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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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runMagic problem too large #213

Open hejing3283 opened 3 years ago

hejing3283 commented 3 years ago

Hi I am using runMagic to get gene activity for ~100 genes across ~60k cells, and it ran into memory issue. I am wondering if there is any way to resolve this?

========================== Error in A %*% A: Cholmod error 'problem too large' at file ../Core/cholmod_sparse.c, line 92 Traceback:

  1. runMagic(obj = x.sp, input.mat = "gmat", step.size = 3)
  2. A %*% A

  3. A %*% A

Thanks! Jing

chemistmarsy commented 3 years ago

Hi Jing,

Please read this post:

https://github.com/r3fang/SnapATAC/issues/105

This method fixed my same issue with large dataset.

Best, Ziyuan