./nnpython3 ./secnet.py3 --input input/ --output output/ --label all

# SecNet, Protein secondary structure prediction software
# 2018-19 (C) Maxim Shapovalov, Roland Dunbrack Lab, Slobodan Vucetic, Fox Chase Cancer Center and Temple University, Philadelphia, PA, USA
# Version 1.1.4
# Jan 13, 2020

None:
=====
If wildcard characters such as * or ? are used to select input sequence files,
please make sure to quote the input argument
with either single or double quotes, for example "/my_input_folder/*.fasta" or '*.seq'

INPUT for processing <-- input/
OUTPUT --> output/


1 of 5] processing of /home/max/16jF_secnet_ubuntu/input/example.fasta
* script: /home/max/16jF_secnet_ubuntu/bin/run_psiblast.py3 /home/max/16jF_secnet_ubuntu/input/example.fasta
* script: psiblast is set to use 8 CPU cores
* command: /home/max/16jF_secnet_ubuntu/3rd_software/unix/ncbi-blast-2.6.0+/bin/psiblast -db /home/max/16jF_secnet_ubuntu/3rd_databases/blast/uniref90.fasta -query /home/max/16jF_secnet_ubuntu/input/example.fasta -inclusion_ethresh 0.001 -evalue 10 -save_pssm_after_last_round -out_ascii_pssm /home/max/16jF_secnet_ubuntu/features/psiblast/example.mtx -num_iterations 2 -num_threads 8 -save_each_pssm > /dev/null 2>&1
* script: /home/max/16jF_secnet_ubuntu/bin/run_hmm.py3 /home/max/16jF_secnet_ubuntu/input/example.fasta
* command: bash /home/max/16jF_secnet_ubuntu/3rd_software/generic/process_hmm.bash -i /home/max/16jF_secnet_ubuntu/input/example.fasta
* hhm: number of detected CPU cores is 8
* hhm: 8 CPU cores will be used
* hhm: input fasta is /home/max/16jF_secnet_ubuntu/input/example.fasta
* hhm: /home/max/16jF_secnet_ubuntu/3rd_software/unix/hh/hh/buildali2.pl /home/max/16jF_secnet_ubuntu/features/temp/example_16589/example.seq -cpu 8 -noss 1>/home/max/16jF_secnet_ubuntu/features/temp/example_16589/example_alignment.output 2>/home/max/16jF_secnet_ubuntu/features/temp/example_16589/example_alignment.error
* hhm: /home/max/16jF_secnet_ubuntu/3rd_software/unix/hh/hh/hhmake -i /home/max/16jF_secnet_ubuntu/features/temp/example_16589/example.a3m -o /home/max/16jF_secnet_ubuntu/features/hhm/example.hhm1 1>/home/max/16jF_secnet_ubuntu/features/temp/example_16589/example_hhmake.output 2>/home/max/16jF_secnet_ubuntu/features/temp/example_16589/example_hhmake.error
* hhm: success
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 8 -i /home/max/16jF_secnet_ubuntu/input/example.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 8 labels: H, E, C, T, G, S, B, I
* predict: label definition: 8 original DSSP labels unchanged (C, S, B, T, I, G, H, E)
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/8label
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/8label/CV1/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/8label/CV2/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/8label/CV3/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/8label/CV4/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/8label/CV5/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/8label/CV6/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/8label/CV7/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/8label/CV8/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/8label/CV9/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/8label/CV10/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/example.fasta
* predict: base name of entry is example
* predict: parsed sequence from the input file is:
STGAANKSLSLLSTETMSILQDAPACCLPLFKFIDIYEKKYGHKLNVSDLYKLTDTIAIREQGNGRLVCLLPSNQ
* predict: prediction file will be output/example.ss8
predict: predicted secondary structure for 10 models
CCCCCCHHHHHHHHHHHHHHHHSTTGCCCHHHHHHHHHHHHSSCCCHHHHHTCCTEEEEEECTTCEEEEECCCCC
CCCCCCCHHHHHHHHHHHHHHHSTTTCCCHHHHHHHHHHHHSSCCCHHHHHTCTTEEEEEEETTEEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHHSTTGCCCHHHHHHHHHHHHSSCCCHHHHTTCCSEEEEEECTTEEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHHSTTGCCCHHHHHHHHHHHHSSCCCHHHHHTCCTEEEEEECTTEEEEEEECCCC
CCCCCCHHHHHHHHHHHHHHHHSTTCCCCHHHHHHHHHHHHSSCCCHHHHHTCTTEEEEEEETTEEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHTSCTGCCCHHHHHHHHHHHHSSCCCHHHHHTCSEEEEEEECTTCEEEEECCCCC
CCCCCCCCHHHHHHHHHHHHHHSTTTCCCHHHHHHHHHHHHSSCCCHHHHTTCCTEEEEEECTTEEEEEEECCCC
CCCCCCHHHHHHHHHHHHHHHHSTTCCCCHHHHHHHHHHHHSSCCCHHHHTTCCTEEEEEEETTEEEEEEECCCC
CCCCCHHHHHHHHHHHHHHHHHSTTTCCCHHHHHHHHHHHHSSCCCHHHHHTCCSEEEEEEETTEEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHHSTTGCCCHHHHHHHHHHHHSSCCCHHHHTTCTTEEEEEECTTEEEEEECCCCC
predict: major vote:
CCCCCCHHHHHHHHHHHHHHHHSTTGCCCHHHHHHHHHHHHSSCCCHHHHHTCCTEEEEEECTTEEEEEECCCCC
* predict: successful (+) prediction at output/example.ss8
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 5 -i /home/max/16jF_secnet_ubuntu/input/example.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 5 labels: H, E, C, T, G
* predict: label definition: (C, S, B) -> C, (H, I) -> H, (E) -> E, (T) -> T, (G) -> G
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/5label_practical
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV1/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV2/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV3/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV4/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV5/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV6/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV7/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV8/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV9/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV10/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/example.fasta
* predict: base name of entry is example
* predict: parsed sequence from the input file is:
STGAANKSLSLLSTETMSILQDAPACCLPLFKFIDIYEKKYGHKLNVSDLYKLTDTIAIREQGNGRLVCLLPSNQ
* predict: prediction file will be output/example.ss5
predict: predicted secondary structure for 10 models
CCCCCCCHHHHHHHHHHHHHHHCTTGCCCHHHHHHHHHHHHCCCCCHHHHHTCCTEEEEEECTTCEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHTCTTCCCCHHHHHHHHHHHHCCCCCHHHHHTCCTEEEEEEETTEEEEEECCCCC
CCCCCCCHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHCCCCCHHHHTTCCEEEEEEECTTEEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHCCCCCHHHHTTCCCEEEEEECTTCEEEEEECCCC
CCCCCCCHHHHHHHHHHHHHHHCTTGCCHHHHHHHHHHHHHCCCCCHHHHTTCCCEEEEEEETTEEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHHCTTGCCCHHHHHHHHHHHHCCCCCHHHHHTCCCEEEEEECTTEEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHCCCCCHHHHHTCCCEEEEEECTTEEEEEEECCCC
CCCCCCHHHHHHHHHHHHHHHHCTTCCCCGGGHHHHHHHHHCCCCCHHHHHTCCCEEEEEECTTEEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHCCCCCHHHHHTCCTEEEEEECTTCEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHCCCCCHHHHTTCCCEEEEEECTTCEEEEECCCCC
predict: major vote:
CCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHCCCCCHHHHHTCCCEEEEEECTTEEEEEECCCCC
* predict: successful (+) prediction at output/example.ss5
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 4 -i /home/max/16jF_secnet_ubuntu/input/example.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 4 labels: H, E, C, T
* predict: label definition: (C, S, B, G) -> C, (H, I) -> H, (E) -> E, (T) -> T
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/4label_practical
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV1/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV2/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV3/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV4/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV5/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV6/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV7/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV8/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV9/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV10/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/example.fasta
* predict: base name of entry is example
* predict: parsed sequence from the input file is:
STGAANKSLSLLSTETMSILQDAPACCLPLFKFIDIYEKKYGHKLNVSDLYKLTDTIAIREQGNGRLVCLLPSNQ
* predict: prediction file will be output/example.ss4
predict: predicted secondary structure for 10 models
CCCCCCCHHHHHHHHHHHHHHHCCTCCCCHHHHHHHHHHHHCCCCCHHHHHTCCCEEEEEECTTCEEEEECCCCC
CCCCCCCHHHHHHHHHHHHHHHCCTCCCCHHHHHHHHHHHHTCCCCHHHHHTCCCEEEEEEETTEEEEEEECCCC
CCCCCCCHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHCCCCCHHHHHTCCCEEEEEETTTEEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHCCCCCHHHHTTCCTEEEEEECTTCEEEEEECCCC
CCCCCCCHHHHHHHHHHHHHHHCCTCCCCHHHHHHHHHHHHCCCCCHHHHHTCCTEEEEEECTTEEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHCCCCCHHHHTTCCCEEEEEECTTEEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHCCCCCHHHHHTCCCEEEEEEETTEEEEEECCCCC
CCCCCCCHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHCCCCCHHHHHTCCCEEEEEECTTCEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHHCCTCCCCHHHHHHHHHHHHCCCCCHHHHHTCCTEEEEEECTTCEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHCCCCCHHHHHTCCEEEEEEECTTCEEEEECCCCC
predict: major vote:
CCCCCCCHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHCCCCCHHHHHTCCCEEEEEECTTCEEEEECCCCC
* predict: successful (+) prediction at output/example.ss4
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 3 -r 1 -i /home/max/16jF_secnet_ubuntu/input/example.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 3 labels of Rule #1: H, E, C
* predict: label definition: (C, S, T) -> C, (H, I, G) -> H, (E, B) -> E
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV1/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV2/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV3/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV4/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV5/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV6/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV7/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV8/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV9/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV10/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/example.fasta
