Converting the data from Seurat to Anndata

[TakuroIwami]

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"

[eva-artano]

Hello,
I have the same error as you. Did you find a solution?

Best,
EA

[yuanG2000]

Hello, I got the same error, did you find a solution? thx a lot

[TakuroIwami]

Hi, I apologize for not noticing your questions earlier. I was able to run the command successfully by switching from the V5 assay to the V3 assay, using the following script. I hope this helps!

sample1[["RNA3"]] <- as(object = sample1[["RNA"]], Class = "Assay")
  DefaultAssay(sample1) <- "RNA3"
  sample1[["RNA"]] <- NULL
 sample1 <- RenameAssays(sample1, RNA3 = 'RNA')
  save_file <- paste0("sample1.h5Seurat")
  SaveH5Seurat(sample1, filename = save_file)
  Convert(save_file, dest = "h5ad")

[yuanG2000]

Hi, I apologize for not noticing your questions earlier. I was able to run the command successfully by switching from the V5 assay to the V3 assay, using the following script. I hope this helps!

sample1[["RNA3"]] <- as(object = sample1[["RNA"]], Class = "Assay")
  DefaultAssay(sample1) <- "RNA3"
  sample1[["RNA"]] <- NULL
 sample1 <- RenameAssays(sample1, RNA3 = 'RNA')
  save_file <- paste0("sample1.h5Seurat")
  SaveH5Seurat(sample1, filename = save_file)
  Convert(save_file, dest = "h5ad")

I work out！thank you very much！