Error: cannot allocate vector of size 80.7 Gb

[mylenaortiz]

Hello!

I'm trying to run SCTransform on my Visium HD data, but I'm getting the error "Error: cannot allocate vector of size 80.7 Gb".

I have already increased the future.globals.maxSize, but it didn't work. I also removed the cells with zero counts to prevent another error (Error in make_cell_attr(umi, cell_attr, latent_var, batch_var, latent_var_nonreg, :
cell attribute "log_umi" contains NA, NaN, or infinite value). Do you have any solution to fix this issue?

pymt_1_cell <- Load10X_Spatial(data.dir = localdir)

pymt_1_cell=pymt_1_cell[,unname(which(colSums(GetAssayData(pymt_1_cell))!=0))]

pymt_1_cell <- Seurat::SCTransform(pymt_1_cell, assay = "Spatial", verbose = FALSE)

Error: cannot allocate vector of size 80.7 Gb
In addition: Warning messages:
1: In size + sum(size_args, na.rm = FALSE) :
  NAs produced by integer overflow
2: In size + sum(size_args, na.rm = FALSE) :
  NAs produced by integer overflow
3: In size + sum(size_args, na.rm = FALSE) :
  NAs produced by integer overflow
4: In size + sum(size_args, na.rm = FALSE) :
  NAs produced by integer overflow

[saketkc]

Hi @mylenaortiz - I can take a look. Can you share your object (or a part of it) with me at saketc@iitb.ac.in?

Thanks!

[mylenaortiz]

Will do!