statistical_analysis and analysis frozen on _counts_validations

Teichlab / cellphonedb

MIT License

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statistical_analysis and analysis frozen on _counts_validations #282

Open edwardkim1 opened 3 years ago

edwardkim1 commented 3 years ago

Hi,

I have tried installing cellphonedb via conda on a remote server running Ubuntu. Every time I try to run cellphonedb on the test data, the command freezes at "Launching Method _counts_validations" and stays in the state for an indefinite period of time.

Trying to quit using Ctrl+C also does not work either in this state.

Screen Shot 2021-03-07 at 10 21 39 PM

prete commented 3 years ago

hi @edwardkim1 could you try upgrading to the beta version pip install -U CellPhoneDB==2.1.8b3 and see if you're still facing this issue?

JonathanCruard commented 2 years ago

Hi there, I'm experiencing the exact same issue running cellphonedb inside a conda on a remote server. Updating to the beta version didn't solved it. Any advice on how to fix that? Thank you :)

prete commented 2 years ago

Hi @JonathanCruard thank you for using CellPhoneDB. Are you sure you've got enough resources (memory) to run CellPhoneDB with a dataset of your size?

JonathanCruard commented 2 years ago

I'm trying to run CellPhoneDB on a sample with 4k cells and i have 300Gb of RAM

prete commented 2 years ago

If this doesn't happen for you with the example datastes but it does happen with your own sample then we'kk need to have a look at your inputs to be able to reproduce the error.

Would it be possible for you to share your meta and counts files so we could check?

JonathanCruard commented 2 years ago

Just tried with example data and it does the same.

prete commented 2 years ago

It's hard to pin down what could be different in your environment, could you please provide:

Operating System and version
Version of cellphonedb, pandas and numpy in your system (pip show cellphonedb pandas numpy)

JonathanCruard commented 2 years ago

System infos, don't know if that helps :

And the infos about the packages :

prete commented 2 years ago

That looks about right.

Only thing that comes to mind is that you're using Python 3.9. Is there a chance you could try to create a new conda environment with python 3.8? This environment file can help you create that by doing: conda env create -f environment.yml.txt It will create an environment called cpdb after that do conda activate cpdb and then you can try again.

JonathanCruard commented 2 years ago

Ok, I will test that option on Monday. Thank you for your help so far btw!