Unable to open HDF5 file

Question

[Christopher]

Hello,

I was wondering if someone could help me:

I am trying to open my raw_feature_bc_matrix for a sample by using Read10x_h5. I have been able to do this for the raw feature matrices for my other three scRNA-Seq samples but I keep encountering this error message.

Error in H5File.open(filename, mode, file_create_pl, file_access_pl) :
HDF5-API Errors:
error #000: ../../src/H5F.c in H5Fopen(): line 620: unable to open file
class: HDF5
major: File accessibility
minor: Unable to open file

error #001: ../../src/H5VLcallback.c in H5VL_file_open(): line 3501: failed to iterate over available VOL connector plugins
    class: HDF5
    major: Virtual Object Layer
    minor: Iteration failed

error #002: ../../src/H5PLpath.c in H5PL__path_table_iterate(): line 578: can't iterate over plugins in plugin path '(null)'
    class: HDF5
    major: Plugin for dynamically loaded library
    minor: Iteration failed

error #003: ../../src/H5PLpath.c in H5PL__path_table_iterate_process_path(): line 712: can't open directory
    class: HDF5
    major: Plugin for dynamically loaded library
    minor: Can't open directory or file

error #004: ../../src/H5VLcallback.c in H5VL__file_open(): line 3351: open failed
    class: HDF5
    major: Virtu

I have checked that the path to the file exists (which it does) and have checked my working directory (as similar errors have mentioned that it may mean the WD has changed). The HDF5 file is not open in another R session etc.

Any advice would be appreciated!

Chris

[bk11]

Could you show us what command you used to read file here? I m not sure but the problem could be associated with hdf5r and HDF5. You could consider reinstalling hdf5r. Also make sure that following code runs TRUE for you.

file.exists("/path_to_your_.h5_file/your_file.h5")