scTransform failed without giving errors

[jingsday]

Hello bioinformaticians,

I was wondering if you could provide any insights regarding me failing to run scTransform. It is 'An object of class Seurat 27475 features across 57058 samples within 1 assay' and all went well until it suddenly quit without any errors in the log.

nohup.out Active assay: RNA (27475 features, 0 variable features) 16 layers present: counts.1, counts.2, counts.3, counts.4, counts.5, counts.6, counts.7, counts.8, counts.9, counts.10, counts.11, counts.12, counts.13, counts.14, counts.15, counts.16 Running SCTransform on assay: RNA Running SCTransform on layer: counts.1 .... Integrating data Merging dataset 2 4 13 5 7 into 11 16 1 3 15 6 10 9 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Integrating data This is the last line.

SCTransform part of the script:

Part II: SCT intergration and save files for furthur analysis

obj.list <- lapply(X = obj.list, FUN = SCTransform) features <- SelectIntegrationFeatures(object.list = obj.list, nfeatures = 3000) obj.list <- PrepSCTIntegration(object.list = obj.list, anchor.features = features)

anchors <- FindIntegrationAnchors(object.list = obj.list, normalization.method = "SCT", anchor.features = features) seurat.integrated <- IntegrateData(anchorset = anchors, normalization.method = "SCT")

seurat.integrated <- ScaleData(object = seurat.integrated) seurat.integrated <- RunPCA(object = seurat.integrated) seurat.integrated <- RunUMAP(object = seurat.integrated, dims = 1:50)

I appreciate your attention and any comments.

Regards, Jing

[saketkc]

Hi @jingsday, I do not see any error in the SCTransform step (or other steps), so would recommend that you open an issue on the seurat repo.