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flying-sheep avatar flying-sheep commented on June 3, 2024 1

Please add the relevant part of jupyter lab’s log.

If it’s a SEGFAULT, please reproduce with the PYTHONFAULTHANDLER env variable set to a non-empty string to get a traceback

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diegorunav avatar diegorunav commented on June 3, 2024

Here it is:

[I 2024-02-06 12:45:46.915 ServerApp] Kernel started: 9fd93000-73b0-4abb-8cf1-505bec376572
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
[I 2024-02-06 12:45:47.931 ServerApp] Connecting to kernel 9fd93000-73b0-4abb-8cf1-505bec376572.
[I 2024-02-06 12:45:47.936 ServerApp] Connecting to kernel 9fd93000-73b0-4abb-8cf1-505bec376572.
[I 2024-02-06 12:45:47.946 ServerApp] Connecting to kernel 9fd93000-73b0-4abb-8cf1-505bec376572.
[I 2024-02-06 12:45:52.822 ServerApp] Creating new directory in
[W 2024-02-06 12:46:00.673 ServerApp] delete /Untitled Folder
[I 2024-02-06 12:46:08.209 ServerApp] Kernel shutdown: 9fd93000-73b0-4abb-8cf1-505bec376572
[W 2024-02-06 12:46:08.330 ServerApp] delete /Untitled.ipynb
[I 2024-02-06 12:46:15.481 ServerApp] Kernel started: 54f6e9a0-500c-48ed-8d4d-49943b2f107c
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
[I 2024-02-06 12:46:16.520 ServerApp] Connecting to kernel 54f6e9a0-500c-48ed-8d4d-49943b2f107c.
[I 2024-02-06 12:48:15.364 ServerApp] Saving file at /Tests/scanpytutorial/Untitled.ipynb
[I 2024-02-06 12:49:18.462 ServerApp] AsyncIOLoopKernelRestarter: restarting kernel (1/5), keep random ports
[W 2024-02-06 12:49:18.462 ServerApp] kernel 54f6e9a0-500c-48ed-8d4d-49943b2f107c restarted
[I 2024-02-06 12:49:18.468 ServerApp] Starting buffering for 54f6e9a0-500c-48ed-8d4d-49943b2f107c:df20bfae-3e78-44d6-b98f-42f032c621cb
[I 2024-02-06 12:49:18.476 ServerApp] Connecting to kernel 54f6e9a0-500c-48ed-8d4d-49943b2f107c.
[I 2024-02-06 12:49:18.476 ServerApp] Restoring connection for 54f6e9a0-500c-48ed-8d4d-49943b2f107c:df20bfae-3e78-44d6-b98f-42f032c621cb
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.

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diegorunav avatar diegorunav commented on June 3, 2024

Same happens when I run sc.pp.regress_out(adata, ['total_counts', 'pct_counts_mt'])

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flying-sheep avatar flying-sheep commented on June 3, 2024

Hmm, there‘s no information in there. You could try converting that notebook to a script and running it with PYTHONFAULTHANDLER on. But if you can’t find a way to get a stack trace, we won’t be able to help you.

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