Open geboro opened 2 years ago
I am having the same issue!
(dvf) delaney@ada:~/software/DeepVirFinder$ ls dvf.py encode.py licence.md models README.md supplementary_tables test train_example training.py (dvf) delaney@ada:~/software/DeepVirFinder$ python dvf.py -i ./test/crAssphage.fa -o ./test/ -l 300 Using Theano backend. WARNING (theano.configdefaults): install mkl with
conda install mkl-service`: No module named 'mkl'
I also have the same issue, I am trying to install the packages in different orders but with no actual rationale behind. It should be due to issues with dependencies: https://stackoverflow.com/questions/53740577/does-any-one-got-attributeerror-str-object-has-no-attribute-decode-whi
I solved it with the following:
conda activate dvf pip3 uninstall keras pip3 uninstall tensorflow pip3 uninstall h5py
pip3 install 'h5py==2.10.0' --force-reinstall pip3 install 'tensorflow==2.4.1' pip3 install 'keras==2.2.4'
I do believe the real problem for me was the version of TF, the older version installed with the instructions given was not working nor the new versions, but a middle ground version did work. h5py and keras are reinstalled as per instructions so I am not sure if uninstalling them and re installing them actually helped. I still do not know why but this worked fine for me. I hope it helps.
Thanks @TomasaSbaffi, your response helped me solve the issue. Reinstalling h5py with the version you mentioned was enough in my case.
@jessieren perhaps the instructions for creating the conda env should be updated with h5py=2.10.0
?
Edit: I can confirm that when I create the environment with conda create --name dvf numpy theano=1.0.3 keras=2.2.4 scikit-learn Biopython h5py=2.10.0
it works out of the box.
DeepVirFinder isn't working in Ubuntu 20.04 after installing dependencies succesfully...
and after installing mkl-service...
Any idea of what's going on here?