Test module falling after installation about deepvirfinder

[fluhus]

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.

[dnolin13]

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'

1. Loading Models.
   model directory /home/delaney/software/DeepVirFinder/models
   Traceback (most recent call last):
   File "dvf.py", line 131, in
   modDict[contigLengthk] = load_model(os.path.join(modDir, modName))
   File "/home/delaney/miniconda3/envs/dvf/lib/python3.6/site-packages/keras/engine/saving.py", line 419, in load_model
   model = _deserialize_model(f, custom_objects, compile)
   File "/home/delaney/miniconda3/envs/dvf/lib/python3.6/site-packages/keras/engine/saving.py", line 224, in _deserialize_model
   model_config = json.loads(model_config.decode('utf-8'))
   AttributeError: 'str' object has no attribute 'decode'
   (dvf) delaney@ada:~/software/DeepVirFinder$
   `

[TomasaSbaffi]

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.

[TomasaSbaffi]

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