mcell_add_gene_stat error about metacell HOT 3 OPEN

Original comment by Yaniv Lubling (Bitbucket: 557058:11761e0c-f009-41f9-a29c-6f6993e0539c, ).

Hi SM,

Looks like a memory issue. Could you tell us what's the size of the umi matrix you're processing (how many cells and how many genes) and how much RAM your machine got?

Thanks,
Yaniv

from metacell.

Original comment by Sasikanth M (Bitbucket: 557058:8a01ef4f-c793-43aa-b940-38f63fa4c750, ).

Hi Yaniv,

We have ~94000 cells and about ~100000 features to start with and we are using 200gb RAM.

Thank you
SM

from metacell.

Original comment by Yaniv Lubling (Bitbucket: 557058:11761e0c-f009-41f9-a29c-6f6993e0539c, ).

Hi SM,

The number of elements in your matrix exceeds 2^32, that might be the problem.
As a quick workaround, you can try to reduce the size of the matrix by removing weak (or non expressing) genes - e.g. rows in the matrix with zero (or close to zero) sum.

Yaniv

from metacell.