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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)
The text was updated successfully, but these errors were encountered:
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
Version (please complete the following information):
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)
The text was updated successfully, but these errors were encountered: