ITADN

Spot extraction error when running pipeline with "lsf" profile

#46Opencgoina 创建于 2023-10-02
bug
C
cgoinacommented
## 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
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