Firstly, I’d like to apologize if I have broken any rules since this is the first time I ask a question in this forum.

So I wanted to add medaka in my Pipeline in order to polish some genome assemblies, but after installing Medaka in my Conda environment and trying to input any command, it raises the same error:

Traceback (most recent call last):
  File "/home/gilmarro/.conda/envs/Medaka/bin/medaka", line 7, in <module>
    from medaka.medaka import main
  File "/home/gilmarro/.conda/envs/Medaka/lib/python3.10/site-packages/medaka/medaka.py", line 8, in <module>
    import medaka.datastore
  File "/home/gilmarro/.conda/envs/Medaka/lib/python3.10/site-packages/medaka/datastore.py", line 20, in <module>
    import h5py
  File "/home/gilmarro/.conda/envs/Medaka/lib/python3.10/site-packages/h5py/__init__.py", line 25, in <module>
    from . import _errors
  File "h5py/_errors.pyx", line 1, in init h5py._errors
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

I’ve looked on the issues site on Github to see if anyone else encountered this problem, but to my surprise nobody had this issue. I also tried installing previous versions of Medaka, installing Medaka in a separate conda environment, downgraded numpy 1.26.4 to any other previous versions… I expected that it would get fixed since I’ve found other people solving this issue by changing the package versions, but it still raises the same error.

¿Has anyone else encountered this issue? Any help is appreciated!