Error executing process > 'NFCORE_SAREK:SAREK:CRAM_HLATYPING_ALL:FASTQ_HLATYPING_OPTITYPE:OPTITYPE (NTC_0001_0001_A23FG3YLT4_2)'

Caused by:
  Process `NFCORE_SAREK:SAREK:CRAM_HLATYPING_ALL:FASTQ_HLATYPING_OPTITYPE:OPTITYPE (NTC_0001_0001_A23FG3YLT4_2)` terminated with an error exit status (1)


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 NTC_0001_0001_A23FG3YLT4_2_R1.fq.gz NTC_0001_0001_A23FG3YLT4_2_R2.fq.gz -c config.ini --dna --beta 0.003 --enumerate 10 --prefix NTC_0001_0001_A23FG3YLT4_2 --outdir NTC_0001_0001_A23FG3YLT4_2
  
  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:
  1

Command output:
  Using custom OptiType reference from: custom_ref/
  total 115152
  drwxr-xr-x. 2 1000 root      130 Feb 14 06:57 .
  drwx------. 4 1000 root     4096 Feb 14 06:57 ..
  -rw-r--r--. 1 1000 root 95958334 Feb 14 06:57 alleles.h5
  -rw-r--r--. 1 1000 root     6094 Feb 14 06:57 freq_alleles.txt
  -rw-r--r--. 1 1000 root 17711099 Feb 14 06:57 hla_reference_dna.fasta
  -rw-r--r--. 1 1000 root  4228813 Feb 14 06:57 hla_reference_rna.fasta

Command error:
  mkdir: cannot create directory ‘//.config’: Permission denied
  mkdir: cannot create directory ‘//.config’: Permission denied
  Traceback (most recent call last):
    File "/usr/local/bin/OptiType/OptiTypePipeline.py", line 369, in <module>
      pos, read_details = ht.pysam_to_hdf(bam_paths[0])
    File "/usr/local/bin/OptiType/hlatyper.py", line 240, in pysam_to_hdf
      pos_df.columns = sam.references[:]
    File "/usr/local/lib/python3.9/site-packages/pandas/core/generic.py", line 6335, in __setattr__
      return object.__setattr__(self, name, value)
    File "pandas/_libs/properties.pyx", line 69, in pandas._libs.properties.AxisProperty.__set__
    File "/usr/local/lib/python3.9/site-packages/pandas/core/generic.py", line 817, in _set_axis
      self._mgr.set_axis(axis, labels)
    File "/usr/local/lib/python3.9/site-packages/pandas/core/internals/managers.py", line 238, in set_axis
      self._validate_set_axis(axis, new_labels)
    File "/usr/local/lib/python3.9/site-packages/pandas/core/internals/base.py", line 98, in _validate_set_axis
      raise ValueError(
  ValueError: Length mismatch: Expected axis has 0 elements, new values have 11179 elements

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/1c57d774155b6836ac4d84020e4cb2

Container:
  quay.io/rsrivas9784/optitype:v3

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