error: non-unique value when setting 'row.names' - even though cell names are already unique

[yls2g13]

I'm having some issues with RunAzimuth. I originally had a larger Seurat object but I've included a 100-cell sample here that produces the same/similar error. cells100.rds.zip

library(Azimuth)
library(Seurat)
library(SeuratData)
# available_data <- AvailableData()

cells100 <- readRDS("cells100.rds")
DefaultAssay(cells100) <-"RNA"
pbmc_out <- RunAzimuth(cells100,assay="RNA", umap.name="umap", reference = "Seurat/Azimuth/pbmcref.SeuratData/inst/azimuth/")
bm_out <- RunAzimuth(cells100, assay="RNA", umap.name="umap", reference = "Seurat/Azimuth/bonemarrowref.SeuratData/inst/azimuth/")

pbmc_out was generated successfully, but bm_out threw some errors. I'm sure each cell name is unique, and I'm not sure where that duplicate cell name would come from

Warning messages:
1: In RunUMAP.default(object = neighborlist, reduction.model = reduction.model,  ... :
  Number of neighbors between query and reference is not equal to the number of neighbors within reference
2: Cannot add objects with duplicate keys (offending key: UMAP_), setting key to 'ref.umap_'
3: non-unique value when setting 'row.names': ‘AGCCTAACATCACGTA-1_3’

I'd really appreciate your guys' input here - thanks!

sessionInfo:

R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /usr/lib64/libblas.so.3.4.2
LAPACK: /usr/lib64/liblapack.so.3.4.2

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

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Signac_1.7.0                SeuratData_0.2.2            Azimuth_0.4.6               shinyBS_0.61.1             
 [5] dittoSeq_1.8.1              ggpubr_0.4.0                ggsci_2.9                   forcats_1.0.0              
 [9] stringr_1.5.0               dplyr_1.1.2                 purrr_1.0.1                 readr_2.1.2                
[13] tidyr_1.3.0                 tibble_3.2.1                ggplot2_3.4.2               tidyverse_1.3.1            
[17] cowplot_1.1.1               DoubletFinder_2.0.3         DropletUtils_1.16.0         SingleCellExperiment_1.18.0
[21] SummarizedExperiment_1.28.0 Biobase_2.58.0              GenomicRanges_1.50.2        GenomeInfoDb_1.34.9        
[25] IRanges_2.32.0              S4Vectors_0.36.2            BiocGenerics_0.44.0         MatrixGenerics_1.10.0      
[29] matrixStats_1.0.0           patchwork_1.1.2.9000        SeuratObject_4.1.3          Seurat_4.3.0.1             

