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cellxgene annotate 'file open' error (Win10) #2668

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kloot opened this issue Apr 8, 2024 · 0 comments
Open

cellxgene annotate 'file open' error (Win10) #2668

kloot opened this issue Apr 8, 2024 · 0 comments
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@kloot
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kloot commented Apr 8, 2024

Describe the bug
File open error

To Reproduce
Command from example annotation workflow:
cellxgene annotate minilung.h5ad -m https://cellxgene-annotation-public.s3.us-west-2.amazonaws.com/cell_type/models/hlca_20220920223732.zip -o minilungAnnotated.h5ad --mlflow-env-manager local --no-use-gpu --gene-column-name feature_name

Expected behavior
Progress or completion messages, a file named 'minilungAnnotated.h5ad' in the launch directory

Observed behaviour

Reading query dataset minilung.h5ad...
Retrieving model from https://cellxgene-annotation-public.s3.us-west-2.amazonaws.com/cell_type/models/hlca_20220920223732.zip
Annotating minilung.h5ad with cell_type...
Traceback (most recent call last):
  File "C:\Users\KL3900X\AppData\Local\Programs\Python\Python310\Scripts\cellxgene-script.py", line 33, in <module>
    sys.exit(load_entry_point('cellxgene==1.2.0', 'console_scripts', 'cellxgene')())
  File "C:\Users\KL3900X\AppData\Local\Programs\Python\Python310\lib\site-packages\click\core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "C:\Users\KL3900X\AppData\Local\Programs\Python\Python310\lib\site-packages\click\core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "C:\Users\KL3900X\AppData\Local\Programs\Python\Python310\lib\site-packages\click\core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "C:\Users\KL3900X\AppData\Local\Programs\Python\Python310\lib\site-packages\click\core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "C:\Users\KL3900X\AppData\Local\Programs\Python\Python310\lib\site-packages\click\core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "C:\Users\KL3900X\AppData\Local\Programs\Python\Python310\lib\site-packages\server\cli\annotate.py", line 200, in annotate
    p = subprocess.Popen(
  File "C:\Users\KL3900X\AppData\Local\Programs\Python\Python310\lib\subprocess.py", line 971, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "C:\Users\KL3900X\AppData\Local\Programs\Python\Python310\lib\subprocess.py", line 1440, in _execute_child
    hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
FileNotFoundError: [WinError 2] The system cannot find the file specified

Version (please complete the following information):

  • Desktop or hosted?: Desktop v 1.2.0
  • Browser (if hosted) [e.g. chrome, safari]:
  • Version [e.g. 0.13.0]:
    Windows 10, running Power Shell or Command (admin or user modes)
    python 3.10, pip 24.0

Additional context
Same error if the model file is downloaded prior to command execution.
Model file download seems succeeds (directory .models_cache is generated)
It is not obvious to me which file cannot be found
cellxgene explorer works fine (hosted)

@kloot kloot added the bug label Apr 8, 2024
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