* predict: base name of entry is example
* predict: parsed sequence from the input file is:
STGAANKSLSLLSTETMSILQDAPACCLPLFKFIDIYEKKYGHKLNVSDLYKLTDTIAIREQGNGRLVCLLPSNQ
* predict: prediction file will be output/example.ss3rule1
predict: predicted secondary structure for 10 models
CCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHHCCCCEEEEEECCCCEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHCCCEEEEEECCCCEEEEEECCCC
CCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHHCCCCEEEEEECCCEEEEEEECCCC
CCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHHCCCCEEEEEECCCEEEEEEECCCC
CCCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHCCCCEEEEEECCCEEEEEECCCCC
CCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHHCCCCEEEEEECCCEEEEEECCCCC
CCCCCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHCCCEEEEEEECCEEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHCCCEEEEEECCCCEEEEECCCCC
CCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHHCCCCEEEEEECCCCEEEEEECCCC
CCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHHCCCCEEEEEECCCEEEEEEECCCC
predict: major vote:
CCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHHCCCCEEEEEECCCEEEEEECCCCC
* predict: successful (+) prediction at output/example.ss3rule1
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 3 -r 2 -i /home/max/16jF_secnet_ubuntu/input/example.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 3 labels of Rule #2: H, E, C
* predict: label definition: (C, S, B, T, I, G) -> C, (H) -> H, (E) -> E
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV1/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV2/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV3/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV4/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV5/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV6/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV7/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV8/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV9/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV10/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/example.fasta
* predict: base name of entry is example
* predict: parsed sequence from the input file is:
STGAANKSLSLLSTETMSILQDAPACCLPLFKFIDIYEKKYGHKLNVSDLYKLTDTIAIREQGNGRLVCLLPSNQ
* predict: prediction file will be output/example.ss3rule2
predict: predicted secondary structure for 10 models
CCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHCCCCCEEEEEECCCCEEEEECCCCC
CCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHCCCCCEEEEEECCCEEEEEECCCCC
CCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHCCCCCEEEEEECCCEEEEEECCCCC
CCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCHHHHCCCCCEEEEEECCCCEEEEECCCCC
CCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHCCCCCEEEEEECCCCEEEEECCCCC
CCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHCCCCCEEEEEECCCCEEEEEECCCC
CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCHHHHCCCCCEEEEEECCCEEEEEECCCCC
CCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHCCCCCEEEEEECCCEEEEEEECCCC
CCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHCCCCCEEEEEECCCCEEEEEECCCC
CCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCHCCHCCCCCEEEEEECCCEEEEEECCCCC
predict: major vote:
CCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCHHHHCCCCCEEEEEECCCCEEEEECCCCC
* predict: successful (+) prediction at output/example.ss3rule2
* predict: returned code is 0 (0 = success, non-zero = failure)

2 of 5] processing of /home/max/16jF_secnet_ubuntu/input/6D0GA.fasta
* script: /home/max/16jF_secnet_ubuntu/bin/run_psiblast.py3 /home/max/16jF_secnet_ubuntu/input/6D0GA.fasta
* script: psiblast is set to use 8 CPU cores
* command: /home/max/16jF_secnet_ubuntu/3rd_software/unix/ncbi-blast-2.6.0+/bin/psiblast -db /home/max/16jF_secnet_ubuntu/3rd_databases/blast/uniref90.fasta -query /home/max/16jF_secnet_ubuntu/input/6D0GA.fasta -inclusion_ethresh 0.001 -evalue 10 -save_pssm_after_last_round -out_ascii_pssm /home/max/16jF_secnet_ubuntu/features/psiblast/6D0GA.mtx -num_iterations 2 -num_threads 8 -save_each_pssm > /dev/null 2>&1
* script: /home/max/16jF_secnet_ubuntu/bin/run_hmm.py3 /home/max/16jF_secnet_ubuntu/input/6D0GA.fasta
* command: bash /home/max/16jF_secnet_ubuntu/3rd_software/generic/process_hmm.bash -i /home/max/16jF_secnet_ubuntu/input/6D0GA.fasta
* hhm: number of detected CPU cores is 8
* hhm: 8 CPU cores will be used
* hhm: input fasta is /home/max/16jF_secnet_ubuntu/input/6D0GA.fasta
* hhm: /home/max/16jF_secnet_ubuntu/3rd_software/unix/hh/hh/buildali2.pl /home/max/16jF_secnet_ubuntu/features/temp/6D0GA_21986/6D0GA.seq -cpu 8 -noss 1>/home/max/16jF_secnet_ubuntu/features/temp/6D0GA_21986/6D0GA_alignment.output 2>/home/max/16jF_secnet_ubuntu/features/temp/6D0GA_21986/6D0GA_alignment.error
* hhm: /home/max/16jF_secnet_ubuntu/3rd_software/unix/hh/hh/hhmake -i /home/max/16jF_secnet_ubuntu/features/temp/6D0GA_21986/6D0GA.a3m -o /home/max/16jF_secnet_ubuntu/features/hhm/6D0GA.hhm1 1>/home/max/16jF_secnet_ubuntu/features/temp/6D0GA_21986/6D0GA_hhmake.output 2>/home/max/16jF_secnet_ubuntu/features/temp/6D0GA_21986/6D0GA_hhmake.error
* hhm: success
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 8 -i /home/max/16jF_secnet_ubuntu/input/6D0GA.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 8 labels: H, E, C, T, G, S, B, I
* predict: label definition: 8 original DSSP labels unchanged (C, S, B, T, I, G, H, E)
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/8label
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/8label/CV1/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/8label/CV2/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/8label/CV3/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/8label/CV4/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/8label/CV5/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/8label/CV6/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/8label/CV7/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/8label/CV8/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/8label/CV9/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/8label/CV10/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/6D0GA.fasta
* predict: base name of entry is 6D0GA
* predict: parsed sequence from the input file is:
SNAMSNNNDYDISDSKDCEKFANQFIQEFPIRSAEIGQGTVIKRALPSRQKRMIGAWCFLDHAGPVTFPAGNGLDVGPHPHIGLQTFTWMIEGTMMHTDSLGSKQLIRPKQVNLMTAGHGISHTEVAPDTETQMHAAQLWIALPDHKRNMDPKFEHYPDLPVVEKDGLEFTVLVGEYLETTSPVVVHTPLVGVDLIATQDTKTRIPLNPEFEYGFMALDGVAHVNGHELTADNMVVLDTGLNEIEIEVKKGNRVLLIGGEPFETPILLWWNFVARTMDDLKEAREQWVNHDVRFGEIPDYVGARLEAPVLPDQMRASK
* predict: prediction file will be output/6D0GA.ss8
predict: predicted secondary structure for 10 models
CCCCCCCCCCCCCCCHHHHHCCCCCEEEECCCEECTTTTCEEEEECCCTTCCCEEEEEEECCCCCCCCCCTSCCCCCCCCTTSEEEEEEEEESEEEEECTTSCEEEECTTCEEEEECSTCEEEEEECCTTSCCEEEEEEEEEECGGGTTSCCCCCCCCCCCEEEETTEEEEEEESEETTCCCSEEEECCEEEEEEEECTTCEEEEECCTTCCEEEEEEESCEEETTEECCTTCEEEECTTCSEEEEEECTTCEEEEEESCCCSSCEEEEEEEEESSHHHHHHHHHHHHTTCCGCCCCTTCCSCCCCCCCCCCGCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEEETTTTCEEEEECTTTTCCCCCEEEEEEEECCSCCCCTSCCCCCCCTTSSCEEEEEEEEEEEEEECTTSCEEEECTTCEEEEECTSEEEEEEECCTTCCCEEEEEEEEECCGGGTTSCCCCECCCCCCEEEETTEEEEEEEEEETTCECSEEEECCEEEEEEEECTTCEEEEECCTTCEEEEEEEESEEEETTEECCTTCEEEECTTCSEEEEEEETTEEEEEEECCCCSSCEEEEEEEEESSHHHHHHHHHHHHTTCCCCCCCTTCCSCCCCCCCCCGGGCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCECCTTTTCEEEEECCCTTCCCEEEEEEEEECCCCCCCTSSCCCCCCCCCSSEEEEEEEEEEEEEEECTTSCEEEECTTEEEEEECSSCEEEEEECCTTCCCEEEEEEEEECCGGGTTSCCCCCCCCCCCEEEETTEEEEEEESCCTTCECSEEEEECEEEEEEEECTTCEEEEECCTTCCEEEEEEESCEEETTEEECTTCEEEECTTCSEEEEEECTTEEEEEEESCCCSSCEEEEEEEECSSHHHHHHHHHHHHTTCCTCCCCTTCCSCCCCCCCCCCGCCCCC
CCCCCCCCCCCCCCCHCCCCCCCCCEEEECCEEECTTTTCEEEEECCCTTCCCEEEEEEEECCCCCCCCTSSSCCCCCCCCCSEEEEEEEEESEEEEECTTSCEEEECTTCEEEEECTSCEEEEEECCTTCCCEEEEEEEEECCGGGTTSCCCCCCCCCCCEEEETTEEEEEEEEEETTCCCSEEEECSEEEEEEEECTTCEEEEECCTTCEEEEEEEESEEEETTEECCTTCEEEECTTCSEEEEEECTTEEEEEECSCCCSSCEEEEEEEEESSHHHHHHHHHHHHTTCCCSCCCTTCCSCCCCCCCCCGGCCCCC
CCCCCCCCCCCCCCCCHHHHCCCCCEEEECCEEECTTTTCEEEEECCCTTCCCEEEEEEEECCCCCCCCTSCCCCCCCCCCTSEEEEEEEEESEEEEECTTSCEEEECTTCEEEEECSSCEEEEEECCTTCCCEEEEEEEEECCGGGTTSCCCCCCCCCCCEEEETTEEEEEEEEEETTCECCCEEECCEEEEEEEECTTCEEEEECCTTCCEEEEEEESEEEETTEEECTTCEEEECTTCSEEEEEECTTCEEEEEESCCCSSCEEEEEEEECSSHHHHHHHHHHHHHTCGGSCCCTTCCSCCCCCCCCCGGGCCCC
CCCCCCCCCCCCCCCHHHHHCCCCCEEEECCCCSCTTTTCEEEEECCCTTCCEEEEEEEEECCCCTCCCTTTCCCCCCCCCTSEEEEEEEEESEEEEECTTSCEEEECTTCEEEEEESSCEEEEEECCSTSCCEEEEEEEEECCGGGTTSCCCCCCCCCCCEEEETTEEEEEEEECTTTCCCSEEEECCEEEEEEEECTTCEEEEECCTTCEEEEEEEESCEEETTEECCTTCEEEECTTCSEEEEEECTTCEEEEEESCCCSSCEEEEEEEECSSHHHHHHHHHHHHTTCTTSCCCTTCCSCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEEETTTTEEEEEECCCSTCCCECEEEEEECCCCSCCCCCSCCECCCCTTSSEEEEEEEEEEEEEEECTTSCEEEECTTCEEEEECSSCEEEEEECCSSSCCEEEEEEEEECCGGGTTSCCCCCECCCCCEEEETTEEEEEEEEECTTEECSEEEECSEEEEEEEECTTCEEEEECCTTCCEEEEEEESEEEETTEECCTTCEEEECTTCSEEEEEECTTEEEEEEECCCCSSCEEEEEEEECSSHHHHHHHHHHHHHTCCTSCCCTTCCSCCCCCCCCCGGCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEECCTTTTCEEEEEECCSSSCCEEEEEEEECCCCSCCCCSSCCCCCCCCCSSEEEEEEEEEEEEEEEETTSCEEEECTTCEEEEECTSEEEEEEECCSSSCCEEEEEEEEEECGGGTTSCCCCCCCCCCCEEEETTEEEEEEEEEETTCCCSEEEECSEEEEEEEECTTCEEEEECCTTCCEEEEEEESEEEETTEECCTTCEEEECSTCSEEEEEECSSEEEEEEESSCCSSCEEEEEEEEESSHHHHHHHHHHHHTTCGGCCCCTTCCSCCCCCCCCCGGGCCCC
CCCCCCCCCCCCCCCCHCCCCCCCCEEEECCCESCTTTTCEEEEECCCTTCCEEEEEEEEECCCCSCCCCCCCCECCCCCTCCCCEEEEEEEEEEEEECTTSCEEEECTTEEEEEEESSCEEEEEECCTTCCCEEEEEEEEECCGGGTTSCCCCCCCCCCCEEEETTEEEEEEEEEETTCECSEEEECSEEEEEEEECTTCEEEEECCTTCCEEEEEEESEEEETTEEECTTCEEEECTTCSEEEEEEETTEEEEEEESCCCSSCEEEEEEEEESSHHHHHHHHHHHHTTCTTCCCCTTCCSCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCHHHHCCCCCCCEEEECCEEEETTTTCEEEEESCCTTSCCEEEEEEEEEECCCCCCTTSCCCCCCCCTSSCEEEEEEEESEEEEECTTSCEEEECTTCEEEEECSSCEEEEEECCTTSCCEEEEEEEEEECGGGTTSCCCCCCCCCCCEEEETTEEEEEEEEEETTCECSEEEECSEEEEEEEECTTCEEEEECCTTSCEEEEEEESEEEETTEECCTTCEEEECTTCSEEEEEECSTEEEEEECSCCCSSCEEEEEEEEESSHHHHHHHHHHHHTTCCTSCCCTTCCSCCCCCCCCCGGGCCCC
