cellphonedb
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Teichlab
statistical_analysis and analysis frozen on _counts_validations
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.
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?
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 :)
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?
I'm trying to run CellPhoneDB on a sample with 4k cells and i have 300Gb of RAM
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?
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)
System infos, don't know if that helps :
And the infos about the packages :
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.
Ok, I will test that option on Monday. Thank you for your help so far btw!