Error: no such option: --data-root
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When I try to run the command deepgoplus --data-root <path_to_data_folder> --in-file <input_fasta_filename> under Running I get this error.
Could you please elaborate more on this. What is your python version? It seems to work for me.
How to reproduce it?
I've tried it on both Python 3.6 and 3.7. I created a folder named 'data' in the root directory, then I called the above command with train_data.fa as the in-file. I've attached a screenshot of my terminal. I see those commands in main.py, but calling it gives me an additional error about diamond not starting correctly.
You are using anaconda and I'm not sure if it works there. Could you please try to install it with virtualenv (or python3 -m venv)? And how did you install diamond? Did you get the binaries?
I am using Windows, so I downloaded and ran the executable (although it didn't look like anything happened). Also, which version of tensorflow needs to be used? I am using the latest version and upon compilation it looks like a number of the methods used are deprecated.
Hi, I would suggest to use tensorflow 1.12.0, because it is the version we tested. And, install all the requirements from requirements.txt with pip install -r requirements.txt
data-root <path_to_data_folder> refers to the specific path where data is stored on your computer, use this path instead of data-root <path_to_data_folder>, no need to write it
I know to replace <path_to_data_folder>; I would still write out --data-root though, right?
Also, point of information, is the model.h5 file pre-trained? If so this would make my job easier; I am working on combining deepgoplus into an ensemble.
you try not to write out data-root,and the model.h5 file should be pre-trained.