predict: major vote:
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEECTTTTCEEEEECCCTTCCCEEEEEEEECCCCCCCCCSSCCCCCCCCCSSEEEEEEEEEEEEEEECTTSCEEEECTTCEEEEECSSCEEEEEECCTTCCCEEEEEEEEECCGGGTTSCCCCCCCCCCCEEEETTEEEEEEEEEETTCECSEEEECCEEEEEEEECTTCEEEEECCTTCCEEEEEEESEEEETTEECCTTCEEEECTTCSEEEEEECTTEEEEEEESCCCSSCEEEEEEEEESSHHHHHHHHHHHHTTCCTCCCCTTCCSCCCCCCCCCGGCCCCC
* predict: successful (+) prediction at output/6D0GA.ss8
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 5 -i /home/max/16jF_secnet_ubuntu/input/6D0GA.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 5 labels: H, E, C, T, G
* predict: label definition: (C, S, B) -> C, (H, I) -> H, (E) -> E, (T) -> T, (G) -> G
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/5label_practical
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV1/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV2/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV3/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV4/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV5/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV6/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV7/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV8/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV9/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV10/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/6D0GA.fasta
* predict: base name of entry is 6D0GA
* predict: parsed sequence from the input file is:
SNAMSNNNDYDISDSKDCEKFANQFIQEFPIRSAEIGQGTVIKRALPSRQKRMIGAWCFLDHAGPVTFPAGNGLDVGPHPHIGLQTFTWMIEGTMMHTDSLGSKQLIRPKQVNLMTAGHGISHTEVAPDTETQMHAAQLWIALPDHKRNMDPKFEHYPDLPVVEKDGLEFTVLVGEYLETTSPVVVHTPLVGVDLIATQDTKTRIPLNPEFEYGFMALDGVAHVNGHELTADNMVVLDTGLNEIEIEVKKGNRVLLIGGEPFETPILLWWNFVARTMDDLKEAREQWVNHDVRFGEIPDYVGARLEAPVLPDQMRASK
* predict: prediction file will be output/6D0GA.ss5
predict: predicted secondary structure for 10 models
CCCCCCCCCCCCCCHHCCCCCCCCCEEEECCCECCTTTTCEEEECCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEECTTCCEEEECTTCEEEECCCCCEEEEEECCCCCCCEEEEEEEEEECGGGTTCCCCCCCCCCCCEEEETTEEEEEEEEETTTCECCEEECCCEEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEECCTTCEEEECTTCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEEECCHHHHHHHHHHHHTTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCECCTTTCCEEEEECCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCTTCCCCEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCGGGTTCCCCCCCCCCCCEEEETTEEEEEEEEEETTCECCCEEECCEEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEECCTTCEEEECTTCCEEEEEECCCEEEEEECCCCCCCCEEEEECCCCCCHHHHHHHHHHHHTTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEECCTTTTCEEEECCCCTTCCCEEEEEEECCCCCCCCCCCCCCCCCCCTTCCCEEEEEEEEEEEEEECTTCCEEEECTTEEEEEECCCCEEEEEECCTTCCCEEEEEEEEECCGGGTTCCCCCCCCCCCCEEEETTEEEEEEEEECTTCCCCEEECCCEEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEEECTTCEEEECTTCCEEEEEECTTCEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHTTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCECCTTTTCEEEECCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEETTCCEEEECTTCEEEEECCCCCEEEEECCCCCCCEEEEEEEEECCGGGTTCCCCCCCCCCCCEEEETTEEEEEEEEEETTCCCCEEEECCCEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEEECTTCEEEECCTCCEEEEEECTCEEEEEECCCCCCCCEEEEECEECCCHHHHHHHHHHHHTTCTTCCCCTTCCCCCCCCCCCCGGCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEECCTTCEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCGGGTTCCCCCECCCCCCEEEETTEEEEEEEECCTTCCCCEEEECCCEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEEECTTCEEEECTTCCEEEEEECCTEEEEEECCCCCCCCEEEEECCECCCHHHHHHHHHHHHTTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCTTTTCEEEEECCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCGGGTTCCCCCCCCCCCCEEEETTEEEEEEEEECTTCCCCEEEECCCEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEECCTTCEEEECTTCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHTTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEECTTTTEEEEECCCCCTCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCCCEEEEEECCTTCCCEEEEEEEEECCGGGTTCCCCCCCCCCCCEEEETTEEEEEEEEEETTCECCEEEECCCEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEEECTTCEEEECTTCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHTTCGCCCCCTTCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEECTTTTCEEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECEEEEECTTCCEEEECTTCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCGGGTTCCCCCCCCCCCCEEEETTEEEEEEEEECTTCCCCCEEECCCEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEEECTTCEEEECTTCCEEEEEECCCEEEEEECCCCCCCCEEEEECCCCCCHHHHHHHHHHHHTTCCCCCCCTTCCCCCCCCCCCCGGGCCCC
CCCCCCCCCCCCCCCHCCCCCCCCCEEEECCCECCTTTCCEEEECCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCTCCCCEEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCCEEEEEEECCCCCCCEEEEEEEEECCGGGTTCCCCCCCCCCCCEEEETTEEEEEEEEECTTCCCCCEECCCCEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEEECTTCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEEECCHHHHHHHHHHHHTTCTTCCCCTTCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEEETTTTCEEEECCCCTTCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCCCEEEEEECCTTCCCEEEEEEEEECCGGGTTCCCCCCCCCCCCEEEETTEEEEEEEEECTTCCCCEEEECCCEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEEECTTCEEEECTTCCEEEEEECTCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHTTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
predict: major vote:
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCECCTTTTCEEEECCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCGGGTTCCCCCCCCCCCCEEEETTEEEEEEEEECTTCCCCEEEECCCEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEEECTTCEEEECTTCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHTTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
* predict: successful (+) prediction at output/6D0GA.ss5
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 4 -i /home/max/16jF_secnet_ubuntu/input/6D0GA.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 4 labels: H, E, C, T
* predict: label definition: (C, S, B, G) -> C, (H, I) -> H, (E) -> E, (T) -> T
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/4label_practical
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV1/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV2/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV3/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV4/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV5/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV6/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV7/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV8/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV9/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV10/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/6D0GA.fasta
* predict: base name of entry is 6D0GA
* predict: parsed sequence from the input file is:
SNAMSNNNDYDISDSKDCEKFANQFIQEFPIRSAEIGQGTVIKRALPSRQKRMIGAWCFLDHAGPVTFPAGNGLDVGPHPHIGLQTFTWMIEGTMMHTDSLGSKQLIRPKQVNLMTAGHGISHTEVAPDTETQMHAAQLWIALPDHKRNMDPKFEHYPDLPVVEKDGLEFTVLVGEYLETTSPVVVHTPLVGVDLIATQDTKTRIPLNPEFEYGFMALDGVAHVNGHELTADNMVVLDTGLNEIEIEVKKGNRVLLIGGEPFETPILLWWNFVARTMDDLKEAREQWVNHDVRFGEIPDYVGARLEAPVLPDQMRASK
* predict: prediction file will be output/6D0GA.ss4
predict: predicted secondary structure for 10 models
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEEETTTEEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCCCEEEEEECCTTCCCEEEEEEEEECCCCCTTCCCCCCCCCCCCEEEETTEEEEEEEEEETTCECCEEEECCEEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEECCTTCEEEECTTCCEEEEEECCCEEEEEEECCCCCCCEEEEEEEECCCHHHHHHHHHHHHTTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCECCTTTTCEEEEECCCTTCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCTCEEEEEECCCTCCCEEEEEEEEECCCCCTTCCCCCCCCCCCCEEEETTEEEEEEEECCTTCCCCEEECCCEEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEEECTTCEEEECTTCCEEEEEECTCCEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHTTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCEECTTTTCEEEECCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCCCEEEEEECCCTCCCEEEEEEEEECCCCCTTCCCCCCCCCCCCEEEETTEEEEEEEECCTTCCCCEEEECCEEEEEEEECTTCEEEEECCTTCCEEEEEEECCEEETTEEECTTCEEEECTTCCEEEEEECCCCEEEEECCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCHCCCCCCCCEEEECCEEECTTTTCEEEEECCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCTTCCCEEEEEEEEEEEEEEETTCCEEEECTTCEEEEECCCEEEEEEECCCCCCCEEEEEEEEECCCCCTTCCCCCCCCCCCCEEEETTEEEEEEEEECTTCCCCEEEECCEEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEEECTTCEEEECTTCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHTTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEECCTTTTCEEEEECCCTTCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCCCEEEEEECCCTCCCEEEEEEEEECCCCCTTCCCCCCCCCCCCEEEETTEEEEEEEEECTTCECCEEEECCCEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEECCTTCEEEECTTCCEEEEEECTTCEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHHTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEEETTTCCEEEECCCCCCCCEEEEEEEEECCCCCCCCCCCCCECCCCTTCCCEEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCCCCTTCCCCCCCCCCCCEEEETTEEEEEEEEECTTCCCCEEEECCEEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEEECTTCEEEECTTCCEEEEEECTTEEEEEECCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEECTTTTCEEEEECCCTTCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCCCCTTCCCCCCCCCCCCEEEETTEEEEEEEEECTTCECCEEEECCCEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEECCTTCEEEECTTCCEEEEEECTTCEEEEECCCCCCCCEEEEEEECCCCHHHHHHHHHHHHTTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCEECTTTTCEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCCCEEEEEECCTTCCCEEEEEEEEECCCCCCTCCCCCCCCCCCCEEEETTEEEEEEEEECTTCCCCCEEECCCEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEEECTTCEEEECCTCCEEEEEECTCCEEEEECCCCCCCCEEEEEEEEECCHHHHHHHHHHHHTTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEEECTTTEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCCCCTTCCCCCCCCCCCCEEEETTEEEEEEEEECTTCCCCCEEECCCEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEECCTTCEEEECTTCCEEEEEECTCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHHTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEECTTTTCEEEEECCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCTTCCCCEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCCCEEEEEECCTTCCCEEEEEEEEECCCCCTTCCCCCCCCCCCCEEEETTEEEEEEEECCTTCCCCCEECCCEEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEEECTTCEEEECTTCCEEEEEECTCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHTTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
