Spot extraction error when running pipeline with "lsf" profile

[cgoina]

Bug report

Description of the problem

Spot extraction fails when running on Janelia's grid with "lsf" profile. (A clear and concise description of the nature of issue.)

Logs

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  SCRATCH_DIR: /groups/scicompsoft/home/kawaset/multifish/work/58/d6089cb2ae561627727ffb120b2cf2
  /app/airlocalize/airlocalize.sh /nrs/scicompsoft/kawaset/nftest4/outputs/LHA3_R3_small/stitching/export.n5 /c0/s0 /nrs/scicompsoft/kawaset/nftest4/outputs/LHA3_R3_small/spots/tiles/29/coords.txt /app/airlocalize/params/air_localize_default_params.txt /nrs/scicompsoft/kawaset/nftest4/outputs/LHA3_R3_small/spots/tiles/29 _c0.txt
  Creating MCR_CACHE_ROOT mcr_cache_16
  Running AirLocalize
  Opening N5 from /nrs/scicompsoft/kawaset/nftest4/outputs/LHA3_R3_small/stitching/export.n5
  Reading vox as 'pixelResolution.dimensions' from /c0/s0
  Got vox [0.23 0.23 0.42]
  N5 Path: /nrs/scicompsoft/kawaset/nftest4/outputs/LHA3_R3_small/stitching/export.n5
  N5 Data Set: /c0/s0
  Shape: (429, 1934, 3653)
  Voxel Size: [0.23 0.23 0.42]
  Non-zero voxel count: 64749568
  Initializing MATLAB runtime...
  Traceback (most recent call last):
    File "/app/airlocalize/scripts/air_localize_mcr.py", line 114, in <module>
      AIRLOCALIZE=AIRLOCALIZE_N5.initialize()
    File "/miniconda/lib/python3.6/site-packages/AIRLOCALIZE_N5/__init__.py", line 305, in initialize
      return _pir.initialize_package()
    File "/miniconda/lib/python3.6/site-packages/AIRLOCALIZE_N5/__init__.py", line 253, in initialize_package
      package_handle.initialize()
    File "/usr/local/MATLAB/MATLAB_Runtime/v95/toolbox/compiler_sdk/pysdk_py/matlab_pysdk/runtime/deployablepackage.py", line 33, in initialize
      mcr_handle = self.__cppext_handle.startMatlabRuntimeInstance(self.__ctf_path)
  SystemError: std::exception
  Cleaned up temporary files at mcr_cache_16

Work dir:
  /groups/scicompsoft/home/kawaset/multifish/work/58/d6089cb2ae561627727ffb120b2cf2

Environment

• EASI-FISH Pipeline version: 1.1.0
• Nextflow version: 23.04.1.5866
• Container runtime: Singularity
• Platform: LSF
• Operating system: oraclelinux 9