How to debug “the process cannot access it” when running imt_gsea ?

[jwli28]

Dear alegiac95,

Thanks for providing this great scripts! I am using this toolbox in my project but meeting a bug.

After PLS analysis, I obtained .pkl file. When I did imt_gsea (below),

imt_gsea –i C:\Users\jwli2\Desktop\update\Imt_PET_pls\pls_analysis.pkl --geneset lake

It showed something wrong.

Traceback (most recent call last):
  File "C:\ProgramData\anaconda3\envs\transcriptomics\lib\runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "C:\ProgramData\anaconda3\envs\transcriptomics\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\ProgramData\anaconda3\envs\transcriptomics\Scripts\imagingtranscriptomics.exe\__main__.py", line 7, in <module>
    sys.exit(main())
  File "C:\ProgramData\anaconda3\envs\transcriptomics\lib\site-packages\imaging_transcriptomics\script\imagingtranscriptomics.py", line 108, in main
    gene_limit=parsed.max_genes)
  File "C:\ProgramData\anaconda3\envs\transcriptomics\lib\site-packages\imaging_transcriptomics\transcriptomics.py", line 334, in run
    gene_limit=gene_limit)
  File "C:\ProgramData\anaconda3\envs\transcriptomics\lib\site-packages\imaging_transcriptomics\transcriptomics.py", line 253, in gsea
    gene_limit=gene_limit)
  File "C:\ProgramData\anaconda3\envs\transcriptomics\lib\site-packages\imaging_transcriptomics\genes.py", line 210, in gsea
    max_size=gene_limit)
  File "C:\ProgramData\anaconda3\envs\transcriptomics\lib\site-packages\gseapy\gsea.py", line 1042, in prerank
    pre.run()
  File "C:\ProgramData\anaconda3\envs\transcriptomics\lib\site-packages\gseapy\gsea.py", line 527, in run
    self._tmpdir.cleanup()
  File "C:\ProgramData\anaconda3\envs\transcriptomics\lib\tempfile.py", line 811, in cleanup
    _shutil.rmtree(self.name)
  File "C:\ProgramData\anaconda3\envs\transcriptomics\lib\shutil.py", line 518, in rmtree
    return _rmtree_unsafe(path, onerror)
  File "C:\ProgramData\anaconda3\envs\transcriptomics\lib\shutil.py", line 402, in _rmtree_unsafe
    onerror(os.unlink, fullname, sys.exc_info())
  File "C:\ProgramData\anaconda3\envs\transcriptomics\lib\shutil.py", line 400, in _rmtree_unsafe
    os.unlink(fullname)
PermissionError: [WinError 32] Another program is using this file and the process cannot access it。: 'C:\\Users\\jwli2\\AppData\\Local\\Temp\\tmpclj7f0r7\\gseapy.prerank.geneset_lake.log'

(I am using imaging-transcriptomics V1.1.7) I tried to solve it but had no idea. I would appreciate your help, thanks!