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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$obj_copy_from(src_loc = source, src_name = "obs", dst_name = "meta.data") :
HDF5-API Errors:
error #000: ../../src/hdf5-1.12.2/src/H5Ocopy.c in H5Ocopy(): line 240: unable to copy object
class: HDF5
major: Object header
minor: Unable to copy object
error #001: ../../src/hdf5-1.12.2/src/H5VLcallback.c in H5VL_object_copy(): line 5495: object copy failed
class: HDF5
major: Virtual Object Layer
minor: Unable to copy object
error #002: ../../src/hdf5-1.12.2/src/H5VLcallback.c in H5VL__object_copy(): line 5456: object copy failed
class: HDF5
major: Virtual Object Layer
minor: Unable to copy object
error #003: ../../src/hdf5-1.12.2/src/H5VLnative_object.c in H5VL__native_object_copy(): line 125: unable to copy object
class: HDF5
major: Object header
minor: Unable to copy object
error #004: ../../src/hdf5-1.12.2/src/H5Ocopy.c in H5O__copy(): line 301: unable to copy object
class: HDF5
major: Object header
minor: Unab
Error in private$closeFun(id) : HDF5-API Errors:
error #000: ../../src/hdf5-1.12.2/src/H5F.c in H5Fclose(): line 711: decrementing file ID failed
class: HDF5
major: File accessibility
minor: Unable to close file
error #001: ../../src/hdf5-1.12.2/src/H5Iint.c in H5I_dec_app_ref(): line 1018: can't decrement ID ref count
class: HDF5
major: Object atom
minor: Unable to decrement reference count
error #002: ../../src/hdf5-1.12.2/src/H5Fint.c in H5F__close_cb(): line 251: unable to close file
class: HDF5
major: File accessibility
minor: Unable to close file
error #003: ../../src/hdf5-1.12.2/src/H5VLcallback.c in H5VL_file_close(): line 3983: file close failed
class: HDF5
major: Virtual Object Layer
minor: Unable to close file
error #004: ../../src/hdf5-1.12.2/src/H5VLcallback.c in H5VL__file_close(): line 3952: file close failed
class: HDF5
major: Virtual Object Layer
min
A h5seurat file is produced despite the errors, and when I ran this:
library(rhdf5)
h5ls("~/Desktop/GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5seurat")
I got a table with the following column names: group, name, otype, dclass, and dim. The table has 57 rows.
I haven't worked with this file format before, so I am unsure if this is what I am supposed to see or if the errors are causing issues.
Has anyone worked with this specific file before, or does anyone have an idea as to why these errors are occurring?
Thank you so much for taking the time to read through this!
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Hi, I'm trying to use R to work with snRNAseq data in the GTEx portal found at this link: https://www.gtexportal.org/home/downloads/adult-gtex/single_cell
The file is called GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad
When I run this code in R:
library(Seurat)
library(SeuratData)
library(SeuratDisk)
Convert("
/Desktop/GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad", dest = "h5seurat", overwrite = TRUE)/Desktop/GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5seurat")sc <- LoadH5Seurat("
I get the following errors:
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$obj_copy_from(src_loc = source, src_name = "obs", dst_name = "meta.data") :
HDF5-API Errors:
error #000: ../../src/hdf5-1.12.2/src/H5Ocopy.c in H5Ocopy(): line 240: unable to copy object
class: HDF5
major: Object header
minor: Unable to copy object
Error in private$closeFun(id) : HDF5-API Errors:
error #000: ../../src/hdf5-1.12.2/src/H5F.c in H5Fclose(): line 711: decrementing file ID failed
class: HDF5
major: File accessibility
minor: Unable to close file
A h5seurat file is produced despite the errors, and when I ran this:
library(rhdf5)
h5ls("~/Desktop/GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5seurat")
I got a table with the following column names: group, name, otype, dclass, and dim. The table has 57 rows.
I haven't worked with this file format before, so I am unsure if this is what I am supposed to see or if the errors are causing issues.
Has anyone worked with this specific file before, or does anyone have an idea as to why these errors are occurring?
Thank you so much for taking the time to read through this!
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