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Published 20 hours ago • verified publisher icon aertslab

[BUG]pySCENIC for Rat

Open Chengshu21 opened this issue 4 years ago • 3 comments

Hi - Recently, I am running pySCENIC on Rat. As for the MOTIF_ANNOTATIONS file, I replace the genes in “motifs-v9-nr.mgi-m0.001-o0.0.tbl” with Rat's genes, but the process was broken like the image shown. So what can I do for running it smoothly? image image

Chengshu21 avatar Aug 10 '21 03:08 Chengshu21

@Chengshu21 Limit the number of workers. Probably you ran out of memory and the OOM killer killed one of the python processes.

ghuls avatar Aug 10 '21 09:08 ghuls

@Chengshu21 Limit the number of workers. Probably you ran out of memory and the OOM killer killed one of the python processes.

Thank you for your reply! But we tried in species of Human and mice, the same process ran successfully....So what can I do more to fix this problem?

Chengshu21 avatar Aug 17 '21 08:08 Chengshu21

Try also client_or_address='custom_multiprocessing' in the prune2df function. This could workaround some dask issues, if that's what is causing this.

cflerin avatar Aug 24 '21 14:08 cflerin