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cole-trapnell-lab / monocle-release

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monocle estimate dispersions out of memory #352

Open eamcmillan88 opened 5 years ago

eamcmillan88 commented 5 years ago

Hi, I'm trying to run a 10x single cell dataset of 50K cells. However, when I run the 'estimatedispersions()', function, I get an out of memory error. I tried increasing the memory with 'Sys.setenv('R_MAX_VSIZE'=3200000000000)', but I'm still getting the same error. Please see below:

Sys.setenv('R_MAX_VSIZE'=3200000000000)

cds<- estimateSizeFactors(cds)

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

Sophia409 commented 5 years ago

@eamcmillan88 Hello,how did you solve it? I'm same as you.

zhaoxi10 commented 3 years ago

same here

KforKuma commented 3 years ago

same here. but after I tried several ways on the internet, i reboot my computer and it just works. my CellDataSet object is about 3.02 Mb.

xiekunwhy commented 3 years ago

same here, @ctrapnell

XiaoqiLuo commented 1 year ago

Same here. I've tried adding options(java.parameters = "-Xmx20g") to larger memory and it works.