search

aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
439 stars 181 forks source link

[BUG]concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruy while the future was running or pending. #556

Open YOUWEIQINGHUAN opened 4 months ago

YOUWEIQINGHUAN commented 4 months ago

when I run the following codes:

pyscenic ctx --num_workers 10 \ --output sce.regulons.csv \ --expression_mtx_fname sce.loom \ --all_modules \ --mask_dropouts \ --mode "dask_multiprocessing" \ --min_genes 10 \

It reported below. what is wrong? concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruy while the future was running or pending.

ghuls commented 4 months ago

You likely ran out of RAM and one of the subprocesses was killed. Try running on a node with more RAM and/or run with less number of concurent workers.