dims in scvi sketch integration

[Flu09]

I was following the v5 integration vignette and I choose 50 dims to continue with the integration of my sketched object ( active slot sketch assay)

DefaultAssay(filtered_obj_sketched) [1] "sketch"

For scvi it did not work beyond 30 dims. Although the object has 50 dims.

filtered_obj_sketched <- FindNeighbors(filtered_obj_sketched, reduction = "integrated.scvi", dims = 1:50) Error in FindNeighbors.Seurat(filtered_obj_sketched, reduction = "integrated.scvi", : More dimensions specified in dims than have been computed

filtered_obj_sketched <- FindNeighbors(filtered_obj_sketched, reduction = "integrated.scvi", dims = 1:40) Error in FindNeighbors.Seurat(filtered_obj_sketched, reduction = "integrated.scvi", : More dimensions specified in dims than have been computed

filtered_obj_sketched <- FindNeighbors(filtered_obj_sketched, reduction = "integrated.scvi", dims = 1:31) Error in FindNeighbors.Seurat(filtered_obj_sketched, reduction = "integrated.scvi", : More dimensions specified in dims than have been computed

filtered_obj_sketched <- FindNeighbors(filtered_obj_sketched, reduction = "integrated.scvi", dims = 1:30) Computing nearest neighbor graph

I decided to skip FindNeighbors step and check if RunUmap() will work .. again it only worked on 30 dims only. filtered_obj_sketched <- RunUMAP(filtered_obj_sketched, reduction = "integrated.scvi", dims = 1:30, return.model = T, reduction.name = "umap.scvi")

Then I faced this issue

DimPlot(filtered_obj_sketched , reduction = "umap.scvi") Rasterizing points since number of points exceeds 100,000. To disable this behavior set raster=FALSE Warning message: Removing 932261 cells missing data for vars requested

CCA, RPCA, harmony, I have no issue at all ( 50 dims in them and no warning message of any missing data)

I would appreciate it if you can help me especially regarding the removing of almost 1million cells