Seurat Object not closing when using SaveH5Seurat

[pshukla63]

Hello, I am trying to save my Seurat object and am getting this error:

Error in H5_close_any(self$id) : HDF5-API Errors:
    error #000: ../../../src/H5F.c in H5Fclose(): line 595: closing file ID failed
        class: HDF5
        major: File accessibility
        minor: Unable to close file

    error #001: ../../../src/H5Fint.c in H5F__close(): line 2113: decrementing file ID failed
        class: HDF5
        major: File accessibility
        minor: Unable to decrement reference count

    error #002: ../../../src/H5I.c in H5I_dec_app_ref(): line 1307: can't decrement ID ref count
        class: HDF5
        major: Object atom
        minor: Unable to decrement reference count

    error #003: ../../../src/H5Fint.c in H5F__close_cb(): line 2173: can't close file
        class: HDF5
        major: File accessibility
        minor: Unable to close file

    error #004: ../../../src/H5Fint.c in H5F_try_close(): line 2346: problems closing file
        class: HDF5
        major: File accessibility
        minor: Unable to close file

    error #005: ../../../src/H5Fint.c in H5F_

There is a .h5seurat object present in the folder. When I try to load this object I get this:

Error in self$read_low_level(file_space = self_space_id, mem_space = mem_space_id,  : 
  HDF5-API Errors:
    error #000: ../../../src/H5Dio.c in H5Dread(): line 198: can't read data
        class: HDF5
        major: Dataset
        minor: Read failed

    error #001: ../../../src/H5Dio.c in H5D__read(): line 599: can't read data
        class: HDF5
        major: Dataset
        minor: Read failed

    error #002: ../../../src/H5Dchunk.c in H5D__chunk_read(): line 2561: error looking up chunk address
        class: HDF5
        major: Dataset
        minor: Can't get value

    error #003: ../../../src/H5Dchunk.c in H5D__chunk_lookup(): line 3280: can't query chunk address
        class: HDF5
        major: Dataset
        minor: Can't get value

    error #004: ../../../src/H5Dbtree.c in H5D__btree_idx_get_addr(): line 1048: can't get chunk info
        class: HDF5
        major: Dataset
        minor: Can't get value

    error #005: ../../../src/H5B.c in H5B_find(): line 355: can't lookup key in subtree
        class: HDF5
        major: B-Tree node
        m

my Rstudio server session then crashes. This does NOT happen with all objects.

Thank you for your help!!

Session Info

R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 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/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
 [1] SeuratDisk_0.0.0.9020 lubridate_1.9.2       forcats_1.0.0         stringr_1.5.0         dplyr_1.1.3           purrr_1.0.2          
 [7] readr_2.1.4           tidyr_1.3.0           tibble_3.2.1          ggplot2_3.4.3         tidyverse_2.0.0       data.table_1.14.8    
[13] Seurat_4.3.0.1        SeuratObject_4.1.3    sp_2.0-0             

loaded via a namespace (and not attached):
  [1] deldir_1.0-9           pbapply_1.7-2          gridExtra_2.3          rlang_1.1.1            magrittr_2.0.3        
  [6] RcppAnnoy_0.0.21       spatstat.geom_3.2-5    matrixStats_1.0.0      ggridges_0.5.4         compiler_4.3.0        
 [11] png_0.1-8              vctrs_0.6.3            reshape2_1.4.4         hdf5r_1.3.8            crayon_1.5.2          
 [16] pkgconfig_2.0.3        fastmap_1.1.1          ellipsis_0.3.2         utf8_1.2.3             promises_1.2.1        
 [21] rmarkdown_2.25         tzdb_0.4.0             bit_4.0.5              xfun_0.40              jsonlite_1.8.7        
 [26] goftest_1.2-3          later_1.3.1            spatstat.utils_3.0-3   irlba_2.3.5.1          parallel_4.3.0        
 [31] cluster_2.1.4          R6_2.5.1               ica_1.0-3              stringi_1.7.12         RColorBrewer_1.1-3    
 [36] spatstat.data_3.0-1    reticulate_1.32.0      parallelly_1.36.0      lmtest_0.9-40          scattermore_1.2       
 [41] Rcpp_1.0.11            knitr_1.44             tensor_1.5             future.apply_1.11.0    zoo_1.8-12            
 [46] sctransform_0.4.0      timechange_0.2.0       httpuv_1.6.11          Matrix_1.6-1.1         splines_4.3.0         
 [51] igraph_1.5.1           tidyselect_1.2.0       rstudioapi_0.15.0      abind_1.4-5            yaml_2.3.7            
 [56] spatstat.random_3.1-6  codetools_0.2-19       miniUI_0.1.1.1         spatstat.explore_3.2-3 listenv_0.9.0         
 [61] lattice_0.21-8         plyr_1.8.8             withr_2.5.0            shiny_1.7.5            ROCR_1.0-11           
 [66] evaluate_0.21          Rtsne_0.16             future_1.33.0          survival_3.5-5         polyclip_1.10-4       
 [71] fitdistrplus_1.1-11    pillar_1.9.0           KernSmooth_2.23-20     plotly_4.10.2          generics_0.1.3        
 [76] hms_1.1.3              munsell_0.5.0          scales_1.2.1           globals_0.16.2         xtable_1.8-4          
 [81] glue_1.6.2             lazyeval_0.2.2         tools_4.3.0            RANN_2.6.1             leiden_0.4.3          
 [86] cowplot_1.1.1          grid_4.3.0             colorspace_2.1-0       nlme_3.1-162           patchwork_1.1.3       
 [91] cli_3.6.1              spatstat.sparse_3.0-2  fansi_1.0.4            viridisLite_0.4.2      uwot_0.1.16           
 [96] gtable_0.3.4           digest_0.6.33          progressr_0.14.0       ggrepel_0.9.3          htmlwidgets_1.6.2     
[101] htmltools_0.5.6        lifecycle_1.0.3        httr_1.4.7             mime_0.12              bit64_4.0.5           
[106] MASS_7.3-59    

[viktorzou]

I have the same issue...