multiple HDF5-API errors when trying to use Convert

[dm8000]

Hello

I have been trying to convert a h5ad file to a Seurat object.

This is the error log

> Convert("adipocytes_integrated_mapped.h5ad", dest = "h5seurat", overwrite = FALSE)
Warning: Unknown file type: h5ad
Warning: 'assay' not set, setting to 'RNA'
Creating h5Seurat file for version 3.1.5.9900
Adding X as data
Adding raw/X as counts
Adding meta.features from raw/var
Error in dfile$obj_copy_from(src_loc = source, src_name = "obs", dst_name = "meta.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 317: unable to copy object
        class: HDF5
        major: Object header
        minor: Unable to copy object

    error #002: ../../../src/H5Ocopy.c in H5O__copy_obj(): line 1221: unable to copy object
        class: HDF5
        major: Object header
        minor: Unable to copy object

    error #003: ../../../src/H5Ocopy.c in H5O__copy_header(): line 1165: unable to copy object
        class: HDF5
        major: Object header
        minor: Unable to copy object

    error #004: ../../../src/H5Ocopy.c in H5O__copy_header_real(): line 872: unable to perform 'post copy' operation on message
        class: HDF5
        major: Object header
        minor: Unable to initialize object

    error #005: ../../../src/H5Ostab.c in H5O
Error in private$closeFun(id) : HDF5-API Errors:
    error #000: ../../../src/H5F.c in H5Fclose(): line 668: closing file ID failed
        class: HDF5
        major: File accessibilty
        minor: Unable to close file

    error #001: ../../../src/H5Fint.c in H5F__close(): line 2047: decrementing file ID failed
        class: HDF5
        major: File accessibilty
        minor: Unable to decrement reference count

    error #002: ../../../src/H5I.c in H5I_dec_app_ref(): line 1309: 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 2105: can't close file
        class: HDF5
        major: File accessibilty
        minor: Unable to close file

    error #004: ../../../src/H5Fint.c in H5F_try_close(): line 2276: problems closing file
        class: HDF5
        major: File accessibilty
        minor: Unable to close file

    error #005: ../../../src/H5Fint.c in H5F__de

This occurs when I try to read the object.

> adipoint <- LoadH5Seurat("adipocytes_integrated_mapped.h5seurat")
Validating h5Seurat file
Error: Cannot find dataset with cell names

And this is what the file I am trying to convert looks like

AnnData object with n_obs × n_vars = 86575 × 3000
    obs: 'orig.ident', 'nCount_RNA', 'nFeature_RNA', 'percent.mt', 'timpoint', 'condition', 'timpoint.condition', 'CellTypeRefined', 'CellTypeRefined.Rajbhandari', 'Sample.type', 'Treatment', 'Author', 'n_genes_by_counts', 'total_counts', 'total_counts_mt', 'pct_counts_mt', 'total_counts_rp', 'pct_counts_rp', 'batch', 'n_genes', 'doublet_scores', 'predicted_doublets', 'doublet_info', '_scvi_batch', '_scvi_labels', '_scvi_local_l_mean', '_scvi_local_l_var', 'leiden_0.1', 'leiden_0.2', 'leiden_0.3', 'leiden_0.4', 'leiden_0.6', 'leiden_0.8', 'leiden_0.9', 'leiden_1'
    var: 'features', 'mt', 'rp', 'n_cells', 'n_cells_by_counts-0', 'mean_counts-0', 'pct_dropout_by_counts-0', 'total_counts-0', 'n_cells_by_counts-0-1', 'mean_counts-0-1', 'pct_dropout_by_counts-0-1', 'total_counts-0-1', 'n_cells_by_counts-1-1', 'mean_counts-1-1', 'pct_dropout_by_counts-1-1', 'total_counts-1-1', 'n_cells_by_counts-2-1', 'mean_counts-2-1', 'pct_dropout_by_counts-2-1', 'total_counts-2-1', 'n_cells_by_counts-3-1', 'mean_counts-3-1', 'pct_dropout_by_counts-3-1', 'total_counts-3-1', 'n_cells_by_counts-4-1', 'mean_counts-4-1', 'pct_dropout_by_counts-4-1', 'total_counts-4-1', 'n_cells_by_counts-5-1', 'mean_counts-5-1', 'pct_dropout_by_counts-5-1', 'total_counts-5-1', 'n_cells_by_counts-6-1', 'mean_counts-6-1', 'pct_dropout_by_counts-6-1', 'total_counts-6-1', 'n_cells_by_counts-7-1', 'mean_counts-7-1', 'pct_dropout_by_counts-7-1', 'total_counts-7-1', 'n_cells_by_counts-8-1', 'mean_counts-8-1', 'pct_dropout_by_counts-8-1', 'total_counts-8-1', 'n_cells_by_counts-9-1', 'mean_counts-9-1', 'pct_dropout_by_counts-9-1', 'total_counts-9-1', 'n_cells_by_counts-0-2', 'mean_counts-0-2', 'pct_dropout_by_counts-0-2', 'total_counts-0-2', 'n_cells_by_counts-1-2', 'mean_counts-1-2', 'pct_dropout_by_counts-1-2', 'total_counts-1-2', 'n_cells_by_counts-2-2', 'mean_counts-2-2', 'pct_dropout_by_counts-2-2', 'total_counts-2-2', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'highly_variable_nbatches', 'highly_variable_intersection'
    uns: '_scvi', 'hvg', 'leiden', 'neighbors', 'pca', 'umap', 'Author_colors', 'leiden_0.1_colors', 'leiden_0.2_colors', 'leiden_0.3_colors', 'leiden_0.4_colors', 'leiden_0.6_colors', 'leiden_0.8_colors', 'leiden_0.9_colors', 'leiden_1_colors'
    obsm: 'X_pca', 'X_scVI', 'X_umap'
    varm: 'PCs'
    layers: 'counts'
    obsp: 'connectivities', 'distances'