Error: Unknown file type: h5seurat

[aodainic7]

Hey everyone,
I am trying to convert Seurat to AnnData via h5Seurat following this guide https://mojaveazure.github.io/seurat-disk/articles/convert-anndata.html. My Object has 3 assays (RNA, ADT and SCT) and multiple reductions. Unfortunately, I have two issues:

1. While saving the h5Seurat I get Error in if (ncol(x = x[[]])) { : argument is of length zero
   SeuratDisk::SaveH5Seurat(CD8_adt.harmony_sct_WNN, filename = "CD8_adt.harmony_sct_WNN.h5Seurat", overwrite = T, verbose = T)
   Although the error comes up, I still get a h5Seurat file saved.
2. The Convert function does not recognize h5Seurat and will give the following error:

SeuratDisk::Convert("CD8_adt.harmony_sct_WNN.h5Seurat", dest = "h5ad")
Validating h5Seurat file
Warning: Cannot find dataset with cell namesWarning: 'assay' not set, setting to 'RNA'Error: Unknown file type: h5seurat

I have tried to save the object both as "h5seurat" and "h5Seurat" without success.
Thanks in advance!

> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

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       

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

other attached packages:
 [1] SeuratDisk_0.0.0.9020   pbmc3k.SeuratData_3.1.4 cbmc.SeuratData_3.1.4   SeuratData_0.2.2        rstatix_0.7.2          
 [6] gt_0.10.0               limma_3.54.2            tidygate_0.4.9          progressr_0.14.0        RColorBrewer_1.1-3     
[11] gitlabr_2.0.1.9000      harmony_1.1.0           Rcpp_1.0.11             glmGamPoi_1.10.2        tidyseurat_0.7.4       
[16] ttservice_0.3.8         patchwork_1.1.3         Seurat_4.4.0            lubridate_1.9.3         forcats_1.0.0          
[21] stringr_1.5.0           dplyr_1.1.3             purrr_1.0.2             readr_2.1.4             tidyr_1.3.0            
[26] tibble_3.2.1            ggplot2_3.4.4           tidyverse_2.0.0         SeuratObject_4.9.9.9091 sp_2.1-1               

loaded via a namespace (and not attached):
  [1] utf8_1.2.4                  spatstat.explore_3.2-5      reticulate_1.34.0           tidyselect_1.2.0           
  [5] htmlwidgets_1.6.2           grid_4.2.1                  BiocParallel_1.32.6         Rtsne_0.16                 
  [9] munsell_0.5.0               ScaledMatrix_1.6.0          preprocessCore_1.60.2       codetools_0.2-18           
 [13] ica_1.0-3                   future_1.33.0               miniUI_0.1.1.1              withr_2.5.1                
 [17] spatstat.random_3.2-1       colorspace_2.1-0            Biobase_2.58.0              knitr_1.44                 
 [21] rstudioapi_0.15.0           stats4_4.2.1                SingleCellExperiment_1.20.1 ROCR_1.0-11                
 [25] tensor_1.5                  listenv_0.9.0               MatrixGenerics_1.10.0       GenomeInfoDbData_1.2.9     
 [29] polyclip_1.10-6             bit64_4.0.5                 rprojroot_2.0.3             parallelly_1.36.0          
 [33] vctrs_0.6.4                 generics_0.1.3              xfun_0.40                   timechange_0.2.0           
 [37] R6_2.5.1                    GenomeInfoDb_1.34.9         ggbeeswarm_0.7.2            rsvd_1.0.5                 
 [41] hdf5r_1.3.8                 cachem_1.0.8                bitops_1.0-7                spatstat.utils_3.0-4       
 [45] DelayedArray_0.24.0         promises_1.2.1              scales_1.2.1                beeswarm_0.4.0             
 [49] gtable_0.3.4                beachmat_2.14.2             globals_0.16.2              processx_3.8.2             
 [53] goftest_1.2-3               spam_2.10-0                 tidybulk_1.10.1             rlang_1.1.1                
 [57] splines_4.2.1               lazyeval_0.2.2              spatstat.geom_3.2-7         broom_1.0.5                
 [61] yaml_2.3.7                  reshape2_1.4.4              abind_1.4-5                 backports_1.4.1            
 [65] httpuv_1.6.12               tools_4.2.1                 ellipsis_0.3.2              jquerylib_0.1.4            
 [69] BiocGenerics_0.44.0         ggridges_0.5.4              plyr_1.8.9                  base64enc_0.1-3            
 [73] sparseMatrixStats_1.10.0    zlibbioc_1.44.0             RCurl_1.98-1.12             prettyunits_1.1.1          
 [77] ps_1.7.5                    deldir_1.0-9                pbapply_1.7-2               viridis_0.6.4              
 [81] cowplot_1.1.1               S4Vectors_0.36.2            zoo_1.8-12                  SummarizedExperiment_1.28.0
 [85] ggrepel_0.9.4               cluster_2.1.3               magrittr_2.0.3              data.table_1.14.8          
 [89] scattermore_1.2             lmtest_0.9-40               RANN_2.6.1                  fitdistrplus_1.1-11        
 [93] matrixStats_1.0.0           evaluate_0.22               hms_1.1.3                   mime_0.12                  
 [97] xtable_1.8-4                IRanges_2.32.0              gridExtra_2.3               compiler_4.2.1             
[101] scater_1.26.1               crayon_1.5.2                KernSmooth_2.23-20          htmltools_0.5.6.1          
[105] later_1.3.1                 tzdb_0.4.0                  rappdirs_0.3.3              MASS_7.3-57                
[109] Matrix_1.5-3                car_3.1-2                   cli_3.6.1                   parallel_4.2.1             
[113] dotCall64_1.1-0             igraph_1.5.1                arpr_0.1.2                  GenomicRanges_1.50.2       
[117] pkgconfig_2.0.3             job_0.3.0                   plotly_4.10.3               scuttle_1.8.4              
[121] spatstat.sparse_3.0-3       xml2_1.3.5                  bslib_0.5.1                 vipor_0.4.5                
[125] XVector_0.38.0              callr_3.7.3                 digest_0.6.33               sctransform_0.4.1          
[129] RcppAnnoy_0.0.21            spatstat.data_3.0-3         rmarkdown_2.25              leiden_0.4.3               
[133] uwot_0.1.16                 DelayedMatrixStats_1.20.0   curl_5.1.0                  shiny_1.7.5.1              
[137] lifecycle_1.0.3             nlme_3.1-157                jsonlite_1.8.7              carData_3.0-5              
[141] BiocNeighbors_1.16.0        desc_1.4.2                  viridisLite_0.4.2           fansi_1.0.5                
[145] pillar_1.9.0                lattice_0.20-45             pkgbuild_1.4.2              ggrastr_1.0.2              
[149] fastmap_1.1.1               httr_1.4.7                  survival_3.3-1              remotes_2.4.2.1            
[153] glue_1.6.2                  png_0.1-8                   bit_4.0.5                   sass_0.4.7                 
[157] stringi_1.7.12              BiocSingular_1.14.0         irlba_2.3.5.1               future.apply_1.11.0 

