Question for the pyscenic grn error

[jeongdo801]

pySCENIC_error.txt

Hello, I was trying to run pySCENIC grn with the following commend, but I got error messages like the attachment file...
Could you guide me how I can resolve this issue? Thanks in advance!

!pyscenic grn --num_workers 20 --output adj.tsv --method grnboost2 PBMC10k_filtered.loom hs_hgnc_tfs.txt

[cflerin]

Hi @jeongdo801 ,

There's a lot going on in your logs, but it looks like pySCENIC was ultimately killed by something external (cluster resources manager perhaps?).

You also get:

OSError: [Errno 24] Too many open files

you could check and increase your ulimit (ulimit -n).

I would also suggest using the multiprocessing implementation of GRNBoost2 unless you really need Dask (see #163 ).