I will try to be as much help as I can, but this is certainly a bit out of my depth.
I am trying to run the metagenomics package 'DeepVirFinder' on my fasta file 'my_seqs.fa' within terminal on my Mac. I have followed the GitHub repository instructions (as found here https://github.com/jessieren/DeepVirFinder). I have created a conda environment with all the necessary packages.
Into my terminal I have inputted
python dvf.py -i ~/Documents/PairwiseANI/my_seqs.fna -o ~/Documents/DeepVirFinder/ -l 1000 -c 2
this receives an output error of
Using Theano backend.
1. Loading Models.
model directory /data2/joshcole/DeepVirFinder/models
Traceback (most recent call last):
File "dvf.py", line 131, in <module>
modDict[contigLengthk] = load_model(os.path.join(modDir, modName))
File "/home/ggb_joshcole/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/ggb_joshcole/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'
From the GitHub repository, what it should return upon a successful run (using example template names) is as follows:
Using Theano backend.
1. Loading Models.
model directory /auto/cmb-panasas2/renj/software/DeepVirFinder/models
2. Encoding and Predicting Sequences.
processing line 1
processing line 1389
3. Done. Thank you for using DeepVirFinder.
output in ./test/crAssphage.fa_gt300bp_dvfpred.txt
Any help for how to fix this error would be greatly appreciated. I have tried to download and jig around with potential conda fixes, but it doesn't appear to be a problem with any dependancies + python is fully up to date.
Thank you for reading
Apologies - I found out it was an error between h5py and tensorflow. Had to downgrade h5py to 2.10.0.