R session aborts when merging seurat objects

[Desi0]

Hi,

I am trying to merge 17 seurat objects (scATAC data) as indicated in the merging obejcts vignette (just without add.cell.ids) to do integration afterwards. But this needs a lot of time (probably >1 day), and after several hours the R session aborts without any error messsage. My computer has 96 GiB RAM. Is that maybe too less?

Can please somebody help with the crashing problem? And if anybody has an idea how to speed up the merging, I'd be happy to hear :)

[timoast]

Can you include the full code you're running and output of sessionInfo()?

[Desi0]

Thnks for your reply. By chance it's working now. I ran it in terminal, not R studio, maybe that was the clue, don't know. and I added the cell_IDs.

However, now I want to integrate the datasets and actually have a question to this, too. In your new vignette, you just use the rownames of one dataset as anchor.features. I think it should also work like this with more than 2 datasets, right? So this is my code

integration.anchors <- FindIntegrationAnchors(list(seu_1423,seu_1529, seu_2895, seu_2940, seu_2980, seu_3275, seu_3363,
                                           seu_3364, seu_3371, seu_3372, seu_3462,seu_48, seu_49, seu_50, seu_53, seu_54, seu_55),
                                           anchor.features = rownames(seu_1423),
                                           reduction = "rlsi", dims = 2:30)

integrated_ATAC<- IntegrateEmbeddings(anchorset = integration.anchors,
                                      reductions = unintegrated[["lsi"]],
                                      new.reduction.name = "integrated_lsi", 
                                      dims.to.integrate = 1:30)

integrated_ATAC <- RunUmap(integrated_ATAC, reduction = "integrated_lsi", dims = 2:30)

Unfortunately, I get this error message for FindIntegrationAnchors: Error in DietSeurat(object = object.list[[i]], assays = assay[i], features = anchor.features, : The default assay is slated to be removed, please change the default assay Additional: Warning: In CheckDuplicateCellNames(object.list = object.list) : Some cell names are duplicated across objects provided. Renaming to enforce unique cell names.

I was wondering if this is a problem with the chromosome coordinates?

head(rownames(unintegrated@assays$peaks@data))
[1] "chr1-3068102-3068488" "chr1-3117873-3118455" "chr1-3119092-3119488"
[4] "chr1-3121252-3121793" "chr1-3292215-3294888" "chr1-3296950-3297308"

If yes, can you help me solving this problem?

Thanks lot

[timoast]

If you include the full code you're running and output of sessionInfo() I can help further

[timoast]

Closing now as I haven't heard back, please reopen if you're still having issues