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akdess / CaSpER

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memory issue with runCaSpER(): cannot allocate vector of size... #60

Closed marlaherr closed 3 years ago

marlaherr commented 3 years ago

Hi there, Thank you for this great tool, I am excited to use it. I am running into some issues during the runCaSpER call, though. I get this error:

final.objects <- runCaSpER(object = CaSpER_object, removeCentromere=T, cytoband= cytoband_hg19, method="iterative") Performing recursive median filtering... Error: cannot allocate vector of size 1024.0 Mb

From googling I infer it is a memory issue. Do you have a suggestion how I could reduce the memory demand? I already cleared my Environment of all objects but the CaSpER_object and cytoband_hg19 (my CaSpER object is 46.5GB), but I am working on an RStudio Server where the maximum memory per session is 64GB, so I suppose the runCaSpER call exceeds this!? Is there a possibility to split the call and run commands separately? I would be very grateful for any suggestions. Thank you