scrub.scrub_doublets() hangs

[obrien-james]

Hi,

I'm trying to run scrublet on some 10x GEX data. I have already run SoupX to correct for ambient RNA. Now I am running:

scrub = scr.Scrublet(adata.X, expected_doublet_rate=0.08 )
doublet_score, predicted_doublet = scrub.scrub_doublets(verbose=True)

However this process never seems to finish, first time I ran it on a sample with 15,000 cells it ran for >100 minutes and never finishes.

I have subsequently restarted etc... and tried again and it still hangs

Theres no error, the output just shows Embedding transcriptomes using PCA...

I'm running this using: Python 3.10.12 numpy 1.26.4 pandas 2.2.2 scanpy 1.9.3 scrublet 0.2.2

I have used scrublet previously and it never took very long to run

I'm not sure what the issue is?

[Cmfffff]

hey, is there anything update?