search

Vivianstats / scImpute

Accurate and robust imputation of scRNA-seq data
https://www.nature.com/articles/s41467-018-03405-7
90 stars 34 forks source link

scimpute using only single thread #5

Closed baracus37 closed 6 years ago

baracus37 commented 6 years ago

Dear Vivian,

I want to use scinpute to impute a 10X dataset with 25.000 cells and 20.000 genes. Unfortunately I noticed that scimpute is only using a single thread, even though ncores=8 is set. Here is how I am invoking scimpute:

scimpute(count_path="./data.csv", out_dir="./", ncores=8, Kcluster=15)

I am using Ubuntu 16.04 and R 3.4.2. I also tested MAGIC, but I would rather use scimpute, for the reason you mentioned in the paper. However, when using MAGIC, all 8 threads are being used. Did I miss something? As this dataset is very large, computation on a single thread takes very long.

Best

baracus37 commented 6 years ago

I just realized that a single thread is only used for the "inferring cell similarities" step. For imputation itself, all threads are used. Sorry