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Published 20 hours ago • verified publisher icon Vivianstats

Processing time

Open morganee261 opened this issue 5 years ago • 1 comments

morganee261 avatar Dec 10 '19 16:12 morganee261

Hi Vivian,

I am trying to run scImpute from a csv of UMI values (22,278 genes and 39,663 cells)

Here is the code I am running:

WS_impute<-scimpute(count_path ="/home-b/morgane/impute/WSdata.csv", infile = "csv", outfile = "csv", type="count", out_dir = "/home-b/morgane/impute/WSimpute",drop_thre = 0.5,Kcluster=3,ncores = 6) [1] "number of genes in raw count matrix 22278" [1] "number of cells in raw count matrix 39663" [1] "reading finished!" [1] "imputation starts ..." [1] "searching candidate neighbors ... " [1] "inferring cell similarities ..." [1] "dimension reduction ..." [1] "calculating cell distances ..."

I has been running for over 5 days now and it is stuck on calculating cell distances. Do you have an idea of how long it would take?

thanks!

morganee261 avatar Dec 10 '19 16:12 morganee261