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Hi! I have a huge 10X scRNA-seq mouse data (~60Gb BAM file | ~50K cells from 12 mice) that I am trying to run on cellSNP-lite. I compiled cellSNP-lite in an HPC environment and I am running it from there on the mode 2A.
The problem is, no matter how much RAM I am using, I am constantly getting the message "Combined max depth is above 1M. Potential memory hog!" and it has been running for 11 days already.
I know it is a lot of data and I am wondering what would be the best approach in that scenario? Perhaps split the cell barcodes file?
Any help is highly appreciated!
Thank you so very much.
The text was updated successfully, but these errors were encountered:
Hi, Mode 2a is more suitable for small datasets. For large datasets, you may try Mode 2b + Mode 1a. Mode 2a does joint calling and genotyping, but it is substantially slower than calling first in a bulk manner by Mode 2b followed by genotyping in Mode 1a. To speed up, you may try --minMAF 0.1 --minCOUNT 100 options in both modes.
Hi! I have a huge 10X scRNA-seq mouse data (~60Gb BAM file | ~50K cells from 12 mice) that I am trying to run on cellSNP-lite. I compiled cellSNP-lite in an HPC environment and I am running it from there on the mode 2A.
The problem is, no matter how much RAM I am using, I am constantly getting the message "Combined max depth is above 1M. Potential memory hog!" and it has been running for 11 days already.
I know it is a lot of data and I am wondering what would be the best approach in that scenario? Perhaps split the cell barcodes file?
Any help is highly appreciated!
Thank you so very much.
The text was updated successfully, but these errors were encountered: