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Vivianstats / scINSIGHT

Matrix factorization model for interpreting single cell gene expression in biologically heterogeneous data
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02649-3
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Question about running time #5

Open XinyeZhao opened 2 years ago

XinyeZhao commented 2 years ago

Hi scINSIGHT team,

When I tried running the examples following the vignette, it took quite a long time to run the sim.scobj = run_scINSIGHT(sim.scobj, K = seq(5,15,2), out.dir = './test_scInsight/test_save_sim/', num.cores = 5) even it's only the simulated data. I've started it two hours ago and it's still running now. Could you please tell me if it's normal？

Thanks

Vivianstats commented 2 years ago

Hi Xinye,

This seems to be much longer than the expected time. Can you provide more detailed information on the computing environment and session info?

Jasper-XYZ commented 2 years ago

Hi Vivian, Of course! I ran it on the cluster with R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.4 LTS scINSIGHT_0.1.4 It seemed to take about 3 hours to finish.

Thanks, Xinye

Vivianstats commented 2 years ago

Hi Xinye,

My apologies. I was thinking of another software tool of our team why I replied last time, so please disregard my response. I will assign this to the developer of this package. He will let you know if this time is regular.

sldyns commented 2 years ago

Hi Xinye,

3 hours is a normal time. In fact, on my machine this took about 4 hours.