[bug] gubbins fails when run under apptainer #667

[35/5c25d1] NOTE: Process `GUBBINS:GUBBINS_MODULE (core-snp)` terminated with an error exit status (1) -- Execution is retried (1)
[c4/33af0d] Re-submitted process > GUBBINS:GUBBINS_MODULE (core-snp)
ERROR ~ Error executing process > 'GUBBINS:GUBBINS_MODULE (core-snp)'

Caused by:
  Process `GUBBINS:GUBBINS_MODULE (core-snp)` terminated with an error exit status (1)


Command executed:

  if [ "true" == "true" ]; then
      gzip -c -d core-snp-clean.full.aln.gz > core-snp-clean.full.aln
  fi

  run_gubbins.py \
      --threads 6 \
      --prefix core-snp \
      --iterations 5 --min-snps 3 --min-window-size 100 --max-window-size 10000 --filter-percentage 25.0 \
      core-snp-clean.full.aln

  # Create masked alignment
  mask_gubbins_aln.py \
      --aln core-snp-clean.full.aln \
      --gff core-snp.recombination_predictions.gff \
      --out core-snp.masked.aln

  # Cleanup
  if [ "true" == "true" ]; then
      rm -rf core-snp-clean.full.aln
  fi
  gzip *.masked.aln *.embl *.fasta *.gff *.vcf

  # Move supplemental outputs to gubbins folder
  mkdir gubbins
  mv core-snp.branch_base_reconstruction.embl.gz        core-snp.recombination_predictions.embl.gz        core-snp.recombination_predictions.gff.gz        core-snp.per_branch_statistics.csv        core-snp.filtered_polymorphic_sites.fasta.gz        core-snp.filtered_polymorphic_sites.phylip        core-snp.final_tree.tre        core-snp.node_labelled.final_tree.tre        core-snp.summary_of_snp_distribution.vcf.gz        gubbins/

  cat <<-END_VERSIONS > versions.yml
  "GUBBINS:GUBBINS_MODULE":
      gubbins: $(run_gubbins.py --version 2>&1)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  /usr/local/lib/python3.10/site-packages/gubbins/__init__.py:12: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
    import pkg_resources
  Traceback (most recent call last):
    File "/usr/local/bin/run_gubbins.py", line 7, in <module>
      from gubbins.run_gubbins import main
    File "/usr/local/lib/python3.10/site-packages/gubbins/__init__.py", line 17, in <module>
      from gubbins import common
    File "/usr/local/lib/python3.10/site-packages/gubbins/common.py", line 44, in <module>
      from gubbins.pyjar import jar, get_base_patterns
    File "/usr/local/lib/python3.10/site-packages/gubbins/pyjar.py", line 237, in <module>
      def seq_to_int(seq,out_seq):
    File "/usr/local/lib/python3.10/site-packages/numba/core/decorators.py", line 227, in wrapper
      disp.enable_caching()
    File "/usr/local/lib/python3.10/site-packages/numba/core/dispatcher.py", line 811, in enable_caching
      self._cache = FunctionCache(self.py_func)
    File "/usr/local/lib/python3.10/site-packages/numba/core/caching.py", line 687, in __init__
      self._impl = self._impl_class(py_func)
    File "/usr/local/lib/python3.10/site-packages/numba/core/caching.py", line 423, in __init__
      raise RuntimeError("cannot cache function %r: no locator available "
  RuntimeError: cannot cache function 'seq_to_int': no locator available for file '/usr/local/lib/python3.10/site-packages/gubbins/pyjar.py'

Work dir:
  /srv/pvh/cholera_analysis/work/c4/33af0d92e8ace59be1817839a9e700

Container:
  /srv/pvh/singularity_cache/depot.galaxyproject.org-singularity-gubbins-3.4.3--py310hfc0ef84_1.img