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diogomribeiro / sc_cop

Single cell local gene co-expression project
MIT License
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`CODer.py` consumed more than 180g VIRT. #4

Closed jiangpuxuan closed 1 year ago

jiangpuxuan commented 1 year ago

Here is my code:

python3 ~/packages/sc_cop-main/CODer.py expression_matrix.bed ./output/ 1000 --fdrCutoff 0.01
#My `CODer.py expression_matrix.bed` has 5000 sample

It consumed more than 180g VIRT so my server cannot run it.

How could I reduce the VIRT cosume? Thank you for your help!

diogomribeiro commented 1 year ago

Yes, I forgot to mention, there is a --lowMem 1 flag you can use. Jobs take a bit longer to run though. It has to do with how the randomisation matrices are stored, which is the heavy bit. Hope this helps, Diogo

jiangpuxuan commented 1 year ago

Yes, I forgot to mention, there is a --lowMem 1 flag you can use. Jobs take a bit longer to run though. It has to do with how the randomisation matrices are stored, which is the heavy bit. Hope this helps, Diogo

Thank you, that worked.