mcell_add_gene_stat error

[aviezerl]

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

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Hi, I got the following error when running mcell_add_gene_stat

Calculating gene statistics... will downsamp done downsamp will gen mat_n done gen mat_n done computing basic gstat, will compute trends Error in asMethod(object) : Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 105

Can you help figuring out what might have caused this error?

Thank you

SM

[aviezerl]

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

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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

[aviezerl]

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

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Hi Yaniv,

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

Thank you SM

[aviezerl]

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

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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