Error from runUMAP

[Liang-Wu-01]

Hi, I just update version of seurat to 4.0.3, but when run the runUMAP function, I get following error: Error in x2set(Xsub, n_neighbors, metric, nn_method = nn_sub, n_trees, : Non-finite entries in the input matrix. I am not sure what happened.

my code:

library(dplyr) library(SeuratData) data("pbmc3k")

pbmc3k <- SCTransform(pbmc3k, ncells = 3000, verbose = FALSE) %>% RunPCA(verbose = FALSE,npcs=30) %>% RunUMAP(dims = 1:30)

Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation' This message will be shown once per session 18:40:12 UMAP embedding parameters a = 0.9922 b = 1.112 18:40:12 Read 2700 rows and found 30 numeric columns 18:40:12 Using Annoy for neighbor search, n_neighbors = 30 18:40:12 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| 18:40:12 Writing NN index file to temp file /tmp/Rtmp7LqWjY/filea87d13b6ebf2 18:40:12 Searching Annoy index using 1 thread, search_k = 3000 18:40:13 Annoy recall = 1.111% 18:40:13 Commencing smooth kNN distance calibration using 1 thread 18:40:13 2700 smooth knn distance failures Error in x2set(Xsub, n_neighbors, metric, nn_method = nn_sub, n_trees, : Non-finite entries in the input matrix

sessionInfo() R version 4.1.0 (2021-05-18) Platform: x86_64-conda-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: ~/software/anaconda3/lib/libmkl_rt.so.1

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] dplyr_1.0.7 pbmc3k.SeuratData_3.1.4 SeuratData_0.2.1 [4] SeuratObject_4.0.2 Seurat_4.0.3

loaded via a namespace (and not attached): [1] nlme_3.1-152 matrixStats_0.60.0 spatstat.sparse_2.0-0 [4] RcppAnnoy_0.0.19 RColorBrewer_1.1-2 httr_1.4.2 [7] sctransform_0.3.2 tools_4.1.0 utf8_1.2.2 [10] R6_2.5.0 irlba_2.3.2 rpart_4.1-15 [13] KernSmooth_2.23-20 uwot_0.1.10 mgcv_1.8-36 [16] DBI_1.1.1 lazyeval_0.2.2 colorspace_2.0-2 [19] tidyselect_1.1.1 gridExtra_2.3 compiler_4.1.0 [22] cli_3.0.1 plotly_4.9.4.1 scales_1.1.1 [25] lmtest_0.9-38 spatstat.data_2.1-0 ggridges_0.5.3 [28] pbapply_1.4-3 rappdirs_0.3.3 goftest_1.2-2 [31] stringr_1.4.0 digest_0.6.27 spatstat.utils_2.2-0 [34] pkgconfig_2.0.3 htmltools_0.5.1.1 parallelly_1.27.0 [37] fastmap_1.1.0 htmlwidgets_1.5.3 rlang_0.4.11 [40] rstudioapi_0.13 shiny_1.6.0 generics_0.1.0 [43] zoo_1.8-9 jsonlite_1.7.2 ica_1.0-2 [46] magrittr_2.0.1 patchwork_1.1.1 Matrix_1.3-4 [49] Rcpp_1.0.7 munsell_0.5.0 fansi_0.5.0 [52] abind_1.4-5 reticulate_1.20 lifecycle_1.0.0 [55] stringi_1.7.3 MASS_7.3-54 Rtsne_0.15 [58] plyr_1.8.6 grid_4.1.0 parallel_4.1.0 [61] listenv_0.8.0 promises_1.2.0.1 ggrepel_0.9.1 [64] crayon_1.4.1 miniUI_0.1.1.1 deldir_0.2-10 [67] lattice_0.20-44 cowplot_1.1.1 splines_4.1.0 [70] tensor_1.5 pillar_1.6.1 igraph_1.2.6 [73] spatstat.geom_2.2-2 future.apply_1.7.0 reshape2_1.4.4 [76] codetools_0.2-18 leiden_0.3.9 glue_1.4.2 [79] data.table_1.14.0 png_0.1-7 vctrs_0.3.8 [82] httpuv_1.6.1 gtable_0.3.0 RANN_2.6.1 [85] purrr_0.3.4 spatstat.core_2.3-0 polyclip_1.10-0 [88] tidyr_1.1.3 scattermore_0.7 future_1.21.0 [91] assertthat_0.2.1 ggplot2_3.3.5 mime_0.11 [94] xtable_1.8-4 later_1.2.0 survival_3.2-11 [97] viridisLite_0.4.0 tibble_3.1.3 cluster_2.1.2 [100] globals_0.14.0 fitdistrplus_1.1-5 ellipsis_0.3.2 [103] ROCR_1.0-11

[yuhanH]

It looks wired. I cannot reproduce the same error.
Does it work if you don't use pipe %>% and run those steps one by one?

[Liang-Wu-01]

Hi yuhan. Thanks for your reply. I also had tried not used %>%, but the same error in the runUMAP function. But this error only appeared in the CentOS Linux 7 (Core) system, the window10 did not show any error in the same script.

[saketkc]

Hi @Liang-BGI, just to follow up I am not able to reproduce this error. Are you still facing issues?

[no-response[bot]]

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[yanpinlu]

@ @I'm having the same problem and I'm curious to know how to fix it. The R used is version 4.2, and the operation process is as follows

A_5s <- ReadVelocity(file = "/home/lvelocyto/190706A_drl_count.loom") bm <- as.Seurat(x = A_5s) bm <- SCTransform(object = bm, assay = "spliced") bm <- RunPCA(object = bm, verbose = FALSE) bm <- FindNeighbors(object = bm, dims = 1:20) bm <- FindClusters(object = bm) bm <- RunUMAP(object = bm, dims = 1:20) Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using th e cosine metric To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation' This message will be shown once per session 20:27:33 UMAP embedding parameters a = 0.9922 b = 1.112 20:27:33 Read 11329 rows and found 20 numeric columns 20:27:33 Using Annoy for neighbor search, n_neighbors = 30 20:27:33 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| 20:27:35 Writing NN index file to temp file /tmp/RtmpoNUZSR/file88363f984c80 20:27:35 Searching Annoy index using 1 thread, search_k = 3000 20:27:37 Annoy recall = 0.2648% 20:27:38 Commencing smooth kNN distance calibration using 1 thread 20:27:38 11329 smooth knn distance failures Error in x2set(Xsub, n_neighbors, metric, nn_method = nn_sub, n_trees, : Non-finite entries in the input matrix @saketkc

[tumorscholar]

Hello @yanpinlu, @saketkc I am facing the same issue, how did you fix?

10:40:19 UMAP embedding parameters a = 0.9922 b = 1.112 Found more than one class "dist" in cache; using the first, from namespace 'spam' Also defined by ‘BiocGenerics’ 10:40:20 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 20 10:40:20 741 smooth knn distance failures Error in x2set(Xsub, n_neighbors, metric, nn_method = nn_sub, n_trees, : Non-finite entries in the input matrix