predict: major vote:
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEECTTTTCEEEEECCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECTTCCEEEECTTCEEEEECCCCEEEEEECCCTCCCEEEEEEEEECCCCCTTCCCCCCCCCCCCEEEETTEEEEEEEEECTTCCCCEEEECCEEEEEEEECTTCEEEEECCTTCCEEEEEEECEEEETTEEECTTCEEEECTTCCEEEEEECTCCEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHTTCCCCCCCTTCCCCCCCCCCCCCCCCCCC
* predict: successful (+) prediction at output/6D0GA.ss4
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 3 -r 1 -i /home/max/16jF_secnet_ubuntu/input/6D0GA.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 3 labels of Rule #1: H, E, C
* predict: label definition: (C, S, T) -> C, (H, I, G) -> H, (E, B) -> E
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV1/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV2/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV3/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV4/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV5/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV6/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV7/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV8/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV9/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV10/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/6D0GA.fasta
* predict: base name of entry is 6D0GA
* predict: parsed sequence from the input file is:
SNAMSNNNDYDISDSKDCEKFANQFIQEFPIRSAEIGQGTVIKRALPSRQKRMIGAWCFLDHAGPVTFPAGNGLDVGPHPHIGLQTFTWMIEGTMMHTDSLGSKQLIRPKQVNLMTAGHGISHTEVAPDTETQMHAAQLWIALPDHKRNMDPKFEHYPDLPVVEKDGLEFTVLVGEYLETTSPVVVHTPLVGVDLIATQDTKTRIPLNPEFEYGFMALDGVAHVNGHELTADNMVVLDTGLNEIEIEVKKGNRVLLIGGEPFETPILLWWNFVARTMDDLKEAREQWVNHDVRFGEIPDYVGARLEAPVLPDQMRASK
* predict: prediction file will be output/6D0GA.ss3rule1
predict: predicted secondary structure for 10 models
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCEEEEECCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECEEEEECCCCCEEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCHHHCCCCCCCCCCCCCCEEEECCEEEEEEEEECCCCCCCEEEECCCEEEEEEECCCCEEEEECCCCCCEEEEEEECEEEECCEECCCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEEECCCCEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECEEEEECCCCCEEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCHHHCCCCCCCCCCCCCCEEEECCEEEEEEEECCCCCECCEEEECCCEEEEEEECCCCEEEEECCCCCCEEEEEEECCEEECCEEECCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCEEEEECCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECEEEEECCCCCEEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCHHHCCCCCCCCCCCCCCEEEECCEEEEEEEEEECCCCCCEEECCCCEEEEEEECCCCEEEEECCCCCCEEEEEEECEEEECCEEECCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEECCCCCCEEEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCEEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEEECHHHHCCCCCCCCCCCCCEEEECCEEEEEEEEECCCCCCCEEEECCEEEEEEEECCCCEEEEECCCCCCEEEEEEECEEEECCEEECCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEEECCCCCEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCHEEEEEEECEEEEECCCCCCEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCHHHCCCCCCCCCCCCCCEEEECCEEEEEEEEECCCCECCEEEECCCEEEEEEECCCCEEEEECCCCCCEEEEEEECEEEECCEEECCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCHHHHCCCCEEEECCCCCCCCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCEEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCHHHCCCCCCCCCCCCCCEEEECCEEEEEEEECCCCCCCCEEEECCCEEEEEEECCCCEEEEECCCCCCEEEEEEECCEEECCEEECCCCEEEECCCCCEEEEEECCCCEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHCCCC
CCCCCCCCCCCCCCHHHCCCCCCCCEEEECCEEECCCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECEEEEECCCCCEEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCHHHCCCCCCCCCCCCCCEEEECCEEEEEEEECCCCCCCCCEEECCCEEEEEEECCCCEEEEECCCCCCEEEEEEECEEEECCEEECCCCEEEECCCCCEEEEEECCCCEEEEECCCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCEEECCEEEECCCCCEEEEECCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECEEEEECCCCCEEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCHHHCCCCCCCCCCCCCCEEEECCEEEEEEEEECCCCECCEEEECCCEEEEEEECCCCEEEEECCCCCCEEEEEEECCEEECCEECCCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCEEEEECCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEEECEEEEECCCCCEEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEEECHHHCCCCCCCCCCCCCCEEEECCEEEEEEEEECCCCCCCEEEECCCEEEEEEECCCCEEEEECCCCCCEEEEEEECCEEECCEEECCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCECCCCCCCCCCCCC
CCCCCCCCCCCCCHHHCCCCCCCCCEEEECCEECCCCCCCEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCECCCCCCCCCEEEEEEEECEEEEECCCCCEEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCHHHCCCCCCCCCCCCCCEEEECCEEEEEEEEECCCCEEEEEEECCEEEEEEEECCCCEEEEECCCCCCEEEEEEECCEEECCEEECCCCEEEECCCCCEEEEEECCCEEEEEEECCCCCCCEEEEEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
predict: major vote:
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEECCCCCCCEEEEECCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECEEEEECCCCCEEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCHHHCCCCCCCCCCCCCCEEEECCEEEEEEEEECCCCCCCEEEECCCEEEEEEECCCCEEEEECCCCCCEEEEEEECCEEECCEEECCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
* predict: successful (+) prediction at output/6D0GA.ss3rule1
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 3 -r 2 -i /home/max/16jF_secnet_ubuntu/input/6D0GA.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 3 labels of Rule #2: H, E, C
* predict: label definition: (C, S, B, T, I, G) -> C, (H) -> H, (E) -> E
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV1/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV2/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV3/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV4/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV5/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV6/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV7/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV8/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV9/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV10/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/6D0GA.fasta
* predict: base name of entry is 6D0GA
* predict: parsed sequence from the input file is:
SNAMSNNNDYDISDSKDCEKFANQFIQEFPIRSAEIGQGTVIKRALPSRQKRMIGAWCFLDHAGPVTFPAGNGLDVGPHPHIGLQTFTWMIEGTMMHTDSLGSKQLIRPKQVNLMTAGHGISHTEVAPDTETQMHAAQLWIALPDHKRNMDPKFEHYPDLPVVEKDGLEFTVLVGEYLETTSPVVVHTPLVGVDLIATQDTKTRIPLNPEFEYGFMALDGVAHVNGHELTADNMVVLDTGLNEIEIEVKKGNRVLLIGGEPFETPILLWWNFVARTMDDLKEAREQWVNHDVRFGEIPDYVGARLEAPVLPDQMRASK
* predict: prediction file will be output/6D0GA.ss3rule2
predict: predicted secondary structure for 10 models
CCCCCCCCCCCCCCCHCCCCCCCCCEEEECCEEEECCCCCEEEECCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEECCCCCEEEECCCCEEEECCCCCEEEEECCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEECCEEEEEEEEECCCCCCCEEEECCEEEEEEEECCCCEEEEECCCCCCEEEEEEECEEEECCEECCCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCEEECCCCCCEEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCEEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEECCEEEEEEEEEECCCECCCEEECCCEEEEEEECCCCEEEEECCCCCCEEEEEEECEEEECCEECCCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCECCCCCCEEEEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECEEEEECCCCCEEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEECCEEEEEEEECCCCCCCCCEEECCCEEEEEEECCCCEEEEECCCCCCEEEEEEECCEEECCEECCCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCEEEEECCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECEEEEECCCCCEEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEECCEEEEEEEECCCCCCCCEEEECCCEEEEEEECCCCEEEEECCCCCCEEEEEEECCEEECCEEECCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCECCCCCCCEEEEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECEEEEECCCCCEEEECCCEEEEEECCCCEEEEECCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEECCEEEEEEEECCCCCCCCEEEECCCEEEEEEECCCCEEEEECCCCCCEEEEEEECEEEECCEEECCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCECCCCCCCEEEECCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECEEEEECCCCCEEEECCCEEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEECCEEEEEEEECCCCCCCCCCCCCCCEEEEEEECCCCEEEEECCCCCCEEEEEEECEEEECCEECCCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCEECCCCCCEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECEEEECCCCCCCEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEECCEEEEEEEECCCCCCCCEEEECCCEEEEEEECCCCEEEEECCCCCCEEEEEEECEEEECCEEECCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCCEEEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCEECCCCCCEEEECCCCCCCCCECCCEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECEEEEECCCCCEEEECCCCEEEEECCCCEEEEECCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEECCEEEEEEEECCCCCCCCEEEECCCEEEEEEECCCCEEEEECCCCCCEEEEEEECEEEECCEECCCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCEEEECCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECEEEEECCCCCEEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEECCEEEEEEEEECCCCCCCEEEECCCEEEEEEECCCCEEEEECCCCCCEEEEEEECEEEECCEEECCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCECCCCCCCEEEECCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECEEEEECCCCCEEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCEEEECCEEEEEEEEECCCCCCCEEEECCEEEEEEEECCCCEEEEECCCCCCEEEEEEECCEEECCEEECCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
