Converting the data from Seurat to Anndata

Hi, thank you for providing with us a great package. I have been analyzing snRNA-seq data using Seurat, and now need to convert the data to Anndata format for the downstream analysis. I tried to replicate the codes described in the article "Converting from Seurat to AnnData via h5Seurat", resulting in getting the error below. I would appreciate your comments based on the attached code and errors. Thank you.

Takuro

R library(Seurat) library(SeuratData) library(SeuratDisk) library(reticulate) anndata <- import("anndata")

sample1 <- readRDS("${dir}/obj1_v2.rds")

sample1 An object of class Seurat 23255 features across 6163 samples within 1 assay Active assay: RNA (23255 features, 2000 variable features) 3 layers present: counts, data, scale.data 2 dimensional reductions calculated: pca, umap

SaveH5Seurat(sample1, filename = "sample1.h5Seurat") "Creating h5Seurat file for version 3.1.5.9900 Adding cell embeddings for pca Adding loadings for pca No projected loadings for pca Adding standard deviations for pca No JackStraw data for pca Adding cell embeddings for umap No loadings for umap No projected loadings for umap No standard deviations for umap No JackStraw data for umap" Convert("sample1.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: H5Ocopy.c in H5Ocopy(): line 247: source object not found class: HDF5 major: Symbol table minor: Object not found

error #001: H5Gloc.c in H5G_loc_find(): line 428: can't find object
    class: HDF5
    major: Symbol table
    minor: Object not found

error #002: H5Gtraverse.c in H5G_traverse(): line 867: internal path traversal failed
    class: HDF5
    major: Symbol table
    minor: Object not found

error #003: H5Gtraverse.c in H5G_traverse_real(): line 639: traversal operator failed
    class: HDF5
    major: Symbol table
    minor: Callback failed

error #004: H5Gloc.c in H5G_loc_find_cb(): line 383: object 'data' doesn't exist
    class: HDF5
    major: Symbol table
    minor: Object not found"

mojaveazure / seurat-disk

Converting the data from Seurat to Anndata #184