Warning message for Quick-TRANSfer

[caitsimop]

I'm running into a Quick-TRANSfer warning when running scPredict. It seems to be related to this Harmony issue.

This is an example of what I'm running:

process_seurats <- function(seuratraw){ 
  seuratraw <- seuratraw %>% 
    NormalizeData() %>% 
    FindVariableFeatures() %>% 
    ScaleData() %>% 
    RunPCA() %>% 
    RunUMAP(dims = 1:30) %>% 
    JackStraw(num.replicate = 100) %>% 
    ScoreJackStraw(dims = 1:20) %>% 
    FindNeighbors(dims = 1:20) %>% 
    FindClusters(resolution = 1:10/10)
  return(seuratraw)
}

set.seed(2248)
query <- process_seurats(query)


# predict using model
query <- scPredict(query, reference, max.iter.harmony = 50)

And the warning message that occurs:

Harmony converged after 2 iterations
Warning message:
Quick-TRANSfer stage steps exceeded maximum (= 4439650)

Can this warning be safely ignored? Or is this an issue with Harmony?

Thanks!

[SmritiChawla]

I had a similar issue when mda model was used during training process. Can this warning be ignored?

[bontix-77]

when i get the quick-transfer warning message i don't see harmony in the reductions list of the seuratObj..