Error executing process > 'NFCORE_SAREK:SAREK:CRAM_HLATYPING_ALL:FASTQ_HLATYPING_OPTITYPE:OPTITYPE (NTC_0001_0001_B23H3TCLT3_1)'

Caused by:
  Process `NFCORE_SAREK:SAREK:CRAM_HLATYPING_ALL:FASTQ_HLATYPING_OPTITYPE:OPTITYPE (NTC_0001_0001_B23H3TCLT3_1)` terminated with an error exit status (1)


Command executed:

  # Matplotlib (used for plots) tries to write to ~/.config by default; in containers this may not be writable.
  export MPLCONFIGDIR="${PWD}/.mplconfig"
  mkdir -p "${MPLCONFIGDIR}"
  
  # 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=72" >> config.ini
  echo "[ilp]" >> config.ini
  echo "solver=cbc" >> config.ini
  echo "threads=72" >> 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_B23H3TCLT3_1_R1.fq.gz NTC_0001_0001_B23H3TCLT3_1_R2.fq.gz -c config.ini --dna --beta 0.003 --enumerate 10 --prefix NTC_0001_0001_B23H3TCLT3_1 --outdir NTC_0001_0001_B23H3TCLT3_1
  
  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 27 18:58 .
  drwx------. 5 1000 root     4096 Feb 27 18:58 ..
  -rw-r--r--. 1 1000 root 95958334 Feb 27 18:58 alleles.h5
  -rw-r--r--. 1 1000 root     6094 Feb 27 18:58 freq_alleles.txt
  -rw-r--r--. 1 1000 root 17711099 Feb 27 18:58 hla_reference_dna.fasta
  -rw-r--r--. 1 1000 root  4228813 Feb 27 18:58 hla_reference_rna.fasta

Command error:
  Failed to read the first read sequence.
  Exiting ...
  Failed to read the first read sequence.
  Exiting ...
  [E::hts_open_format] Failed to open file "NTC_0001_0001_B23H3TCLT3_1/NTC_0001_0001_B23H3TCLT3_1_1.bam" : No such file or directory
  Traceback (most recent call last):
    File "/usr/local/bin/OptiType/OptiTypePipeline.py", line 396, in <module>
      pos, read_details = ht.pysam_to_hdf(bam_paths[0])
    File "/usr/local/bin/OptiType/hlatyper.py", line 186, in pysam_to_hdf
      sam = pysam.AlignmentFile(samfile, sam_or_bam)
    File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.__cinit__
    File "pysam/libcalignmentfile.pyx", line 951, in pysam.libcalignmentfile.AlignmentFile._open
  FileNotFoundError: [Errno 2] Could not open alignment file: No such file or directory: 'NTC_0001_0001_B23H3TCLT3_1/NTC_0001_0001_B23H3TCLT3_1_1.bam'

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/95a77c5c6ab7fcf4e8a4b27332d2c7

Container:
  quay.io/rsrivas9784/optitype:v4

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