KeyError: "Unable to open object (unable to open external file, external link file name = 'ag1000g.phase1.ar3.3L.h5

1

Hello,
I met this error to open a h5df file:

Traceback (most recent call last):
File “”, line 1, in
File “h5py/_objects.pyx”, line 54, in h5py._objects.with_phil.wrapper
File “h5py/_objects.pyx”, line 55, in h5py._objects.with_phil.wrapper
File “/home/yifang/miniconda3/envs/allel/lib/python3.12/site-packages/h5py/_hl/group.py”, line 357, in getitem
oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “h5py/_objects.pyx”, line 54, in h5py._objects.with_phil.wrapper
File “h5py/_objects.pyx”, line 55, in h5py._objects.with_phil.wrapper
File “h5py/h5o.pyx”, line 241, in h5py.h5o.open
KeyError: “Unable to open object (unable to open external file, external link file name = ‘ag1000g.phase1.ar3.3L.h5’)”
I’m using h5py version 3.11.0 under conda environment.
The file was downloaded from a bioinformatic pkg demo. The problem seems with the H5DF format that sounds complicated to me. Can anyone give me any clue? Thanks!

2

It looks to be trying to open an external link, which is a link to a separate HDF5 file, and it can’t find the file. The file name it’s looking for is “ag1000g.phase1.ar3.3L.h5”. You can either try to find the external file then download it and put it in the right directory, modify your python code to avoid trying to open it (or be resilient to a failure), or delete the link from the HDF5 file.

Thanks