[Rohit-Satyam]

I am also getting the same error

[Rohit-Satyam]

Okay this is weird. When I run FindVariableFeatures the error Error in guess_dtype(x = x, ...) : unknown type disappears

ring.mca<-mca[,c(mca$STAGE_HR == "ring" & mca$singleR %in% c("2hpi","4hpi") )] %>% NormalizeData()%>% FindVariableFeatures( selection.method = "vst", nfeatures = 2000)
SaveH5Seurat(ring.mca, filename = "ring.h5Seurat",verbose = TRUE, overwrite = TRUE)
Warning: Overwriting previous file ring.h5Seurat
Creating h5Seurat file for version 3.1.5.9900

But then a new error emerges when I run Convert("ring.h5Seurat", dest = "h5ad")

> Convert("ring.h5Seurat", dest = "h5ad")
Validating h5Seurat file
Adding data from RNA as X
Error in assay.group$obj_copy_to(dst_loc = dfile, dst_name = "X", src_name = x.data) : 
  HDF5-API Errors:
    error #000: ../../../src/H5Ocopy.c in H5Ocopy(): line 233: unable to copy object
        class: HDF5
        major: Object header
        minor: Unable to copy object

    error #001: ../../../src/H5Ocopy.c in H5O__copy(): line 289: source object not found
        class: HDF5
        major: Symbol table
        minor: Object not found

    error #002: ../../../src/H5Gloc.c in H5G_loc_find(): line 422: can't find object
        class: HDF5
        major: Symbol table
        minor: Object not found

    error #003: ../../../src/H5Gtraverse.c in H5G_traverse(): line 851: internal path traversal failed
        class: HDF5
        major: Symbol table
        minor: Object not found

    error #004: ../../../src/H5Gtraverse.c in H5G__traverse_real(): line 627: traversal operator failed
        class: HDF5
        major: Symbol table
        minor: Callback failed

    error #005: ../../../src/H5Gloc.c in H5G__loc_find_cb(): line 378: object 'data' doesn't exist

[Rohit-Satyam]

Hi @mojaveazure, I was wondering if you guys looked into this behavior of the package?

Edit1: I even tried UpdateSeuratObject function to update my Seurat object as per latest recommendation but the error persists.

>SaveH5Seurat(ring.mca, filename = "ring.h5seurat", overwrite = TRUE, verbose = TRUE)
Creating h5Seurat file for version 3.1.5.9900
Error in guess_dtype(x = x, ...) : unknown type
> Convert("ring.h5seurat", dest = "h5ad", overwrite = TRUE)
Validating h5Seurat file
Warning: Cannot find dataset with cell names
Warning: 'assay' not set, setting to 'RNA'
Error: Unknown file type: h5seurat

[chloesavignac]

@Rohit-Satyam I faced the same problem. Downgrading Seurat and SeuratObject to v4 solved the issue for me.

[greensii]

I have this same problem when trying to convert a (source) h5Seurat file to a (dest) h5ad file.
Looking at the source code, I think it might stem from the Convert function calling the Convert.H5File method when it should be calling Convert.h5Seurat ?
the error message

stop("Unknown file type: ", stype, call. = FALSE)

only exists in Convert.H5File

[emidalla]

Downgrading Seurat and SeuratObject to v4 solved the issue for me.

Thank you very much @chloesavignac downgrading fixed the issue for me