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Published 20 hours ago • verified publisher icon zhanghao-njmu

RunDEtest not running

Open giorgiatosoni opened this issue 2 years ago • 2 comments

Hi,

I used RunDEtest before and it worked just fine. Now that I'm using the latest SCP version (SCP 0.5.4) because of the velocity genes error, this doesn't work anymore (not running, still 0% after half an hour). The dataset is small, around 30K of cells. Any ideas on why?

image

Thank in advance,

Best, Giorgia

giorgiatosoni avatar Nov 02 '23 15:11 giorgiatosoni

This may be a parallelization issue. SCP uses a different multi-threading strategy compared to Seurat, using BiocParallel instead of future. When using SCP, do not enable future, as it may slow down some function executions. Please try restarting a new R session, making sure not to use future in that session, and then run the RunDEtest function.

zhanghao-njmu avatar Nov 15 '23 06:11 zhanghao-njmu

I tried several times, it didn't work either. I'm sure that I was using BiocParallel not future. image image Also, I have changed the parameter 'BPPARAM' for several times, but it didn't help. That's quite wired since I was using two different HPCs and both of them didn't work.

GuoJoey avatar Sep 06 '24 09:09 GuoJoey