chromvar from signac wrapper is stuck (not progressing)

Hello, I would really appreciate your help. I am running chromvar from a Seurat object on 29K cells and 192K peaks. R version 4.1.1 (2021-08-10) chromVAR version 1.16.0 Signac version 1.6.0 Seurat version 4.1.0

It starts running fine:

register(MulticoreParam(10, progressbar = TRUE)) mySeurat <- RunChromVAR(

• object = mySeurat,
• genome = BSgenome.Mmusculus.UCSC.mm10,
• verbose=TRUE
• ) Computing GC bias per region Selecting background regions Computing deviations from background | | 0%

Basically, it gets stuck at this stage forever. Any suggestions? Thanks in advance

Hi, I'm facing the same issue. I let my job run for almost 4 days and still nothing changed. I'd love some help here.

Before chromvar command run register(SerialParam())

From: hsriniva1104 @.> Sent: Friday, August 12, 2022 9:30 PM To: GreenleafLab/chromVAR @.> Cc: Dena Leshkowitz @.>; Author @.> Subject: Re: [GreenleafLab/chromVAR] chromvar from signac wrapper is stuck (not progressing) (Issue #98)

Hi, I'm facing the same issue. I let my job run for almost 4 days and still nothing changed. I'd love some help here.

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