Is this expected run time really expected?

[li-xuyang28]

Loaded expression matrix of 6659 cells and 33538 genes in 10.464452981948853 seconds...
Loaded 1639 TFs...
starting grnboost2 using 20 processes...
  0%|                                                                                                                                | 6/33538 [01:03<96:47:35, 10.39s/it]

I'm using the arboreto_with_multiprocessing.py on a cluster, the expected run time only seems to get longer after waiting for it to run for a bit...

[wbrett87]

Many people are having the same problem, but it seems like no one is checking this page anymore.

[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

[ghuls]

@li-xuyang28 Could you share your input files?