Issue with step3. analysis on the RNA assay: unable to run UMAP

[yojetsharma]

I have total of 4-multiome dataset(1-control, 3-patients), which I merge and use it for downstream analysis. Everything is fine until I reach step3 of analysis on the RNA assay. I get an error after running the RunUMAP function:

> library(simspec)
> alldata <- cluster_sim_spectrum(alldata,
+                                label_tag = "orig.ident",
+                                cluster_resolution = 0.6,
+                                reduction.name = "css_rna",
+                                reduction.key = "CSSRNA_")
Start to do clustering for each sample...
  Done clustering of sample d149npcs.
  Done clustering of sample ls002npcs.
  Done clustering of sample ls003npcs.
  Done clustering of sample ls004npcs.
Finished clustering.
Calculating average profiles of clusters...
Calculating standardized similarities to clusters...
Doing z-transformation...
Done. Returning results...
> alldata <- RunUMAP(alldata,
+                   reduction = "css_rna",
+                   dims = 1:ncol(Embeddings(alldata,"css_rna")),
+                   reduction.name = "umap_css_rna",
+                   reduction.key = "UMAPCSSRNA_")
07:04:52 UMAP embedding parameters a = 0.9922 b = 1.112
Error in checkna(X) : Missing values found in 'X'
> alldata
An object of class Seurat 
388143 features across 73587 samples within 2 assays 
Active assay: RNA (36601 features, 3000 variable features)
 1 other assay present: ATAC
 3 dimensional reductions calculated: pca, umap_rna, css_rna
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

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

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

other attached packages:
[1] simspec_0.0.0.9000 dplyr_1.1.4        Matrix_1.6-5       Signac_1.11.0      SeuratObject_4.1.4
[6] Seurat_4.4.0      

loaded via a namespace (and not attached):
  [1] Rtsne_0.17             colorspace_2.1-0       deldir_2.0-2           ellipsis_0.3.2        
  [5] ggridges_0.5.6         XVector_0.36.0         fs_1.6.3               GenomicRanges_1.48.0  
  [9] rstudioapi_0.15.0      spatstat.data_3.0-4    leiden_0.4.3.1         listenv_0.9.1         
 [13] remotes_2.4.2.1        ggrepel_0.9.5          fansi_1.0.6            codetools_0.2-19      
 [17] splines_4.2.1          cachem_1.0.8           pkgload_1.3.4          RcppRoll_0.3.0        
 [21] polyclip_1.10-6        jsonlite_1.8.8         Rsamtools_2.12.0       ica_1.0-3             
 [25] cluster_2.1.6          png_0.1-8              uwot_0.1.16            shiny_1.8.0           
 [29] sctransform_0.4.1      spatstat.sparse_3.0-3  compiler_4.2.1         httr_1.4.7            
 [33] fastmap_1.1.1          lazyeval_0.2.2         cli_3.6.2              later_1.3.2           
 [37] htmltools_0.5.7        tools_4.2.1            igraph_2.0.2           gtable_0.3.4          
 [41] glue_1.7.0             GenomeInfoDbData_1.2.8 RANN_2.6.1             reshape2_1.4.4        
 [45] fastmatch_1.1-4        Rcpp_1.0.12            scattermore_1.2        Biostrings_2.64.1     
 [49] vctrs_0.6.5            spatstat.explore_3.2-6 nlme_3.1-164           progressr_0.14.0      
 [53] lmtest_0.9-40          spatstat.random_3.2-2  stringr_1.5.1          ps_1.7.6              
 [57] globals_0.16.2         mime_0.12              miniUI_0.1.1.1         lifecycle_1.0.4       
 [61] irlba_2.3.5.1          devtools_2.4.5         goftest_1.2-3          future_1.33.1         
 [65] zlibbioc_1.42.0        MASS_7.3-60.0.1        zoo_1.8-12             scales_1.3.0          
 [69] promises_1.2.1         spatstat.utils_3.0-4   parallel_4.2.1         RColorBrewer_1.1-3    
 [73] curl_5.2.0             memoise_2.0.1          reticulate_1.35.0      pbapply_1.7-2         
 [77] gridExtra_2.3          ggplot2_3.5.0          stringi_1.8.3          desc_1.4.3            
 [81] S4Vectors_0.34.0       BiocGenerics_0.42.0    pkgbuild_1.4.3         BiocParallel_1.30.4   
 [85] GenomeInfoDb_1.32.4    rlang_1.1.3            pkgconfig_2.0.3        matrixStats_1.2.0     
 [89] bitops_1.0-7           lattice_0.22-5         ROCR_1.0-11            purrr_1.0.2           
 [93] tensor_1.5             patchwork_1.2.0        htmlwidgets_1.6.4      processx_3.8.3        
 [97] cowplot_1.1.3          tidyselect_1.2.0       parallelly_1.37.0      RcppAnnoy_0.0.22      
[101] plyr_1.8.9             magrittr_2.0.3         R6_2.5.1               profvis_0.3.8         
[105] IRanges_2.30.1         generics_0.1.3         pillar_1.9.0           fitdistrplus_1.1-11   
[109] survival_3.5-8         abind_1.4-5            RCurl_1.98-1.14        sp_2.1-3              
[113] tibble_3.2.1           future.apply_1.11.1    crayon_1.5.2           KernSmooth_2.23-22    
[117] utf8_1.2.4             spatstat.geom_3.2-8    plotly_4.10.4          urlchecker_1.0.1      
[121] usethis_2.2.3          grid_4.2.1             data.table_1.15.0      callr_3.7.5           
[125] digest_0.6.34          xtable_1.8-4           tidyr_1.3.1            httpuv_1.6.14         
[129] stats4_4.2.1           munsell_0.5.0          viridisLite_0.4.2      sessioninfo_1.2.2