loaded via a namespace (and not attached):
  [1] shinydashboard_0.7.2      utf8_1.2.3                spatstat.explore_3.2-1    reticulate_1.30          
  [5] R.utils_2.12.2            ks_1.13.5                 tidyselect_1.2.0          htmlwidgets_1.6.2        
  [9] grid_4.2.0                BiocParallel_1.32.6       Rtsne_0.16                munsell_0.5.0            
 [13] codetools_0.2-18          ica_1.0-3                 DT_0.27                   future_1.33.0            
 [17] miniUI_0.1.1.1            withr_2.5.0               spatstat.random_3.1-5     colorspace_2.1-0         
 [21] progressr_0.13.0          knitr_1.43                rstudioapi_0.14           ROCR_1.0-11              
 [25] ggsignif_0.6.3            tensor_1.5                listenv_0.9.0             GenomeInfoDbData_1.2.9   
 [29] polyclip_1.10-4           bit64_4.0.5               pheatmap_1.0.12           Nebulosa_1.8.0           
 [33] rhdf5_2.42.1              parallelly_1.36.0         vctrs_0.6.3               generics_0.1.3           
 [37] xfun_0.39                 R6_2.5.1                  locfit_1.5-9.7            hdf5r_1.3.5              
 [41] bitops_1.0-7              rhdf5filters_1.10.1       spatstat.utils_3.0-3      DelayedArray_0.24.0      
 [45] promises_1.2.0.1          scales_1.2.1              googlesheets4_1.0.0       rgeos_0.5-9              
 [49] gtable_0.3.3              beachmat_2.14.2           globals_0.16.2            goftest_1.2-3            
 [53] rlang_1.1.1               RcppRoll_0.3.0            splines_4.2.0             rstatix_0.7.0            
 [57] lazyeval_0.2.2            gargle_1.2.0              spatstat.geom_3.2-4       broom_1.0.4              
 [61] modelr_0.1.8              yaml_2.3.7                reshape2_1.4.4            abind_1.4-5              
 [65] backports_1.4.1           httpuv_1.6.11             SeuratDisk_0.0.0.9020     tools_4.2.0              
 [69] ellipsis_0.3.2            RColorBrewer_1.1-3        ggridges_0.5.4            Rcpp_1.0.11              
 [73] plyr_1.8.8                sparseMatrixStats_1.10.0  zlibbioc_1.44.0           RCurl_1.98-1.12          
 [77] deldir_1.0-9              pbapply_1.7-2             zoo_1.8-12                haven_2.5.0              
 [81] ggrepel_0.9.3             cluster_2.1.3             fs_1.6.3                  magrittr_2.0.3           
 [85] data.table_1.14.8         scattermore_1.2           reprex_2.0.1              lmtest_0.9-40            
 [89] RANN_2.6.1                googledrive_2.0.0         mvtnorm_1.1-3             fitdistrplus_1.1-11      
 [93] shinyjs_2.1.0             hms_1.1.3                 mime_0.12                 evaluate_0.21            
 [97] xtable_1.8-4              readxl_1.4.0              mclust_5.4.10             gridExtra_2.3            
[101] compiler_4.2.0            crayon_1.5.2              KernSmooth_2.23-20        R.oo_1.25.0              
[105] htmltools_0.5.5           tzdb_0.4.0                later_1.3.1               lubridate_1.8.0          
[109] DBI_1.1.3                 dbplyr_2.3.2              rappdirs_0.3.3            MASS_7.3-57              
[113] Matrix_1.5-4              car_3.0-13                cli_3.6.1                 R.methodsS3_1.8.2        
[117] parallel_4.2.0            igraph_1.5.0.1            pkgconfig_2.0.3           sp_2.0-0                 
[121] plotly_4.10.2             scuttle_1.6.2             spatstat.sparse_3.0-2     xml2_1.3.4               
[125] dqrng_0.3.0               XVector_0.38.0            rvest_1.0.2               digest_0.6.33            
[129] sctransform_0.3.5         RcppAnnoy_0.0.21          pracma_2.4.2              Biostrings_2.66.0        
[133] spatstat.data_3.0-1       fastmatch_1.1-3           cellranger_1.1.0          rmarkdown_2.23           
[137] leiden_0.4.3              uwot_0.1.16               edgeR_3.40.2              DelayedMatrixStats_1.20.0
[141] curl_5.0.1                Rsamtools_2.14.0          shiny_1.7.4.1             lifecycle_1.0.3          
[145] nlme_3.1-157              jsonlite_1.8.7            Rhdf5lib_1.20.0           carData_3.0-5            
[149] viridisLite_0.4.2         limma_3.54.2              fansi_1.0.4               pillar_1.9.0             
[153] lattice_0.20-45           fastmap_1.1.1             httr_1.4.6                survival_3.3-1           
[157] glue_1.6.2                png_0.1-8                 bit_4.0.5                 presto_1.0.0             
[161] stringi_1.7.12            HDF5Array_1.26.0          irlba_2.3.5.1             future.apply_1.11.0    

[yls2g13]

Touching base here as I haven't heard from Seurat in a while and I still have not solved this

[Gesmira]

Hi,
This should now be fixed in the newest release of Seurat (5.0.1). Please restart your session and reinstall.