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cole-trapnell-lab / monocle3

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preprocess_cds running for hours #717

Open alicerlam opened 2 months ago

alicerlam commented 2 months ago

Hi!

When I try to run preprocess_cds on my data (~50k cells, ~41k genes), it runs for hours without completing, as shown below:

Screenshot 2024-04-29 at 22 49 48

I've checked that my matrix is sparse (I created the cell data set object from a 10x matrix) and that my kernel is not frozen. Am I missing another preparation step somewhere? I've also tried to import the same dataset from a Seurat object using SeuratWrappers, and have run into the same issue.

gsx-ucas commented 1 month ago

Same problem. install.packages("irlba") reinstall irlba solved the issue.