Error: vector memory exhausted (limit reached?) during Seurat integration datasets

Question

[davide]

Hi,

I am running (in R-studio) an integration analysis of scRNA-seq with Seurat, this is part of the script:

TD60_merge.features <- SelectIntegrationFeatures(object.list = TD60_merge.list, nfeatures = 3000)

TD60_merge.list <- PrepSCTIntegration(object.list = TD60_merge.list, anchor.features = TD60_merge.features, 
                                    verbose = FALSE)

TD60_merge.anchors <- FindIntegrationAnchors(object.list = TD60_merge.list, normalization.method = "SCT", 
                                           anchor.features = TD60_merge.features, verbose = FALSE)

TD60_merge.integrated <- IntegrateData(anchorset = TD60_merge.anchors, normalization.method = "SCT", 
                                     verbose = FALSE)

After the last command, I got this message:

Error: vector memory exhausted (limit reached?)

I have a MacBook Pro with 16 GB 2133 MHz LPDDR3

Can someone help me with this issue? Thank you

[ATpoint]

What did you try? https://stackoverflow.com/questions/51295402/r-on-macos-error-vector-memory-exhausted-limit-reached Did you monitor memory consumption during the process using the Activity Monitor? How big are the elements in your global environment?

Answer 1

[davide]

Thank you for the suggestion. I did two things:

1. I increase this value at the beginning of the script

options (future.globals.maxSize = 4000 * 1024^2) to options (future.globals.maxSize = 4000 * 1024^5)

AND also I follow the link you sent me https://stackoverflow.com/questions/51295402/r-on-macos-error-vector-memory-exhausted-limit-reached

from the terminal I increase cd ~ touch .Renviron open .Renviron Step 3: Save the following as the first line of .Renviron:

R_MAX_VSIZE=100Gb

Now It works

[Julia]

Thank you, I am also on MacBook Pro with 16 GB and this helped