Issue with running UMAP with Seurat v5?

[ChawlaP1994]

Hi all,

I had some error running UMAP with Seurat v5. The same dataset worked fine with the previous version of Seurat. Any help if appreciated :)

sample <- RunUMAP(sample, dims = 1:30)
09:50:59 UMAP embedding parameters a = 0.9922 b = 1.112
09:50:59 Read 38737 rows and found 30 numeric columns
09:50:59 Using Annoy for neighbor search, n_neighbors = 30
09:50:59 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
09:51:05 Writing NN index file to temp file /tmp/Rtmp64A3uB/file1b85213ca28
09:51:05 Searching Annoy index using 1 thread, search_k = 3000
09:51:14 Annoy recall = 0.07745%
09:51:15 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
09:51:16 38737 smooth knn distance failures
Error in x2set(Xsub, n_neighbors, metric, nn_method = nn_sub, n_trees, :
Non-finite entries in the input matrix