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Description
Hello,
I'm trying to use DeepCapTail software to predict phage tail proteins and Im getting the following error:
>>> python predict_sequence.py --p_fasta ../Myoviridae_GCA_002594545.1_genomic.faa --capsid_tail tail --p_output output_test/prot_myo_tail_prediction.csv
Using TensorFlow backend.
Traceback (most recent call last):
File "predict_sequence.py", line 98, in <module>
main()
File "predict_sequence.py", line 89, in main
df_prediction = predict_sequence(args.capsid_tail, df_data, p_model_json, p_model_h5)
File "predict_sequence.py", line 14, in predict_sequence
model.load_weights(p_model_h5)
File "/home/mdz/bio_env/lib/python3.6/site-packages/keras/engine/network.py", line 1157, in load_weights
with h5py.File(filepath, mode='r') as f:
File "/home/mdz/bio_env/lib/python3.6/site-packages/h5py/_hl/files.py", line 394, in __init__
swmr=swmr)
File "/home/mdz/bio_env/lib/python3.6/site-packages/h5py/_hl/files.py", line 170, in make_fid
fid = h5f.open(name, flags, fapl=fapl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5f.pyx", line 85, in h5py.h5f.open
OSError: Unable to open file (unable to open file: name = 'model/tail.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
My setup:
Ubuntu 14.04 LTS
Python 3.6
installed python packages:
absl-py==0.7.0
astor==0.7.1
biopython==1.73
gast==0.2.2
grpcio==1.18.0
h5py==2.9.0
Keras==2.2.4
Keras-Applications==1.0.7
Keras-Preprocessing==1.0.6
Markdown==3.0.1
numpy==1.16.0
pandas==0.24.0
protobuf==3.6.1
python-dateutil==2.7.5
pytz==2018.9
PyYAML==3.13
scipy==1.2.0
six==1.12.0
tensorboard==1.12.2
tensorflow==1.12.0
termcolor==1.1.0
Werkzeug==0.14.1
What's interesting is that when I run predictions for capsid (--capsid_tail capsid) the software runs without any errors.
I tried redownloading the repo, just to make sure that the models/tail.h5 file hasn't been corrupted during the downloading process, but unfortunately it did not help.