[BUG]

[xujie1020]

pyscenic grn --num_workers 10 \
>   --sparse \
>   --method grnboost2 \
>   --output sce.adj.csv \
>   sce.loom \
> hs_hgnc_tfs.txt

2023-05-30 14:26:20,464 - pyscenic.cli.pyscenic - INFO - Loading expression matrix.

2023-05-30 14:26:20,744 - pyscenic.cli.pyscenic - INFO - Inferring regulatory networks.
preparing dask client
parsing input
creating dask graph
10 partitions
computing dask graph

Why is the calculation speed so slow? It took 6 hours to calculate 100 cells and still no results. I am using a server with 1500 GB of memory, so insufficient computing power should not be an issue. The Python version I am using is 3.7. It seems like the calculation will never finish. Is there any issue that could be causing this?

[tyxdavid]

#463 Not the author, but we have fixed this problem by using an older version of pySCENIC. This problem may be caused by some bugs in the most recently updated version of pySCENIC, which causes incompatibility with other python packages.

[ghuls]

Try the containerized versions of pySCENIC: https://pyscenic.readthedocs.io/en/latest/installation.html#docker-podman-and-singularity-apptainer-images

Different Dask versions has been problematic for pySCENIC in the past.

[xujie1020]

Try the containerized versions of pySCENIC: https://pyscenic.readthedocs.io/en/latest/installation.html#docker-podman-and-singularity-apptainer-images

Different Dask versions has been problematic for pySCENIC in the past.

Thank you and I will have a try.