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
448 stars 183 forks source link

pyscenic ctx error - EOFError #586

Open yulchen810 opened 1 month ago

yulchen810 commented 1 month ago

Hi, Thank you for your great work. I run the pyscenic ctx in singularity, and encountered an error as below image

the version info: 1) singularity/3.7.0 2) singularity_pyscenic/0.11.2

Is the python version incorrect or the file is corrupt? Thank you. Best

ghuls commented 1 month ago

It might be that you use to many processes for pyscenic and one or more of the workers died. Try with less threads or run on a node with more RAM. (for pyscenic ctx each worker load the database file, so if you have 16 workers, you will need at least 16x the amount of RAM of the database size).

yulchen810 commented 1 month ago

It might be that you use to many processes for pyscenic and one or more of the workers died. Try with less threads or run on a node with more RAM. (for pyscenic ctx each worker load the database file, so if you have 16 workers, you will need at least 16x the amount of RAM of the database size).

Yes, I added the following two codes which resolved this problem, although I don't know why. --mode "custom_multiprocessing" \ --num_workers 4