BITFAM taking way too much time

jaleesr / BITFAM

BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.

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BITFAM taking way too much time #11

Open Sophon-0 opened 1 year ago

Sophon-0 commented 1 year ago

Hello, I was running BITFAM on a subset of 200 cells: BITFAM_res <- BITFAM(data = data_matrix_normalized, species = "human", scATAC_obj = NA, ncores = parallel::detectCores() ) And it would not finish even in 3 days. I have 128GB RAM and 32 CPUs. Thanks !

sgao30 commented 1 year ago

Hi,

Thank you for trying our tools and your feedback!

It is really weird to run such long time on a small dataset. Could you please provide more information? Like at which step it stuck?

Best, Shang