0 overlapping genes between query and reference error

[billyt-gene]

Hi! I am getting an error when running

RCTD <- create.RCTD(query, reference, max_cores = 9)

The error is:

End: process_cell_type_info
create.RCTD: getting regression differentially expressed genes: 
Error in get_de_genes(cell_type_info$info, puck.original, fc_thresh = config$fc_cutoff_reg,  : 
  get_de_genes: Error: 0 common genes between SpatialRNA and Reference objects. Please check for gene list nonempty intersection.
In addition: Warning messages:
1: In asMethod(object) :
  sparse->dense coercion: allocating vector of size 1.6 GiB
2: In asMethod(object) :
  sparse->dense coercion: allocating vector of size 1.6 GiB
3: In asMethod(object) :
  sparse->dense coercion: allocating vector of size 1.6 GiB

However the below code indicates that 478 of the 480 genes in the query match the reference:

> q.genes <- query@counts@Dimnames[[1]]
> ref.genes <- reference@counts@Dimnames[[1]]
> 
> matching_genes <- intersect(q.genes,ref.genes)
> 
> length(matching_genes)
[1] 478

Any suggestions on how to move forward would be greatly appreciated!