predict: major vote:
CCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCECCCCCCCEEEECCCCCCCCCECEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECEEEEECCCCCEEEECCCCEEEEECCCCEEEEEECCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEECCEEEEEEEECCCCCCCCEEEECCCEEEEEEECCCCEEEEECCCCCCEEEEEEECEEEECCEECCCCCEEEECCCCCEEEEEECCCEEEEEECCCCCCCCEEEEEEEECCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
* predict: successful (+) prediction at output/6D0GA.ss3rule2
* predict: returned code is 0 (0 = success, non-zero = failure)

3 of 5] processing of /home/max/16jF_secnet_ubuntu/input/6G44A.fasta
* script: /home/max/16jF_secnet_ubuntu/bin/run_psiblast.py3 /home/max/16jF_secnet_ubuntu/input/6G44A.fasta
* script: psiblast is set to use 8 CPU cores
* command: /home/max/16jF_secnet_ubuntu/3rd_software/unix/ncbi-blast-2.6.0+/bin/psiblast -db /home/max/16jF_secnet_ubuntu/3rd_databases/blast/uniref90.fasta -query /home/max/16jF_secnet_ubuntu/input/6G44A.fasta -inclusion_ethresh 0.001 -evalue 10 -save_pssm_after_last_round -out_ascii_pssm /home/max/16jF_secnet_ubuntu/features/psiblast/6G44A.mtx -num_iterations 2 -num_threads 8 -save_each_pssm > /dev/null 2>&1
* script: /home/max/16jF_secnet_ubuntu/bin/run_hmm.py3 /home/max/16jF_secnet_ubuntu/input/6G44A.fasta
* command: bash /home/max/16jF_secnet_ubuntu/3rd_software/generic/process_hmm.bash -i /home/max/16jF_secnet_ubuntu/input/6G44A.fasta
* hhm: number of detected CPU cores is 8
* hhm: 8 CPU cores will be used
* hhm: input fasta is /home/max/16jF_secnet_ubuntu/input/6G44A.fasta
* hhm: /home/max/16jF_secnet_ubuntu/3rd_software/unix/hh/hh/buildali2.pl /home/max/16jF_secnet_ubuntu/features/temp/6G44A_25074/6G44A.seq -cpu 8 -noss 1>/home/max/16jF_secnet_ubuntu/features/temp/6G44A_25074/6G44A_alignment.output 2>/home/max/16jF_secnet_ubuntu/features/temp/6G44A_25074/6G44A_alignment.error
* hhm: /home/max/16jF_secnet_ubuntu/3rd_software/unix/hh/hh/hhmake -i /home/max/16jF_secnet_ubuntu/features/temp/6G44A_25074/6G44A.a3m -o /home/max/16jF_secnet_ubuntu/features/hhm/6G44A.hhm1 1>/home/max/16jF_secnet_ubuntu/features/temp/6G44A_25074/6G44A_hhmake.output 2>/home/max/16jF_secnet_ubuntu/features/temp/6G44A_25074/6G44A_hhmake.error
* hhm: success
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 8 -i /home/max/16jF_secnet_ubuntu/input/6G44A.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 8 labels: H, E, C, T, G, S, B, I
* predict: label definition: 8 original DSSP labels unchanged (C, S, B, T, I, G, H, E)
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/8label
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/8label/CV1/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/8label/CV2/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/8label/CV3/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/8label/CV4/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/8label/CV5/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/8label/CV6/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/8label/CV7/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/8label/CV8/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/8label/CV9/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/8label/CV10/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/6G44A.fasta
* predict: base name of entry is 6G44A
* predict: parsed sequence from the input file is:
GAMGMNTPPELDTVLQAPYAYNWPTSKNVKIASRIGIPYSTFQTIQPVSDAPNNGIGQITFNQPLGNLTGGAPRLRVSFTAEIKNILADSSLKDQIGLKSFPVNRSIPVAVINMNGKTFTSYPAQLIKLHQYNADPLELALLSPCSDVDEYNKIKAVSMNNPYRQGTESTDSRMSRGLGCNYAYYIHPRAAGSTSVKIDFVVDEALVANPTQYKNIKDPVPFRNLNTFKVILDGQFKPENMIGIADDVKLVAGKADFEVDITGFKINMLVQNWVAPLEIGDIPKTIIYNTPLISLEGNISSMCLNTKDPYGIPGERNKHILTTHSMAMNNVPSMFAVMVSQETPTKKFAPDQLAGIIGLEIKVDSDVGIFRELEQQQLYELSSSNGYNKRFSCFSGALANGLTVADPAVAAGNKFKEAIFGAGSVIFFRPSDLGLKDYNVMANANKSINMQVQATFVTPEAAGTGAHYKLEVFSIRDNLTYSFEDGTFMDDLTLYTPDQLLRSPLKLTDDNNKLMRVMGG
* predict: prediction file will be output/6G44A.ss8
predict: predicted secondary structure for 10 models
CCCCCCCCCHHHHHHCCCCEECCCCCHHHHHHHHTTCCGEEEEEEEECCSCTTCCEEEEEESSCCECCCTCCCEEEEEEEEEHHHHHHHHHHHHHTCCCCCCCCCCCCEEEEETTTCEEEECHHHHHHHHHTTCCHHHHHHHSCCCCHHHHHHHHHHHHTCTTCCCCCCHHHHHCCCCCCEEEEEEECCCTSCEEEEEEEEEEEEEHSCGGGGGCTCSCCCCEEEEEEEEEETTEECGGGEEEHHHHHHHHHTSEEEEEEETTEEEEEEEEEECCCCCGTCCCSEEEEECCEEEEEECHHHHHHECCCTTCCCCCCCEEEEEEHHHHHTCCCHEHHHEHECSCCTCCCCHHHHEEEEEEEEEEETTTTEEEHHHHHHHHHHHHTTTCEEEEEEEEHHHHTTCEECCHHHHHHHHHHHEEETTTEEEEECGGGTTCCCEEEEEEEEEEEEEEEEEEEECCTGCTSSCEEEEEEEEEETTEEEEETTTEEEEEEEEECHHHHECSCCEECCTTHHHHHHHCC
CCCCCCCCCCHHHHHTSCGEECCCCCHHHHHHHHTTCCGGEEEEEEECCCCCTTCEEEEEEESCCECCTSCCCEEEEEEEEEEEEEEECHHHHHHHCCCCSCCCTEECEEEEETTSCEEEEECHHHEHHHHTTCCHHHHHEESCCCSHHHHHHHHHEEECCCCCCCCCCCCCCCCCCCCCEEEEEECCCETTCEEEEEEEEEEEEEECCGGGHTTCTSCCCEEEEEEEEEEEETEECGGGEEEEHHEEEEHHTSEEEEEEETTEEEEEEEEEECCCCCETCCCEEEEEEEEEEEEEECEEEEHHECSCTTCCCCCCCEEEEEEEEEEETTCCEEEEEEEEECCCTCCCCCCEEEEEEEEEEEECTTTCEEEEHHHHHHHHHHHTTTCHEEEEEEEEEEETTCEEECHHHHHHHHHHHHHHTTTEEEEECGGGTTCCCEEEEEEEEEEEEEEEEEEEECCCCTTTTCEEEEEEEEEETEEEEEETTTEEEEEEEEECHHHHHTSCCECCCTTCCEEEECCC
CCCCCCCCCCHHHHHTSCEEECCCCCCCHHHHHHTTCCHGGEEEEEECCCCTTCCEEEEEEESCCCCCTSCCCEEEEEEEEEEEEEECHHHHHHHHTCCCSCCCTCSCEEEEETTTCEEEECCHHHHHHHHHTCCHHHHHHECCCSCHHHHHHHHHHHHCCCCCCCCCCCCHCCCCCCCCEEEEEECECCTTCEEEEEEEEEEEEEHSCGGGHHTCCSCCCCEETEEEEEEEETECCGGGEEHHHHHHEEEETEEEEEEEEETEEEEEEEEEECCCCCGTCCCEEEEEEEEEEEEESCHHHHHHCCCCTTCCCTCCCEEEEEEEEEECTCCCEEEEEEEECSSCCCCCCHHHEEEEEEEEEEEETTTTEEEEEHHHHHHHHHHHTTHEEEEEEEHHHHHTTCEEECHHHHHHHHEEEEEECTTEEEEECGGGGTCCCEEEEEEEEEEEEEEEEEEEECCGGTTSSEEEEEEEEEEETEEEEEETTTEEEEEEEEECHHHHHCSCEEEECTTHHHHEECCC
CCCCCCCCCHHHHHHHCCEEEECCCHHHHHHHHHTTCCGGGEEEEEECCCCCTTCEEEEEEESCCECCESCCCEEEEEEEEEEEEEEEHHHHHHHTCCCGSCCCSCCCEEEEETTSCEEEECCHHHEEHHHTTSCHHHHHHECCCSCGGGHHHHHHHHTTCCCCCCCCCCCCCCCCCCCEEEEEEECCCSTSCEEEEEEEEEEEHHHHCGGGCCCTSSCCCCGEEEEEEEEETTEECGGGHEEEEHEEEEEETEEEEEEEETHHEEEEEEEEECCCCCTTCCCSEEEEECCEEEEESCEEEEEEECCCTTCCCTCHHHEEEEHEEEEETCHCHEEEEEEESSCCCCCCCHHHHHHEEEEEEEEETTTHEEEEHHHHHHHHHHHTTSCEEEEEEEEHHHHTTCEEECHHHHHHHHHHHEHHTTTEEEEECGGGGTCCHHEEEEETTSEEEEEEEEEEECCCGTTSSCEEEEEEEEEETTEEEEEETTEEEEEEEECCHHHHHCSCCCECCTTHHHEEECCC
CCCCCCCCCHHHHHHTSCEEECCCCHHHHHHHHHHTCCGGEEEEEEECCCCCCCCEEEEEEEECCCCCTTCCCEEEEEEEEEEEHHHHHHHHHHHHCCCCSCCCCCCCEEEEETTSCEEEECHHHHHHHHHHCCCHHHHHHHSCCCCHHHHHHHHHHHHCCCCCCCCCCCCHHCCCCEEEEEEEEECCCSTSEEEEEEEEEEEEHHHSCGGGGTTCCSCCCEEEEEEEEEEETTECCGGGHHHHHHHHHHHHTEEEEEEEETTHEEEEEEEHHSCCCCGTCCCEEEEEECCEEEEEHHHHHHHHHCCCTTCCCCCCCEEEEEEEEEECCCCCEEEEEEEEHCCCTCCCCCHHHEEEEEEEEEECTTTHHHHHHHHHHHHHHHHHTTCCEEEEEEHEEEETTEEECCHHHHHHHHHHHHETTTTEEEEECGGGGTCCHHHHEEEEEEEEEEEEEEEEECCTGTTSSCEEEEEEEEEETTEEEEEETTCEEEEEEEECHHHHHTSCEEEECTTCCEEEEECC
CCCCCCCCCCHHHHHTSCEEEECCCHHHHHHHHHHTCCGGGEEEEEECCCCCTCCEEEEEEEECCCCECTSCCEEEEEEEEEEHHHHHHHHHHHHHTCCTSCCCTTECEEEEETTSCEEEEECHHHHHHHHHHCCHHHHHHTSCCCGHHHHHHHHHHHHTCCTCCCCCCCCHCCCCCCEEEEEEEECCCCTTCEEEEEEEEEEHHEHSCGGGCCCTTSCCCCEEEEEEEEEEEEEECGGGEEEEHHHHEHHEEEEEEEEEETTEEEEEEEEEESCCCCGTCCCSEEEEECEEEEEESCEEEEEEETSCTTCCCCCCCEEEEEEEEEEETTCCEEEEEEEECSCCCCCCCHHHHHTEEEEEEEEETTEHEEHHHHHHHHEEEHHTTTCCEEEEEECHHHHTTCCECCHHHHHHHHHHHHHTTTTEEEEECGGGGTCCCEEEEEETTSEEEEEEEEEEECCCCTTSSCEEEEEEEEEETTEEEEEETTCEEEEEEEECHHHHHTSCEEEECTTCCEEEECCC
CCCCCCCCCCHHHHHTCCEEECCCCCCCHHHHHHTTCCGGGEEEEEECGGSCTTCEEEEEESSCCCCCCTCCCEEEEEEEEEEEEEEHHHHHHHHHCCCCCCCCTTSCEEEEETTSCEEEECHHHHHHHHHHTCCHHHHHHHSCCCCHHHHHHHHHHHHCCTTCCCCCCCCCCCCCCCCCEEEEEEECCSTTCEEEEEEEEEEEEEHSCGGGCCTTCSCCCEEEEEEEEEEETTEECGGGHEEEEEHHEEEETEEEEEEEETTEEEEEEEEEECSCCCGTCCCEEEEEEECEEEEESCEEEEEEECSCTTCCCTCCCEEEEEEEEECCTSCCEEHHHHHECSCCCCCCCCCHHEEEEEEEEEEETTEEEEEHHHHHHHHHHHHTTTCCEEEEEECHHHHTTCEECCHHHHHHHHHHHHHHTTTEEEEECGGGGTCCCEEEEETSTEEEEEEEEEEEECGGGTTSSEEEEEEEEEECTTEEEEEETTEEEEEEEEECHHHHCCSCCEECCTTHHHEEEHCC
CCCCCCCCCHHHHHHHSCEEECCCCHHHHHHHHHTTCCHHEEEEEEECCCCCTTCEEEEEEESCCCCCTTCCCEEEEEEEEEEEHHHHHHHHHHHHCCCCCCCCTCSCEEEEETTTCEEEECHHHHHHHHHHTCCHHHHHHHSCCSCHHHHHHHHHHHHCCTTCCCCCCCCCCCCCCCCCEEEEEECCCCTTCEEEEEEEEEEHHHHSCHGGHHTCCCCCCCEECEEEEEEETTEECGGGHHEHHHHHEEHTTEEEEEEEETTHEEEEEEEEECCCCCGGGCCSEEEEECCEEEEESHHHHHHHECCCTTCCCTCCCEEEEEEEEEECTCCCHHHHHEEHCCCCCCCCCHHHHHHHHEEEEEEETTTHHHHHHHHHHHHHHHHHTTCEEEEEEEEEEHHTTCEHHCHHHHHHHHHHHHHTTTTEEEEECGGGGTCCHHHHHHHTTEEEEEEEEEEEECCCCTTTTCEEEEEEEEEETTEEEEEETTEEEEEEEEECHGGHEESCCEEECTTCCEEEECCC
CCCCCCCCCCCCEHETCCEEECCCTTCCEEEHHHTTCCGGEEEEEEECCCCCTCEEEEEEEESCCGCCTTSCCEEEEEEEEEEHHHHHHHHHHHHHTCCGCCCCTTCCEEEEETTTCEEEECCHEHEHHHHHCCCHHHHHHHSCCCCHHHHHHHHHEHTCCTTCCCCCCHCHHHCHCCCCEEEEEECCTCCSCCEEEEEEEEEEEEHHCGGGHTTTTCCCCCCEEEEEEEEEETEECGGGEEEEHHHHHEHHTEEEEEEEETTEEEEEEEEEECCCCCGTCCCEEEEEECEEEEEEEEEHHHEEEECCTTCCTCCCCEEEEEEEEECCTTCCEEEEEEEECCCCCCCCCHHEEEEEEEEEEEEETTTCEEEEHHHHHHHHHHHTTTCEEEEEEEESHHHTTCEEHCHHHHHHHHHHHEEETTTEEEEECGGGTTCCCEEEEEEETSEEEEEEEEEEECCTGTTTSCEEEEEEEEEETTEEEEETTSEEEEEEEECCHHHHHTSCCEECCTTSCEEEEECC
CCCCCCCCHHHHHHHTSCEEECCCCCHHHHHHHHTTCCGGGEEEEEECCSSCTCSEEEEEEESCCGCCTTCCCEEEEEEEEEEEEEHHHHHHHHHHCCCCSCCCTTCCEEEEEETTEEEEEHHHHHHHHHHTTCCHHHHHHECCCCCHHHHHHHHHHCCCCCCCCCCCCHCCCCCCCCCCCEEEEEECCCTTCCEEEEEEEEEEEEHSCGGGHHTTTSCCCEEEEEEEEEEETTEECGGGHEEEHHHEEEEHTEEEEEEEEEEEEEEEEEEEECCCCCGTCCCSEEEEECEEEEEEHHHHHHHHCCCCTTCCCTCCCEEEEEEEEEECTSCCEEEEEEEEESCCCCCCCHHHHHTEEEEEEEEETTTHHHHHHHHHHHHHHHHTTSCEEHEEEHHHHHHTTCCECCHHHHHHHHHHHHHHTTTCEEEECGGGGTCCHHHHHHHHCEEEEEEEEEEEECCGGTTSSEEEEEEEEEEETTEEEEETTTCEEEEEEEECHHHHECSCCEECCTTCCEEEECCC
predict: major vote:
CCCCCCCCCCHHHHHTSCEEECCCCCHHHHHHHHTTCCGGEEEEEEECCCCCTCCEEEEEEESCCCCCTTCCCEEEEEEEEEEEEEHHHHHHHHHHCCCCSCCCTCCCEEEEETTSCEEEECCHHHHHHHHHTCCHHHHHHHSCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCTTCEEEEEEEEEEEEEHSCGGGHCTTCSCCCCEEEEEEEEEETTEECGGGEEEEHHHHEEHHTEEEEEEEETTEEEEEEEEEECCCCCGTCCCEEEEEECCEEEEESCEHHHHHECCCTTCCCCCCCEEEEEEEEEECTCCCEEEEEEEECSCCCCCCCHHHHEEEEEEEEEEETTTHEEEHHHHHHHHHHHHTTTCEEEEEEEEHHHHTTCEECCHHHHHHHHHHHHHHTTTEEEEECGGGGTCCCEEEEEEETEEEEEEEEEEEECCCGTTSSCEEEEEEEEEETTEEEEEETTEEEEEEEEECHHHHHCSCCEECCTTCCEEEECCC
