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zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
https://zhanghao-njmu.github.io/SCP/
GNU General Public License v3.0
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RunDEtest not running #198

Open giorgiatosoni opened 8 months ago

giorgiatosoni commented 8 months ago

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

zhanghao-njmu commented 8 months ago

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.