Error in converting h5ad to h5Seurat Error: (converted from warning) Unknown file type: h5ad

[Sophia409]

Hi,

Thanks for developing this great tool.

I'm running into an error in Convert() step, stated that: Error: (converted from warning) Unknown file type: h5ad'.

My data was downloaded from the tutorial you provide.

Many thanks.

Regards, Sophia

url <- "https://seurat.nygenome.org/pbmc3k_final.h5ad"
curl::curl_download(url, basename(url))
Convert("pbmc3k_final.h5ad", dest = "h5seurat", overwrite = TRUE)
Error: (converted from warning) Unknown file type: h5ad

> sessionInfo()
R version 4.2.3 (2023-03-15 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8  LC_CTYPE=Chinese (Simplified)_China.utf8    LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

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

other attached packages:
 [1] SeuratDisk_0.0.0.9020     readr_2.1.4               ComplexHeatmap_2.15.4     RColorBrewer_1.1-3        Hmisc_5.1-0               corrplot_0.92            
 [7] circlize_0.4.15           scales_1.2.1              datapasta_3.1.0           cowplot_1.1.1             dplyr_1.1.2               patchwork_1.1.2          
[13] ggplot2_3.4.2             stxBrain.SeuratData_0.1.1 SeuratData_0.2.2.9001     Seurat_4.9.9.9045         SeuratObject_4.9.9.9084   sp_1.6-0                 

loaded via a namespace (and not attached):
  [1] utf8_1.2.3                  spatstat.explore_3.2-1      reticulate_1.28             tidyselect_1.2.0            htmlwidgets_1.6.2           Rtsne_0.16                 
  [7] munsell_0.5.0               ragg_1.2.5                  codetools_0.2-19            ica_1.0-3                   future_1.32.0               miniUI_0.1.1.1             
 [13] withr_2.5.0                 spatstat.random_3.1-5       colorspace_2.1-0            progressr_0.13.0            Biobase_2.58.0              knitr_1.43                 
 [19] rstudioapi_0.14             stats4_4.2.3                ROCR_1.0-11                 tensor_1.5                  listenv_0.9.0               MatrixGenerics_1.10.0      
 [25] labeling_0.4.2              GenomeInfoDbData_1.2.9      polyclip_1.10-4             bit64_4.0.5                 farver_2.1.1                parallelly_1.36.0          
 [31] vctrs_0.6.2                 generics_0.1.3              xfun_0.39                   R6_2.5.1                    doParallel_1.0.17           GenomeInfoDb_1.34.9        
 [37] clue_0.3-64                 hdf5r_1.3.8                 bitops_1.0-7                spatstat.utils_3.0-3        DelayedArray_0.24.0         vroom_1.6.3                
 [43] promises_1.2.0.1            nnet_7.3-19                 gtable_0.3.3                globals_0.16.2              goftest_1.2-3               spam_2.9-1                 
 [49] rlang_1.1.1                 systemfonts_1.0.4           GlobalOptions_0.1.2         splines_4.2.3               lazyeval_0.2.2              spatstat.geom_3.2-1        
 [55] checkmate_2.2.0             reshape2_1.4.4              abind_1.4-5                 backports_1.4.1             httpuv_1.6.11               tools_4.2.3                
 [61] ellipsis_0.3.2              BiocGenerics_0.44.0         ggridges_0.5.4              Rcpp_1.0.10                 plyr_1.8.8                  base64enc_0.1-3            
 [67] sparseMatrixStats_1.10.0    zlibbioc_1.44.0             purrr_1.0.1                 RCurl_1.98-1.12             rpart_4.1.19                deldir_1.0-9               
 [73] pbapply_1.7-0               GetoptLong_1.0.5            viridis_0.6.3               S4Vectors_0.36.2            zoo_1.8-12                  SummarizedExperiment_1.28.0
 [79] ggrepel_0.9.3               cluster_2.1.4               magrittr_2.0.3              data.table_1.14.8           RSpectra_0.16-1             glmGamPoi_1.10.2           
 [85] scattermore_1.1             openxlsx_4.2.5.2            lmtest_0.9-40               RANN_2.6.1                  fitdistrplus_1.1-11         matrixStats_0.63.0         
 [91] hms_1.1.3                   evaluate_0.21               mime_0.12                   xtable_1.8-4                fastDummies_1.6.3           IRanges_2.32.0             
 [97] gridExtra_2.3               shape_1.4.6                 compiler_4.2.3              tibble_3.2.1                KernSmooth_2.23-21          crayon_1.5.2               
[103] htmltools_0.5.5             tzdb_0.4.0                  later_1.3.1                 Formula_1.2-5               tidyr_1.3.0                 MASS_7.3-60                
[109] rappdirs_0.3.3              Matrix_1.5-4.1              cli_3.6.1                   parallel_4.2.3              dotCall64_1.0-2             igraph_1.4.3               
[115] GenomicRanges_1.50.2        pkgconfig_2.0.3             foreign_0.8-84              plotly_4.10.2               spatstat.sparse_3.0-1       foreach_1.5.2              
[121] XVector_0.38.0              stringr_1.5.0               digest_0.6.31               sctransform_0.3.5           RcppAnnoy_0.0.20            spatstat.data_3.0-1        
[127] rmarkdown_2.22              leiden_0.4.3                htmlTable_2.4.1             dendextend_1.17.1           uwot_0.1.14                 DelayedMatrixStats_1.20.0  
[133] curl_5.0.0                  shiny_1.7.4                 rjson_0.2.21                lifecycle_1.0.3             nlme_3.1-162                jsonlite_1.8.4             
[139] viridisLite_0.4.2           fansi_1.0.4                 pillar_1.9.0                lattice_0.21-8              fastmap_1.1.1               httr_1.4.6                 
[145] survival_3.5-5              glue_1.6.2                  zip_2.3.0                   png_0.1-8                   iterators_1.0.14            bit_4.0.5                  
[151] stringi_1.7.12              textshaping_0.3.6           RcppHNSW_0.4.1              irlba_2.3.5.1               future.apply_1.11.0      

[anglixue]

Did you load all the required libraries?

library(Seurat)
library(SeuratData)
library(SeuratDisk)