Error: Counts slot not found in your Seurat object

[apal6]

Hi, Thank you for an amazing package. I was successfully able to run this on my other seurat objects but not with this one. Is it the version issue? Following is the error:

query.projected <- Run.ProjecTILs(tcell_combined_filtered, ref = ref.cd8, split.by = "sample.type", ncores = 4)
  |                                                                                                                    |   0%[1] "Using assay integrated for Untreated"
Pre-filtering cells with scGate...

### Detected a total of 2222 pure 'Target' cells (32.52% of total)
[1] "4611 out of 6833 ( 67% ) non-pure cells removed. Use filter.cells=FALSE to avoid pre-filtering"

  |=======================================                                                                             |  33%Stop worker failed with the error: wrong args for environment subassignment

Error: BiocParallel errors
  1 remote errors, element index: 1
  2 unevaluated and other errors
  first remote error:
Error in projection.helper(query = query.list[[i]], ref = ref, filter.cells = filter.cells, : Counts slot not found in your Seurat object. If you already normalized your data, re-run with option skip.normalize=TRUE

I tried running with skip.normalize=TRUE too which gives the below error:

query.projected <- Run.ProjecTILs(tcell_combined_filtered, ref = ref.cd8, split.by = "sample.type", ncores = 4,skip.normalize=TRUE)
  |                                                                                                                    |   0%[1] "Using assay integrated for Untreated"
Pre-filtering cells with scGate...

### Detected a total of 2222 pure 'Target' cells (32.52% of total)
[1] "4611 out of 6833 ( 67% ) non-pure cells removed. Use filter.cells=FALSE to avoid pre-filtering"

  |=======================================                                                                             |  33%Stop worker failed with the error: wrong args for environment subassignment

Error: BiocParallel errors
  1 remote errors, element index: 1
  2 unevaluated and other errors
  first remote error:
Error in projection.helper(query = query.list[[i]], ref = ref, filter.cells = filter.cells, : Too many genes missing. Check input object format

Additonally, I checked my slots and they are not empty.tcell_combined_filtered@assays$RNA$counts

Appreciate your help. Thank you!

[mass-a]

Hi, can you figure out what is different between this object and others that do work for you? e.g. names of existing slots, split vs. merged layers, assay vs. assay5 data type, ...? also can you post your sessioninfo() information?