TSSEnrichment Error: unable to allocate 2147483648.00Mb for a hash table

[gbloeb]

I'm not sure if this is a problem with the annotation as I get errors at that point as well.

smallatac<-readRDS(file="~/Downloads/smallatac.rds") #Will email you this file
annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v86)

Get multiple instances of: The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)

seqlevelsStyle(annotations) <- 'UCSC'
genome(annotations) <- "hg38"
Annotation(smallatac) <- annotations
atac<-TSSEnrichment(object=atac, fast=TRUE)

Extracting TSS positions
Extracting fragments at TSSs
Error: unable to allocate 2147483648.00Mb for a hash table

[timoast]

This issue occurs if the cells information is not set for the fragment object, which happens if you create a fragment object without setting the cells parameter and then add it to the assay. I've pushed a fix to the develop branch, but I'd also recommend setting the cells parameter in the fragment object

[BioInfoUCI]

Hello! I didn't use 10x data and I don't have a metadata file/cell info to add. I am running the develop branch and got the same error. Any tips on how to go around this would be much appreciated.

[timoast]

@BioInfoUCI can you open a new issue with a reproducible example and the output of sessionInfo()?

[BioInfoUCI]

I created a metadata file similar to the 10x file and it worked. Thank you!