Not able to convert loom to seurat

[millerkaplanlab]

Hello. I used velocyto to generate the loom file required to RNA Velocity using seurat wrappers. I am unable to convert the loom object to Seurat as shown in the tutorial. I get the following error. Any help would be appreciated.

P7loom <- as.Seurat(x = loom.data) | | 0%Error in validObject(.Object) : invalid class “LogMap” object: Duplicate rownames not allowed

[FlyingFa]

Similar problem, did you figure out ?

[jcy258]

Same problem!

[jwtobias]

Please add me to the list. Same function, same error.

[TaoBern]

same as me , does anyone solve it?

[hwick]

I am having the same issue

> ldat <- ReadVelocity(file = "../velocyto_out/merged_loom/all_merged.loom")
reading loom file via hdf5r...
> # Turn loom to seurat
> bm <- as.Seurat(x = ldat)
  |                                                                                                                  |   0%Error in validObject(.Object) : 
  invalid class “LogMap” object: Duplicate rownames not allowed

> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /n/app/openblas/0.3.19-gcc-9.2.0/lib/libopenblas_haswellp-r0.3.19.so;  LAPACK version 3.9.0

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       

time zone: US/Eastern
tzcode source: system (glibc)

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

other attached packages:
 [1] loomR_0.2.0           itertools_0.1-3       iterators_1.0.14      hdf5r_1.3.11         
 [5] R6_2.5.1              SeuratWrappers_0.3.5  SeuratDisk_0.0.0.9021 Seurat_5.1.0         
 [9] SeuratObject_5.0.2    sp_2.1-4              pcaMethods_1.96.0     Biobase_2.64.0       
[13] BiocGenerics_0.50.0   devtools_2.4.5        usethis_3.0.0        

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3     rstudioapi_0.16.0      jsonlite_1.8.8         magrittr_2.0.3        
  [5] spatstat.utils_3.0-5   fs_1.6.4               vctrs_0.6.5            ROCR_1.0-11           
  [9] memoise_2.0.1          spatstat.explore_3.3-1 htmltools_0.5.8.1      curl_5.2.1            
 [13] sctransform_0.4.1      parallelly_1.38.0      KernSmooth_2.23-22     htmlwidgets_1.6.4     
 [17] desc_1.4.3             ica_1.0-3              plyr_1.8.9             plotly_4.10.4         
 [21] zoo_1.8-12             cachem_1.1.0           igraph_2.0.3           mime_0.12             
 [25] lifecycle_1.0.4        pkgconfig_2.0.3        rsvd_1.0.5             Matrix_1.7-0          
 [29] fastmap_1.2.0          fitdistrplus_1.2-1     future_1.34.0          shiny_1.9.1           
 [33] digest_0.6.36          colorspace_2.1-1       patchwork_1.2.0        ps_1.7.7              
 [37] tensor_1.5             RSpectra_0.16-2        irlba_2.3.5.1          pkgload_1.4.0         
 [41] progressr_0.14.0       fansi_1.0.6            spatstat.sparse_3.1-0  mgcv_1.9-1            
 [45] httr_1.4.7             polyclip_1.10-7        abind_1.4-5            compiler_4.4.0        
 [49] remotes_2.5.0          withr_3.0.1            bit64_4.0.5            fastDummies_1.7.3     
 [53] pkgbuild_1.4.4         R.utils_2.12.3         MASS_7.3-60.2          sessioninfo_1.2.2     
 [57] tools_4.4.0            lmtest_0.9-40          httpuv_1.6.15          future.apply_1.11.2   
 [61] goftest_1.2-3          R.oo_1.26.0            glue_1.7.0             callr_3.7.6           
 [65] nlme_3.1-164           promises_1.3.0         grid_4.4.0             Rtsne_0.17            
 [69] cluster_2.1.6          reshape2_1.4.4         generics_0.1.3         gtable_0.3.5          
 [73] spatstat.data_3.1-2    R.methodsS3_1.8.2      tidyr_1.3.1            data.table_1.15.4     
 [77] utf8_1.2.4             spatstat.geom_3.3-2    RcppAnnoy_0.0.22       ggrepel_0.9.5         
 [81] RANN_2.6.1             pillar_1.9.0           stringr_1.5.1          spam_2.10-0           
 [85] RcppHNSW_0.6.0         later_1.3.2            splines_4.4.0          dplyr_1.1.4           
 [89] lattice_0.22-6         bit_4.0.5              survival_3.5-8         deldir_2.0-4          
 [93] tidyselect_1.2.1       miniUI_0.1.1.1         pbapply_1.7-2          gridExtra_2.3         
 [97] scattermore_1.2        matrixStats_1.3.0      stringi_1.8.4          lazyeval_0.2.2        
[101] codetools_0.2-20       tibble_3.2.1           BiocManager_1.30.23    cli_3.6.3             
[105] uwot_0.2.2             xtable_1.8-4           reticulate_1.38.0      munsell_0.5.1         
[109] processx_3.8.4         Rcpp_1.0.13            globals_0.16.3         spatstat.random_3.3-1 
[113] png_0.1-8              spatstat.univar_3.0-0  parallel_4.4.0         ellipsis_0.3.2        
[117] ggplot2_3.5.1          velocyto.R_0.6         dotCall64_1.1-1        profvis_0.3.8         
[121] urlchecker_1.0.1       listenv_0.9.1          viridisLite_0.4.2      scales_1.3.0          
[125] ggridges_0.5.6         crayon_1.5.3           leiden_0.4.3.1         purrr_1.0.2           
[129] rlang_1.1.4            cowplot_1.1.3  

[ivonyao]

same here