kai-jz
commented
5 months ago Sorry, I have never encountered such an error. Restarting your computer might be an option?
Open irleader opened 6 months ago
kai-jz
commented
5 months ago Sorry, I have never encountered such an error. Restarting your computer might be an option?
At eval or denovo mode, when it finishes inference, the following error occurs before writing any output file, so I have no output,. I tried two different windows PCs with conda, the same error is reproduced:
Traceback (most recent call last): File "C:\Users\PilotLab\miniconda3\envs\contranovo\Lib\shutil.py", line 634, in _rmtree_unsafe os.unlink(fullname) PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\Users\PilotLab\AppData\Local\Temp\tmpl0ej9j5f\eval_52a4e37204e84f17b63625486cc4b5d7'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "", line 198, in _run_module_as_main
File "", line 88, in _run_code
File "C:\OneDrive\Evaluate_Denovo_Project\ContraNovo\ContraNovo\ContraNovo.py", line 211, in
main()
File "C:\Users\PilotLab\miniconda3\envs\contranovo\Lib\site-packages\click\core.py", line 1157, in call
return self.main(args, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\PilotLab\miniconda3\envs\contranovo\Lib\site-packages\click\core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "C:\Users\PilotLab\miniconda3\envs\contranovo\Lib\site-packages\click\core.py", line 1434, in invoke
return ctx.invoke(self.callback, ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\PilotLab\miniconda3\envs\contranovo\Lib\site-packages\click\core.py", line 783, in invoke
return __callback(args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\OneDrive\Evaluate_Denovo_Project\ContraNovo\ContraNovo\ContraNovo.py", line 205, in main
model_runner.evaluate(peak_path, model, config)
File "C:\OneDrive\Evaluate_Denovo_Project\ContraNovo\ContraNovo\denovo\model_runner.py", line 58, in evaluate
_execute_existing(peak_path, model_filename, config, True)
File "C:\OneDrive\Evaluate_Denovo_Project\ContraNovo\ContraNovo\denovo\model_runner.py", line 171, in _execute_existing
tmp_dir.cleanup()
File "C:\Users\PilotLab\miniconda3\envs\contranovo\Lib\tempfile.py", line 950, in cleanup
self._rmtree(self.name, ignore_errors=self._ignore_cleanup_errors)
File "C:\Users\PilotLab\miniconda3\envs\contranovo\Lib\tempfile.py", line 930, in _rmtree
_shutil.rmtree(name, onexc=onexc)
File "C:\Users\PilotLab\miniconda3\envs\contranovo\Lib\shutil.py", line 808, in rmtree
return _rmtree_unsafe(path, onexc)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\PilotLab\miniconda3\envs\contranovo\Lib\shutil.py", line 636, in _rmtree_unsafe
onexc(os.unlink, fullname, err)
File "C:\Users\PilotLab\miniconda3\envs\contranovo\Lib\tempfile.py", line 905, in onexc
_os.unlink(path)
PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\Users\PilotLab\AppData\Local\Temp\tmpl0ej9j5f\eval_52a4e37204e84f17b63625486cc4b5d7'
The only change I do to the code is https://github.com/BEAM-Labs/ContraNovo/blob/503fdb3bb7146b46aa3e205d1b70b70e2a4be7b8/ContraNovo/denovo/db_index.py#L117
The map size is too large for my disk, so I change to 40GB instead.
Can you kindly help to resolve this error so I can use ContrNovo?