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Vivianstats / scImpute

Accurate and robust imputation of scRNA-seq data
https://www.nature.com/articles/s41467-018-03405-7
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resume scImpute? #36

Open dpschreiner opened 3 years ago

dpschreiner commented 3 years ago

hi, i am running scImpute (thank you!) on our cluster with:

[1] "number of genes in raw count matrix 11213" [1] "number of cells in raw count matrix 14865"

and just got a timeout after 24 hours. is it possible to set scImpute to resume since i already have 11 out of 16 scImputepars*.rds files? would it be valid to subset the object and do only the last 5 clusters?

wangwenyue712 commented 1 year ago

I also have the same problem. Have you solved your problem?

dpschreiner commented 1 year ago

no, i abandoned the effort!

wangwenyue712 commented 1 year ago

Hi Vivian, Thank you very much for providing such wonderful tools for us. My data has 180,000 cells and 30,000 genes, and it's always limited by memory at runtime. Applying for memory failed to solve the problem. Do you have any suggestion on this error? Thanks in advance! 集群 @Vivianstats