatically detected by OptiTypePipeline.py
  # when files are staged to custom_ref/ (mounted at /data/custom_ref in container)
  if [ "true" = "true" ]; then
      echo "Using custom OptiType reference from: custom_ref/"
      ls -la custom_ref/
  else
      echo "Using built-in OptiType reference"
  fi
  
  # Run the actual OptiType typing with args
  # Input can be FASTQ files (1 or 2) or BAM file
  OptiTypePipeline.py -i 1029_BICA-N1-BDNA-1_2375WFLT3_s32_R1.fq.gz 1029_BICA-N1-BDNA-1_2375WFLT3_s32_R2.fq.gz -c config.ini --dna --beta 0.003 --enumerate 10 --prefix 1029_BICA-N1-BDNA-1_2375WFLT3_s32 --outdir 1029_BICA-N1-BDNA-1_2375WFLT3_s32
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:CRAM_HLATYPING_ALL:FASTQ_HLATYPING_OPTITYPE:OPTITYPE":
      optitype: $(cat $(which OptiTypePipeline.py) | grep -e "Version:" | sed -e "s/Version: //g")
  END_VERSIONS

Command exit status:
  -

Command output:
  (empty)

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/53b49279325ee668c05521c668234d

Container:
  quay.io/rsrivas9784/optitype:v3

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line