Error in indices.ba

[jcorn427]

Hello,
I'm trying to use RunAzimuth to annotate cell calls and I get an error at the "Finding anchors" step. Here's the entire text of the run for reference:

> combo_seurat <- RunAzimuth(combo_seurat, reference = "pbmcref", assay = "SCT")
Warning: Overwriting miscellanous data for model
Warning: Adding a dimensional reduction (refUMAP) without the associated assay being present
Warning: Adding a dimensional reduction (refUMAP) without the associated assay being present
detected inputs from HUMAN with id type Gene.name
reference rownames detected HUMAN with id type Gene.name
Normalizing query using reference SCT model
Warning: 1164 features of the features specified were not present in both the reference query assays. 
Continuing with remaining 3836 features.
Projecting cell embeddings
Finding query neighbors
Finding neighborhoods
Finding anchors
Error in indices.ba[neighbors.ab, 1:k.anchor, drop = FALSE] : 
  subscript out of bounds

I get this same error when running azimuth on standard normalized data as well so I don't think SCT is the issue. Any help would be much appreciated.

[sang-15]

Hi!

I had the same issue, I think the problem is having multiple layers in the Seurat object. If I do JoinLayers(), or subset each layer out as individual Seurat object, then everything worked out fine.

Hope it helps.