Cholmod error when using decontX package

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3.8 years ago

abiuma ▴ 30

Hi, I am trying remove the ambient RNA from my sequencing data. But I keep running into this error. Can you please tell me how to clear this error.

Error in asMethod(object) : 
  Cholmod error 'out of memory' at file ../Core/cholmod_memory.c, line 147

This is my code

decontxModel <- decontX(counts = as.matrix(GetAssayData(control, assay="RNA", slot="counts")), 
                        z = as.integer(control$RNA_snn_res.0.5),
                        batch = as.integer(control$orig.ident))

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server x64 (build 19042)

Matrix products: default

R RNA-Seq sequencing • 2.6k views

ADD COMMENT • link updated 3.7 years ago by Biostar 20 • written 3.8 years ago by abiuma ▴ 30

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'out of memory'

Looks like you are running out of memory.

ADD REPLY • link 3.8 years ago by GenoMax 147k

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Have you read the error message, in particular the part that says ''out of memory'? So compare the size of the data to the amount of RAM available.

ADD REPLY • link 3.8 years ago by Jean-Karim Heriche 27k

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Is there any way to overcome the memory issue without having to upgrade the RAM!

ADD REPLY • link 3.8 years ago by abiuma ▴ 30

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Work on a smaller data set or maybe use a less memory-hungry approach/tool. You also don't need to upgrade the RAM of your machine if you can get access to one with what you need, e.g. in your local HPC or in the cloud.

ADD REPLY • link 3.8 years ago by Jean-Karim Heriche 27k

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Thanks! I tried to run the script in the local server, but I got the same error.

ADD REPLY • link 3.8 years ago by abiuma ▴ 30

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Are you running this via cygwin on windows? Perhaps the default memory allocated to that environment is small and you could look at increasing that?