* predict: successful (+) prediction at output/6G44A.ss8
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 5 -i /home/max/16jF_secnet_ubuntu/input/6G44A.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 5 labels: H, E, C, T, G
* predict: label definition: (C, S, B) -> C, (H, I) -> H, (E) -> E, (T) -> T, (G) -> G
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/5label_practical
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV1/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV2/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV3/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV4/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV5/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV6/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV7/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV8/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV9/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV10/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/6G44A.fasta
* predict: base name of entry is 6G44A
* predict: parsed sequence from the input file is:
GAMGMNTPPELDTVLQAPYAYNWPTSKNVKIASRIGIPYSTFQTIQPVSDAPNNGIGQITFNQPLGNLTGGAPRLRVSFTAEIKNILADSSLKDQIGLKSFPVNRSIPVAVINMNGKTFTSYPAQLIKLHQYNADPLELALLSPCSDVDEYNKIKAVSMNNPYRQGTESTDSRMSRGLGCNYAYYIHPRAAGSTSVKIDFVVDEALVANPTQYKNIKDPVPFRNLNTFKVILDGQFKPENMIGIADDVKLVAGKADFEVDITGFKINMLVQNWVAPLEIGDIPKTIIYNTPLISLEGNISSMCLNTKDPYGIPGERNKHILTTHSMAMNNVPSMFAVMVSQETPTKKFAPDQLAGIIGLEIKVDSDVGIFRELEQQQLYELSSSNGYNKRFSCFSGALANGLTVADPAVAAGNKFKEAIFGAGSVIFFRPSDLGLKDYNVMANANKSINMQVQATFVTPEAAGTGAHYKLEVFSIRDNLTYSFEDGTFMDDLTLYTPDQLLRSPLKLTDDNNKLMRVMGG
* predict: prediction file will be output/6G44A.ss5
predict: predicted secondary structure for 10 models
CCCCCCCCCHHHHHHTCCCEECCCCCHHHHHHHHTTCCGGEEEEEEECCCCCTCCCEEEEECCCCCCCCCCCCEEEEEEEEEEEHHECCHHHHHHTCCCCCCCCCCCCEEEEETTCCEEEECHHHHHHHHHHTCCHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCTTCCEEEEEEEEEEEECCCGGGCCCCCCCCCCEEEEEEEEEETTECCGGGEEEEHHHHHHHHTCEEEEEEETTHEEEEEEEECCCCCCCCCCCEEEEEECCEEEEECCHHHHHHCCCCTTCCCCCCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCHHEEEEEEEEEEEECTTTCEEEEHHHHHHEEEHCTTCCCEEEEEECHHHCTTCEECCHHHHHHHHHHHHHHCCCEEEEECGGGCCCCCEEEEECCCCEEEEEEEEEEECCCCCTCCCEEEEEEEEECTTEEEEEETTEEEEEEEECCHHHHHCCCCCCCCTCCHHHHHHCC
CCCCCCCCCCHHHHHHCCCEECCCCCCHHHHHHHTTCCGGGEEEEEECCCCCCCCEEEEEECCCCCCCCCCCCEEEEEEEEEEEEHHCCHHHHHHHCCCCCCCCCCCCEEEEETTCCEEECCHHHHHHHHHHTCCHHHHHHHCCCCCCGHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEEEECCCCCCGGGCCCCCCCCCCEECCEEEEEETCECCGGGEEEEHCCEEEEEEEEEEEEEETTEEEEEEEEECCCCCCECCCCCEEEECCCEEEEECCHEEEEECCCCTTCCCCCCCCEEEEEEEHHHTCCCHHEEEEEECCCCCCCCCCCCEEEEEEEEEEEETTTCEEEHHHHHHHHHEHCTTCCCEEEEEECCHHHTTCEECCHHHHHHHHEHHHHHCCCEEEEECGGGTTCCCEEEEEECCEEEEEEEEEEEECCCCCCCCCEEEEEEEEECTTEEEEETTCEEEEEEEECCHHHHCCCCCCCCCTTCCEEECCCC
CCCCCCCCCCHHHHHHCCCEECCCCCCCHHEHHHTTCCGGGEEEEEECCCCCCCCEEEEEECCCCCCCCCCCCEEEEEEEEEEEEEECCHHHHHHHCCCCCCCCCCCCEEEEETTCCEEEECCHHHHHHHHTCCCHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHEEEECCCCCCCCEEEEEEEEEECCCCCHHHHTTCCCCCCCEECEEEEEEETTECCGGGHHHHHHHHHHHHEEEEEEEEETTEEEEEEEEECCCCCCGCCCCCEEEECCCEEEEECCHHHHEEECCCTTCCCCCCCCEEEEEEEEECTCCCEEEEEEEECCCCCCCCCCCCEEEEEEEEEEEETTTEEEEEEHHHHHHHHHHTTCCEEEEEECCHHHHTTCEECCHHHHHHHHHEHEECCTCCEEEECGGGGTCCCEEEEEECCCEEEEEEEEEEECCCCCCCCCEEEEEEEEEETTEEEEEETTEEEEEEEECCHHHHHCCCEEECCTTCCEEEECCC
CCCCCCCCCHHHHHHTCCCEECCCCCHHHHHHHHTTCCGGGEEEEEECCCCCTCCEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEHHCHHHHHHHCCCCCCCCCCCCEEEEEETTEEEEECHHHHHHHHHTCCCHHHHHHTCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCTCCEEEEEEEEECCHCCCGGGHHTCCCCCCCCCCEEEEEEEETEECGGGEEEEEHHHEHHHTCCEEEEEETTEEEEEEEEECCCCCCGTCCCCEEEEECCEEEEECCHHHHHHCCCCTTCCCCCCCCEEEEEEEEECTTCCCEEEEEEECCCCCCCCCCCHEEEEEEEEEEECTTTCCEEHHHHHHHHHHHHTTCCCEEEEECCCCHHTTCEECCHHHHHHHHHHHHHTCTTCEEEECGGGGTCCCHEEEEECCCEEEEEEEEEEECCCCTTCCCEEEEEEEEEETTEEEEETTTEEEEEEEECCHHHHHCCCEEEECTTCHHEEECCC
CCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHTTCCGGGEEEEEECCCCCCCCCEEEEEECCCCCCCCCCCEEEEEEEEEEEECCCCHHHHHHHCCCCCCCCCCCEEEEEETTCCEEECCCHHHHHHHHTTCCHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCTTCCEEEEEEEEEEHHHCCGGGCCCCCCCCCEEECEEEEEEETTCCCGGGEEEECHHHHHHHTCCEEEEEETHHEEEEEEEECCCCCCGTCCCCEEEECCCEEEEECCHHHHHHCCCCTTCCCCCCCCEEEEECCCCCCCCCHHHEHHHHCCCCCCCCCCHCCEEEEEEEEEECTTTCEEEHHHHHHHHHHHHHTCCEEEEEEEEEEHHTTCEEHCHHHHTHHHHHHHHCCCCEEEEECGGGCTCCCHHHHHCCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEEETTEEEEETTCCEEEEEEECCHGGCCCCCEEEECTTCCEEEEECC
CCCCCCCCCHHHHHHCCCCEECCCCCCHHHHHHHTTCCGGGEEEECCCCCCCCCCEEEEEECCCCCCCCCCCCEEEEEEEEEEEEHHHHHHHHHHHCCCCCCCCCCCCEEEEETTCCEEEECHHHHHHHHHHTCCHHHHHHHCCCCCHHHHHHHHHHHTCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCTTCCEEEEEEEECCHHHCCGGGCCCCCCCCCCEECEEEEEEETTECCCGCEEEEEHHHEEEETCEEEEEEETCCEEEEEEEEECCCCCCCCCCCEEEECCCEEEEECCEEEEEECCCCTTCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCCCCCCCEEEEEEEEEEEECTTCCEEEHHHHHHHHHHHHHTCCCEEEEECHHHHHHTCCHCCHHHHHHHHHHHHHTTCEEEEEECGGGTCCCCEEEEECCCCCEEEEEEEEEECCCCCCCCCEEEEEEEEECTTEEEEEETTEEEEEEEECCHHHHCCCCCCCCCCCHHHHHCCCC
CCCCCCCCCCCHHHHHCCEEECCCCCHHHHHHHHTTCCGGGEEECECCCCCCTCCCEEEEEECCCCCCCCCCCEEEEEEEEEEEEHHHCHHHHHHCCCCCCCCCCCCEEEEEETTCCEEECCCHHHHHHHHHTCCHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHCCCCCCCCEEEEECCCCCCCCEEEEEEEEEEECCCCGGGCHTCCCCCCCEEEEEEEEEEETEECGGGHEEEHHHHHHHHTEEEEEEEETTEEEEEEEEECCCCCCGCCCCEEEEECCCEEEEECCHHHHHECCCCTTCCCCCCCCEEEEEEEEECCCCCHHHHEEEECCCCCCCCCCCCEEEEEEEEEEECTTCCHHEHHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCCCCCHHHHHHHHHHHHHTCCCEEEEECGGGCCCCCEEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEEETTEEEEEETTEEEEEEEEECCHHHHCCCEEECCTTCCCEECCCC
CCCCCCCCCHHHHHHHCCCCCCCCCCCHHHHHHHTTCCGGGEEEEEECCCCCTCCEEEEEEECCCCCCCCCCCEEEEEEEEEHHEECCCHHHHHHHCCCCCCCCCCCCEEEEEETTCEEEECCHHHHHHHHHTCCHHHHHHHCCCCCHHHHHHHHHHHHCCTTCCCCCCCCCCCCCCCCCCEEEEECCCCTTCCEEEEEEEEEEEHHCCGGGCCCCCCCCCCEEEEEEEEEEECECCGGGEEEEEHHHHHHHTCCEEEEEETCCEEEEEEEECCCCCCGCCCCCEEEEECCEEEEEECEEHHEECCCCTTCCCCCCCCEEEECCCCCCCCCCHEEHHHHECCCCCCCCCCHHHEEEEEEEEEEETTCCEEEEEHHHHHHHHHHTTCCCEEEEECCCHHHTTCEECCHHHHHHHHHHHEECCCCEEEEECGGGTTCCCHEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECTTEEEEETTCCEEEEEEEECHHHHCCCCCEECCTTCCEEEECCC
CCCCCCCCCHHHHHHHCCCCCCCCCCHHHHHHHHTTCCGGGEEEEECCCCCCCCCCEEEEECCCCCCCCCCCCEEEEEEEEEEHHHHHCHHHHHHHCCCCCCCCCCCCEEEEETTCCEEEECHHHHHHHHHHCCCHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCEEEEEEEECHHHHHCGGGCCCCCCCCCCECCEEEEEEEECECCGGGHEEEHHHHEEHETEEEEEEEETTEEEEEEEEECCCCCCCTCCCCEEEECCCCCEEECCEEEEEECCCCTTCCCCCCCCEEEEEECCCCCCCCEEEEEEEECCCCTCCCCCCCEHHHEEEEEEECTTCCEEEEEHHHHHHHHHHTTCCCEEEEECCCHHHTCCEECCHHHHHHHHHHHHHHCCCEEEEECGGGTCCCCEEEEECCCEEEEEEEEEEEECCCCCTCCCEEEEEEEEECTTEEEEEETTEEEEEEEEECHHHHHCCCCECCCCTCEEEHHCCC
CCCCCCCCCHHHHHHCCCEEECCCCCHHHHHHHHTTCCGGGEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCEEEEEEEEEEEHHCCCHHHHHHHCCCCCCCCCCCCEEEEETTCCEEEECHHHHHHHHHHCCCHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHCCCCHCCHHEEEECCCCTCCCEEEEEEEEECHHCCCGGGCCCCCCCCCCEECEEEEEEETTCCCGGGHHHHHHHHHEHETCCEEEEEECTEEEEEEEEECCCCCCGGCCCCEEEEECCEEEEECCHHHHHCCCCCTTCCCCCCCCEEEEECCCCCCCCCCEEEEEEECCCCCCCCCCCCEEEEEEEEEEECTTCCEEEEHHHHEEEHHHHTTCCCEEEEEECCCECTTCEECCHHHHHHHHHHHHHHCCCEEEEECGGGCTCCCEEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEEETTEEEEETTTEEEEEEEECCHHHHCCCCCECCCTTCEEEEECCC
predict: major vote:
CCCCCCCCCHHHHHHHCCCEECCCCCHHHHHHHHTTCCGGGEEEEEECCCCCCCCEEEEEECCCCCCCCCCCCEEEEEEEEEEEEHHCCHHHHHHHCCCCCCCCCCCCEEEEETTCCEEEECHHHHHHHHHHTCCHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEEEEEHHCCCGGGCCCCCCCCCCEECEEEEEEETTECCGGGEEEEHHHHHHHHTCEEEEEEETTEEEEEEEEECCCCCCGCCCCCEEEECCCEEEEECCHHHHEECCCCTTCCCCCCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCEEEEEEEEEEECTTCCEEEEHHHHHHHHHHHTTCCCEEEEECCCHHHTTCEECCHHHHHHHHHHHHHHCCCEEEEECGGGCTCCCEEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECTTEEEEEETTEEEEEEEECCHHHHCCCCCECCCTTCCEEEECCC
* predict: successful (+) prediction at output/6G44A.ss5
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 4 -i /home/max/16jF_secnet_ubuntu/input/6G44A.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 4 labels: H, E, C, T
* predict: label definition: (C, S, B, G) -> C, (H, I) -> H, (E) -> E, (T) -> T
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/4label_practical
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV1/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV2/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV3/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV4/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV5/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV6/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV7/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV8/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV9/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV10/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/6G44A.fasta
* predict: base name of entry is 6G44A
* predict: parsed sequence from the input file is:
GAMGMNTPPELDTVLQAPYAYNWPTSKNVKIASRIGIPYSTFQTIQPVSDAPNNGIGQITFNQPLGNLTGGAPRLRVSFTAEIKNILADSSLKDQIGLKSFPVNRSIPVAVINMNGKTFTSYPAQLIKLHQYNADPLELALLSPCSDVDEYNKIKAVSMNNPYRQGTESTDSRMSRGLGCNYAYYIHPRAAGSTSVKIDFVVDEALVANPTQYKNIKDPVPFRNLNTFKVILDGQFKPENMIGIADDVKLVAGKADFEVDITGFKINMLVQNWVAPLEIGDIPKTIIYNTPLISLEGNISSMCLNTKDPYGIPGERNKHILTTHSMAMNNVPSMFAVMVSQETPTKKFAPDQLAGIIGLEIKVDSDVGIFRELEQQQLYELSSSNGYNKRFSCFSGALANGLTVADPAVAAGNKFKEAIFGAGSVIFFRPSDLGLKDYNVMANANKSINMQVQATFVTPEAAGTGAHYKLEVFSIRDNLTYSFEDGTFMDDLTLYTPDQLLRSPLKLTDDNNKLMRVMGG
* predict: prediction file will be output/6G44A.ss4
predict: predicted secondary structure for 10 models
CCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHHHTTCCCCCEEEEEECCCCCCCCCEEEEEECCCCCCCCCCCEEEEEEEEEHHHHHHHHHHHHCTCCCCCCCCCCCCEEEEEETTEEEECCCHHHHHHHHHTCCHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCCHHCCCCCCCCEEEEECCCCCCCCEEEEEEEEECCCHHCCCCCCCCCCCCCCCCCCEEEEEETTEECCCCEEHHHHHHEEEEEEEEEEEEETTEEEEEEEEECCCCCCCCCCCCEEEECCCEEEEECCEEEEEECCCCTTCCCCCCCCEEEECCCCCCCCCCEEEEEEEEECCCCCCCCCCCHHEEEEEEEEEETTCCEEEHHHHHHHHHHHHTTCCCEEEEEECCCHHTTCEEECHHHHHHHHHEEEECCTCEEEEECCCCCCCCCHHEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECTTEEEEEETTEEEEEEEECCHHHHHCCCCEECCTCHHHHHHCCC
CCCCCCCCCHHHHHHTCCCCCCCCCCHHHHHHHHTTCCCEEEEEEEECCCCCCCCEEEEEECCCCCCCCCCCCEEEEEEEEEEEEEHCHHHHHHHHCCCCCCCCCCCCEEEEEETTEEEEECHHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHTCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCTTCCEEEEEEEEECCCCCCCCCCCCCCCCCCEEECTEEEEEETTECCCCCHEEHHHHHHHHHTCCEEEEEETTEEEEEEEEEECCCCCCCCCCCEEEECCCEEEEECCEEEEEEECCCTTCCCCCCCEEEEEEECCCCTCCCHEEEEEEECCCCCCCCCCCCCEEEEEEEEEEETTTCEEEEEHHHHHHHHHCTTCCCEEEECCCCCCCTTCEECCHHHHHTHHEEEEECCTCEEEEECCCCCCCCCHHHHHHCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEEETCEEEEEETTEEEEEEEECCCHCHCCCCCEECCTTCCEEEECCC
CCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHTTCCCCCEEEEECCCCCCCCCEEEEEEECCCCCCCCCCCEEEEEEEEEEEEECCHHHHHHHHCCCCCCCCCCCCEEEEETTTEEEEECCHHHHHHHHTCCCHHHHHHHCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEEEECCCHCCCCCCCCCCCCCCEEEEEEEEEEEETEECCCCEEEECCCHEHHECCCEEEEEETCEEEEEEEEECCCCCCCCCCCCEEEEECCEEEEECCHHHHEEECCCTTCCCCCCCCEEEEEEECCCCCCCEEEEEEEECCCCCCCCCCCCEEEEEEEEEEEETTCCEEEEHHHHHHHHHHCCTCCCCEEEEEECEECTTCEECCHHHHHHHHHHHHHCCCCEEEEECCCCCTCCCEEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECTCEEEEEETTEEEEEEEEECHHHHHCCCCECCCTCCCCECCCCC
CCCCCCCCCHHHHHHHCCCCECCCCCCHHHHHHHTTCCCCCEEEEEECCCCCCCCCEEEEEECCCCCCCCCCCEEEEEEEEEEEECCCCHHHHHHHCCCCCCCCCCCCEEEEETTCCEEEECHHHHHHHHHHCCCHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEEEEEECCHHCCCCCCCCCCCCCCCCCEEEEEEEETTECCCCCEEEEEHHHEEEETCEEEEEEETTEEEEEEEEEECCCCCCCCCCCEEEECCCEEEEEHHHHHHHHCCCCTTCCCTCCCEEEEEEEEHHHTCCCEEEEEEEECCCCCCCCCCCCEEEEEEEEEEEETTTCEEEHHHHHHHEEHHHTTCCCCCECCCCCHHHTTCECCCHHHHHHHHHHHHHCCTCEEEEECCCCCCCCCEEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECTCEEEEEETTEEEEEEEECCHHHHHHCCCCCCCCCCCEEECCCC
CCCCCCCCCCHHHHHCCCEEECCCCCCHHHHHHHTTCCCCCEEEEECCCCCCCCCCEEEEEECCCCCCCCCCCCEEEEEEEEEEEECCCHHHHHHTCCCCCCCCCCEEEEEEEETTEEEEECHHHHHHHHHCCCCHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHCCCCCHHHHHHEECCCCCTCCEEEEEEEEECCCCCCCCCCCCCCCCCCEEEECEEEEEETTEECCCCHHHHHHHHHHHEEEEEEEEEETTEEEEEEEEEECCCCCCCCCCCEEEECCCEEEEEHHHHHHHHCCCCTTCCCCCCCCEEEECCCCCCCCCCHHHHHHHHCCCCCCCCCCHHHEEEEEEEEEEETCCCCEEEHHHHHHHHHHHHTCCCEEEEECCHHHHTTCEEECHHHHHTHHHHHEEECTTCEEEECCCCCCCCHEEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECTCEEEEETTCCEEEEEEECCHHHHHCCCEEEECTTCHEEEECCC
CCCCCCCCCHHHHHHTCCCEECCCCCCCHHHHHHTTCCCCCEEEEEECCCCCTCCCEEEEEECCCCCCCCCCCEEEEEEEEEEEEECCCHHHHHHHCCCCCCCCCCCCEEEEETTCCEEEECCHEHHHHHHHHCCHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCECCCEEEEEEETECCCCCEEHHHHHEEEEETCEEEEEEETTEEEEEEEEEECCCCCCCCCCCEEEECCCEEEEECCCEEEEECCCCTTCCCCCCCCEEEEEECCCCCCCCHEEEEEEECCCCCCCCCHHHHETEEEEEEEECTCCCCEEHHHHHHHHHHHHTTCCCEEEEECCCHHHHHEEECCHHHHHHHHHEEEEECCCEEEEECCCCCCCCCCEEEHCCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEEETCEEEEEETTEEEEEEEECCHHHHCCCCEEECCTTCCEEEECCC
CCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHTTCCCCCEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCEEEEEEEEEHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEETTTCEEEECCHHHHHHHHHCCCHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHCCCCCCCCCEEEEECCCCCTCCEEEEEEEECCCCHCCCCCCCCCCCCCCCCCCEEEEEEETTCCCCCCHHEHCHHHEEHEEEEEEEEEETTEEEEEEEEEECCCCCCCCCCCEEEEECCEEEEECCEEEEEECCCCTTCCCCCCCCEEEEEECCCCTCCCHHEEEEEECCCCCCCCCCCCCEEEEEEEEEEETTTCEEEEECHHHHEEECCTTCCEEEEEECHHHHHTTCEECCHHHHHHHHHHHHHHCCCCEEEECCCCCTCCCEEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECTTEEEEETTCCEEEEEEEECHHCCCCCCCEECCTTCCEEEHCCC
CCCCCCCCCCHHHHHHCCCCCCCCCCCHHHHHHHTTCCCCHEEEEEECCCCCCCCCEEEEEECCCCCCCCCCCCEEEEEEEEEEEHHHHHHHHHHHCCCCCCCCCCCCEEEEEETTCEEEECCHHHHHHHHTCCCHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCTCCEEEEEEEEECCCHCCCCCCCCCCCCCCCEEEEEEEEEETTEECCCCHHEHHHHHHHHHEECEEEEEETTEEEEEEEEECCCCCCCCCCCCEEEEECCEEEEECCEEEHHHCCCCTTCCCCCCCCEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEEEEEEEEETTTCEEEEHHHHHHHHHHHTTCCCHHEEHHHHHHHTTCCHCCHHHHHHHHHHHHHHCCEEEEEECCCCCTCCCEEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEEETCEEEEETTCEEEEEEEECCHHHHCCCCCEEECTTCCEEECCCC
CCCCCCCCHHHHHHHHCCCECCCCCCCCHHHHHHTTCCCCCEEEEECCCCCCCCCCEEEEEECCCCCCCCCCCEEEEEEEEEEEECCCCHHHHHHHCCCCCCCCCCCCEEEEETTCCEEEECCEEEEHHHHHCCCHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCECCEEEEEEETCCCCCCEEEEEEHHHHHHTCEEEEEEETTEEEEEEEEECCCCCCCCCCCCEEEEECCEEEEECCHHHHHHCCCCTTCCCCCCCEEEEEEEECCCCCCCEEEEEEEECCCCCCCCCCCCEEEEEEEEEEEETTTEEEEEEHHHEEEEEHCTTCCCEEEEEEEEHHHTTCECCCHHHHHHHHHHHHHCCTCCEEEECCCCCCCCCEEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECTCEEEEETTTEEEEEEEEECHHCHCCCCCEECCTTCCEEEEECC
CCCCCCCCCHHHHHHHCCCCCCCCCCCCEEHHHHTTCCCCCEEEECCCCCCCCCCCEEEEEECCCCCCCCCCCEEEEEEEEEEEECCCCHHHHHHTCCCCCCCCCCCCEEEEETTCCEEEECCEHHHHHHHHCCCHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCCEEEEEECCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCEEEHHHHHHHHHEEEEEEEEETTEEEEEEEEECCCCCCCCCCCCEEEECCCEEEEECCCCCCEECCCCTTCCCCCCCCEEEEECCCCCCCCCHEEEEEHECCCCCCCCCCCEEEEEEEEEEEECTTCCCEHHHHHHHHHHHHCTTCCEEEEEEECCCCCTCCCECCCCCHCHHHHHHHHHCCCEEEEECCCCCTCCCCEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECTTEEEEETTCCEEEEEEEECHHHHHCCCCCCCCTCCHHHHCCCC
predict: major vote:
CCCCCCCCCHHHHHHHCCCCCCCCCCCHHHHHHHTTCCCCCEEEEEECCCCCCCCCEEEEEECCCCCCCCCCCEEEEEEEEEEEEECCCHHHHHHHCCCCCCCCCCCCEEEEETTTCEEEECCHHHHHHHHHCCCHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEETTECCCCCEEEHHHHHEHHEECEEEEEEETTEEEEEEEEECCCCCCCCCCCCEEEECCCEEEEECCEEEHEECCCCTTCCCCCCCCEEEEEECCCCCCCCHEEEEEEECCCCCCCCCCCCEEEEEEEEEEEETTCCEEEEHHHHHHHHHHCTTCCCEEEEECCCHHHTTCEECCHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCEEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECTCEEEEEETTEEEEEEEECCHHHHCCCCCEECCTTCCEEECCCC
* predict: successful (+) prediction at output/6G44A.ss4
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 3 -r 1 -i /home/max/16jF_secnet_ubuntu/input/6G44A.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 3 labels of Rule #1: H, E, C
* predict: label definition: (C, S, T) -> C, (H, I, G) -> H, (E, B) -> E
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV1/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV2/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV3/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV4/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV5/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV6/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV7/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV8/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV9/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV10/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/6G44A.fasta
* predict: base name of entry is 6G44A
* predict: parsed sequence from the input file is:
GAMGMNTPPELDTVLQAPYAYNWPTSKNVKIASRIGIPYSTFQTIQPVSDAPNNGIGQITFNQPLGNLTGGAPRLRVSFTAEIKNILADSSLKDQIGLKSFPVNRSIPVAVINMNGKTFTSYPAQLIKLHQYNADPLELALLSPCSDVDEYNKIKAVSMNNPYRQGTESTDSRMSRGLGCNYAYYIHPRAAGSTSVKIDFVVDEALVANPTQYKNIKDPVPFRNLNTFKVILDGQFKPENMIGIADDVKLVAGKADFEVDITGFKINMLVQNWVAPLEIGDIPKTIIYNTPLISLEGNISSMCLNTKDPYGIPGERNKHILTTHSMAMNNVPSMFAVMVSQETPTKKFAPDQLAGIIGLEIKVDSDVGIFRELEQQQLYELSSSNGYNKRFSCFSGALANGLTVADPAVAAGNKFKEAIFGAGSVIFFRPSDLGLKDYNVMANANKSINMQVQATFVTPEAAGTGAHYKLEVFSIRDNLTYSFEDGTFMDDLTLYTPDQLLRSPLKLTDDNNKLMRVMGG
* predict: prediction file will be output/6G44A.ss3rule1
predict: predicted secondary structure for 10 models
CCCCCCCCCCHHHHCCCCCECCCCCCHHHHHHHHCCCCHHHEEEEEECCCCCCCCEEEEEECCCCCCCCCCCCEEEEEEEEEEEEECCCCHHHHHCCCCCCCCCCCCCEEEEEECCEEEEECCHHHHHHHHHCCCHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHEEECCCCCCCCEEEEEEEECCCCCCCHHHHCCCCCCCCCCCCCEEEEEECCECCCHHEEEEHHHHEEECCCEEEEEEECCEEEEEEEECCCCCCCHCCCCCEEEECCCEEEEECCHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCHHEEEEEECCCCCCCCCCHHEEEEEEEEEEECCCCCHEEHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCEECCHHHHHHHHHHHHHCCCCEEEEECHHHCCCCCEEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCCEEEEEEECCCHHCCCCCCECCCCCCCEEEECCC
CCCCCCCCCCHHHHHCCCCCCCCCCCCCHHHHHHHCCCHHHEEEEECCCCCCCCCCEEEEECCCCCCCCCCCCEEEEEEEEEEEEHHCCHHHHHHCCCCCCCCCCCCCEEEEECCCCEEEECCHHHHHHHHHCCCHHHHHHCCCCCCCCHCCHHEEEECCCCCCCCCCCCCCCCCCCCCCEHHEEECCCCCCCCEEEEEEEEECCHHCCHHHHHCCCCCCCCEECCEEEEEEECCCCHHHEEHHHHHHHHECCEEEEEEEECCCEEEEEEEECCCCCCECCCCCEEEECCCEEEEECCCEEEEEECCCCCCCCCCCCCEEEECCCHHHCCCCCEEEEEECCCCCCCCCCCCHHEEEEEEEEEECCCCCCEEECCHHHHHHHHCCCCCCEEEEEEEHHHCCCCCCCCHHHHHHHHEEHHCCCCCCEEEECHHHCCCCCEEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCCEEEEEEECCHHHHCCCCCEECCCCCCEEEECCC
CCCCCCCCCCHHHHHCCCCEECCCCCCCEEHHHHHCCCHHHHEEEEECCCCCCCCCEEEEECCCCCCCCCCCCEEEEEEEEEEEEEECCHHHHHHCCCCCCCCCCCCEEEEEECCCCEEEECHHHHHHHHHHCCCHHHEEECCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEEEECCHCCCHHHHHCCCCCCCCECCCEEEEEECCEECCHHHEEHHHHHHHHCCEEEEEEEECCCEEEEEEEEECCCCCCCCCCCEEEECCCEEEEECCEEEEEECCCCCCCCCCCCCCEEEEEEECCCCCCCEEEEEEEEECCCCCCCCCCCEEEEEEEEEEECCCCCHEHHHHHHHHHHECCCCCCCHEEEECCCCCCCCEEECCHHHHHHHHHHHHHCCCCCEEEECHHHHCCCCEEEEEECCCEEEEEEEEEEECHHHCCCCCEEEEEEEEECCCEEEEECCCCEEEEEEECCHHHHCCCCCEECCCCCCEEEECCC
CCCCCCCCCCHHHHHCCCCECCCCCCHHHHHHHHHCCCCCEEEEEEECCCCCCCCEEEEEECCCCCCCCCCCCEEEEEEEEEEHHHHHCHHHHHHHCCCCCCCCCCCEEEEEEECCCEEEECCHHHHHHHHHCCCHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCEEEEEEEEECCCCCCHHHHHCCCCCCCCCCCCEEEEEECCCCCHHHEEEEEHHHEEHECCEEEEEEECCEEEEEEEEECCCCCCCCCCCCEEEECCCEEEECCCHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCCCCEEEEEEEECCCCCCCCCCHHHEEEEEEEEEECCCCCEEEECCHHHHHHHHHCCCCCCEEEECCHHHHCCCCECCHHHHHHHHHHHHHCCCCCEEEECHHHHCCCCHEEEECCCCCEEEEEEEEEECCCHCCCCCEEEEEEEEECCCEEEEECCCCEEEEEEECCHHHHCCCCEEECCCCHHHHEECCC
CCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHCCCCHHHEEEEECCCCCCCCCEEEEEECCCCCCCCCCCCEEEEEEEEEEEECCCCHHHHHHHCCCCCCCCCCCCEEEEECCCCEEEECCHEHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHEEEECCCCCCCCEEEEEEEEECCCCCCCHHHHCCCCCCCCEECCEEEEEEECEECCCCEEEEEEEEEEEECCEEEEEECCCCEEEEEEEECCCCCCCCCCCCEEEECCCEEEEECCHHHHEECCCCCCCCCCCCCCEEEEEEEHHHCCCCEEEEEEEECCCCCCCCCCHHEEEEEEEEEEECCCCCEEEEEHHHHHHHHHHCCCCEEEEEEECCCCCCCCEECCHHHHHHHHHHHHHCCCCEEEEECHHHCCCCHHEEECCCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCCEEEEEEECCCHHHCCCCCCCCCCCCCEEEECCC
CCCCCCCCCCHCHHHCCCCCCCCCCHHHHHHHHHHCCCHHHEEEECCCCCCCCCCEEEEEECCCCCCCCCCCCEEEEEEEEEEEHHHCCHHHHHHCCCCCCCCCCCCCEEEEECCCCEEEECCHHHHHHHHHCCCHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHCCCCCCCEEEEEEECCCCCCCEEEEEEEEEHHECCCHHHHHHCCCCCCCCCCCEEEEEEECEECCHHCEEEECHHEEEECCEEEEEEECCCEEEEEEEHCCCCHHHCCCCHEEEEECCEEEECCCCEEEEECCCCCCCCCCCCCHHEEEEEEEECCCCCEEEEEEECCCCCCCCCCCCCECEEEEEEEEEECCCCHEEHHHHHHHHHHCCCCCCEEEEEECCCCHHCCCEECCHHHHHHHHHHHHHCCCCEEEEECHHHCCCCCEEEECCCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEEECCEEEEECCCCEEECEEECCCHHHCCCCCCCCCCCHHHHHHCCC
CCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHHHHCCCCHHHEEEEEECCCCCCCCEEEEEECCCCCCCCCCCCEEEEEEEEEEEEEHHHHHHHHHCCCCCCCCCCCCEEEEEEECCCEEEECCHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCEEEEEEEEECCCCCCHHHHHCCCCCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHCCCCEEEEEECCCEEEEEEECCCCCCCHCCCCCEEEECCCEEEEECCEEEEEEECCCCCCCCCCCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCHHHHCCEEEEEEEECCCCCEEEEHHHHHHHHHHHCCCCEEEEEECCCCCCCCCEECCHHHHHHHHHHHECCCCCEEEEECHHHCCCCHHEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCCEEEEEEECCHHHHCCCCCEEECCCCHHEECCCC
CCCCCCCCCHHHHHHCCCCCCCCCCCCCHHHHHHCCCCHHHEEECCCCCCCCCCCEEEEEECCCCCCCCCCCCEEEEEEEEEHHHHHCHHHHHHHHCCCCCCCCCCCCEEEEECCCCEEEECCHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHEEEECCCCCCCCEEEEEEEEEHHHHCCHHHHHCCCCCCCCCCCCEEEEEEECCCCCHHEEEEEEEEHHHCCCCEEEEEECCEEEEEEEEECCCCCCCCCCCCEEEEECCEEEEECCHHHHHCCCCCCCCCCCCCCCEEEEEEEHHCCCCCHHHEEHHHCCCCCCCCCCHHCCEEEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECHHHCCCEECCHHHHHHHHHHHHHCCCCCEEEECHHHCCCCCHEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCCEEEEEECCCHHHHHCCCCCECCCHHHHHHHCCC
CCCCCCCCCHHHHHHHCCCCCCCCCCCCHHHHHHCCCCHHHEEECCCCCCCCCCCCEEEEECCCCCCCCCCCCEEEEEEEEEEHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCEEEECHHHHHHHHHHCCCHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCEEEEEEEEECCCCCCHHHHCCCCCCCCCECCCEEEEEEECCCCCCCEEEEEEEEEEEECEEEEEEEECCEEEEEEEEECCCCCCHCCCCCEEEECCCEEEECCCHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCCCCHHHHHEEECCCCCCCCCCHHHHCEEEEEEEECCCCCEEEECCHHHEEEEECCCCCEEEEEECHHHHHHCCCCCCHHHHHCHHHHHHCCCCCEEEEECHHHCCCCHHEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEEECCEEEEECCCCEEEEEEECCCHHHCCCCEEECCCCCCEEEECCC
CCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHCCCCHHHHEEEECCCCCCCCCCEEEEECCCCCHCCCCCCEEEEEEEEEEEEECCCCHHHHHCCCCCCCCCCCCCEEEEECCCCEEEECCHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCEEEEEEEEECCHHCCHHHHHCCCCCCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHCCEEEEEEECCEEEEEEEEECCCCCCCCCCCCEEEECCCEEEEECCHHHEECCCCCCCCCCCCCCCEEEEECCECCCCCCHEEEEEEECCCCCCCCCCHHEEEEEEEEEEECCCCCHEEEHHHHHHHHHHHCCCCCCEEEECCCCCCCCCECCCHHHHHHCEEEECCCCCCCEEEECHHHHCCCCCHEECCCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCCEEEEEEECCCCHCCCCCCEECCCCCHHHHCCCC
predict: major vote:
CCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHCCCCHHHEEEEECCCCCCCCCEEEEEECCCCCCCCCCCCEEEEEEEEEEEEHHCCHHHHHHCCCCCCCCCCCCCEEEEECCCCEEEECCHHHHHHHHHCCCHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCEEEEEEEEECCCCCCHHHHHCCCCCCCCCCCCEEEEEEECCCCCHHEEEEEHHHEEECCCEEEEEEECCCEEEEEEEECCCCCCCCCCCCEEEECCCEEEEECCHHHEEECCCCCCCCCCCCCCEEEEEEECCCCCCCEEEEEEEECCCCCCCCCCHHEEEEEEEEEEECCCCCHEEEHHHHHHHHHHHCCCCCEEEEECCCCCCCCCEECCHHHHHHHHHHHHHCCCCCEEEECHHHCCCCCHEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCCEEEEEEECCCHHHCCCCCEECCCCCCEEEECCC
* predict: successful (+) prediction at output/6G44A.ss3rule1
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 3 -r 2 -i /home/max/16jF_secnet_ubuntu/input/6G44A.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 3 labels of Rule #2: H, E, C
* predict: label definition: (C, S, B, T, I, G) -> C, (H) -> H, (E) -> E
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV1/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV2/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV3/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV4/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV5/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV6/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV7/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV8/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV9/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV10/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/6G44A.fasta
* predict: base name of entry is 6G44A
* predict: parsed sequence from the input file is:
GAMGMNTPPELDTVLQAPYAYNWPTSKNVKIASRIGIPYSTFQTIQPVSDAPNNGIGQITFNQPLGNLTGGAPRLRVSFTAEIKNILADSSLKDQIGLKSFPVNRSIPVAVINMNGKTFTSYPAQLIKLHQYNADPLELALLSPCSDVDEYNKIKAVSMNNPYRQGTESTDSRMSRGLGCNYAYYIHPRAAGSTSVKIDFVVDEALVANPTQYKNIKDPVPFRNLNTFKVILDGQFKPENMIGIADDVKLVAGKADFEVDITGFKINMLVQNWVAPLEIGDIPKTIIYNTPLISLEGNISSMCLNTKDPYGIPGERNKHILTTHSMAMNNVPSMFAVMVSQETPTKKFAPDQLAGIIGLEIKVDSDVGIFRELEQQQLYELSSSNGYNKRFSCFSGALANGLTVADPAVAAGNKFKEAIFGAGSVIFFRPSDLGLKDYNVMANANKSINMQVQATFVTPEAAGTGAHYKLEVFSIRDNLTYSFEDGTFMDDLTLYTPDQLLRSPLKLTDDNNKLMRVMGG
* predict: prediction file will be output/6G44A.ss3rule2
predict: predicted secondary structure for 10 models
CCCCCCCCCCHHHHCCCCCEECCCCCCHHHHHHHCCCCCCCCEEECCCCCCCCCCEEEEEEECCCCCCCCCCCEEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCEEEECCHHHHHHHHCCCCHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCEEEEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEECCECCCCCCHHHHHHHHHECCEEEEEEEECCEEEEEEEEECCCCCCCCCCCCEEEEECCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECEEECCCCCEEEEEEEECCCCCCCCCCCCECEEEEEEEEECCCCCEEEHHHHHHHHHECCCCCCEEEEEEECCEECCCCECCCHHHHHCHHHHHHCCCCCCEEEECCCCCCCCCEEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCEEEEEEEECCCCCCCCCCCECCCCCCCEEHHCCC
CCCCCCCCCCHCCCCCCCCCCCCCCCCCHEEHHHCCCCCCCCEEEEECCCCCCCCCCEEECCCCCCCCCCCCCEEEEEEEEEEEECCCCCCHHCCCCCCCCCCCCCCCEEEEEECCCEEECCCHHHHHHHCCCCCHHHHHCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHEECCCCCCCCEEEEEEEECCCCHCCCCCCCCCCCCCCCCCCEEEEEEEECECCCCCCCCCCCHHHHHCCCCEEEEECCCCEEEEEEECCCCCCCCCCCCCEEEECCCCEEECCCCCEEEECCCCCCCCCCCCCCEEECCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCHHHHHHHCCCCCCCCEEECCCCCCCCCCECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCEECCCCCCEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCEEEEECCCEEEEEEEECCHHHHCCCCCCCCCCCCCCHCCCCC
CCCCCCCCCHHHHHHHCCCCCCCCCCCHHHHHHHCCCCCCCEEEEECCCCCCCCCCEEEEEECCCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHCCCCCCCCCCCEEEEEEECCCCEEECCCHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEEECCHHHCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEEECCEEEEEEEEECCCCCCCCCCCCEEEECCCEEEEECCHHHHHECCCCCCCCCCCCCCEEEEECCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCEEEECCHHEEEEEECCCCCCEEEECCCCCCCCCEEECCCHHHCCHHHHHHHCCCCEEEEECCCCCCCCCEEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCCEEEEEEEECHHHHCCCCCCECCCCCCEEEECCC
CCCCCCCCCHHHHHHCCCCCCCCCCCCCCEHHHHCCCCCCCEEEECCCCCCCCCCCEEEEECCCCCCCCCCCCCEEEEEEHHHHHHHHCHHHHHHCCCCCCCCCCCEEEEEEECCCCEEEECCHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEHHCCHEHHCCCEEEEEECCCHEHEHHHECCCCCCCCCCCCCEEEECCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCEEEEEEHCCCCCCCCCCCCCCCEEEEEEEECCCCCHEHHHHHHHHHHHHHCCCCCCCEECCCCCCCCCCCECCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCEECCCCCCEEEEEEEEEECCCCCCCCCEEEEEEEECCCCEEEECCCCCEEEEEEECCCCCCCCCCCEECCCCCCEEEECCC
CCCCCCCCCCCCHHCCCCCCCCCCCCHHHHHHHHCCCCCCCEEEEEECCCCCCCCCCEEEECCCCCCCCCCCCEEEEEEEEEEEECCCCHHHHHHCCCCCCCCCCCCCEEEEEECCCEEEECCCCEEEEHCCCCCHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCEEEECCEEEECCEEEEEEEECCEEEEEEEEEECCCCCCCCCCEEEEEECCEEEECCCHHHHHECCCCCCCCCCCCCCEEEEEECECCCCCCHHEEEEEECCCCCCCCCCCCCCEEEEEEEEECCCCCCEEEHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCEEEECCCCCEEECEECCCCCCCCCCCEEECCCCCCEEEEECC
CCCCCCCCCCHHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCHEEEECCCCCCCCCEEEEEECCCCCCCCCCCCEEEEEEEEEEHHHHHCCCHHCCCCCCCCCCCCCCEEEEEECCCCEEEECCHHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEEEECEECCCCEEEEHCCHHHHCCCEEEEEEECCCEEEEEEEHCCCCCCCCCCCEEEEECCCEEEECCCEEEHHECCCCCCCCCCCCCCEEEEECCCCCCCCCEEEEEHEECCCCCCCCCCCCCCCEEEEEEEECCCCCHEHHHHHHHHHHHHCCCCCCEEEEECCCCHHCCCCCCCHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCEEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCCEEEEEEECCCCCCCCCCCCCCCCCCHEEEECCC
CCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHCCCCCCCEEEECCCCCCCCCCCEEEEECCCCCCCCCCCCEEEEEEEEEEHCHCCCHHHHHHCCCCCCCCCCCCCEEEEECCCCEEEECCCHHHHHHHHCCCHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHCCCEEEEECCCCEEEEEEEECCCCCCCCCCCCEEEECCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCEEEEEEEECCCCCEEEECCHHHHHHHCCCCCCCCEEEECCCCCCCCCEECCHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCEEEECCCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEECCCCCEEEEEEECCHHHHCCCCCCCCCCCCCHHHHCCC
CCCCCCCCHHHHHHHCCCCEECCCCCCCHEHHHHCCCCCCCEEEEECCCCCCCCCCEEEEECCCCCCCCCCCCEEEEEEEEEEECCCCCHHHHHHCCCCCCCCCCCCEEEEEEECCCEEEECCCEEEHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHCCCCCCCCCEEEEECCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEEECECCCCCCEEHEHHEEEECCCEEEEEEECCCEEEEEEEECCCCCCCCCCCCEEEEECCEEEEECCCCEEEEECCCCCCCCCCCCCEEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCEEEEEEEECCCCCCEEHHHHHHHHHHHCCCCCCEEEEEECCCCCCCEEECCHHHHCHHHHHHHHCCCCCEEEECCCCCCCCCCEEECCCCCCEEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEECCCCCEEEEEEECCCCHHCCCCCEECCCCCCEEECCCC
CCCCCCCCCCHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCCEEEECECCCCCCCCCEEEEECCCCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHCCCCCCCCCCCCEEEEEEECCCEEEECCCEEEEHCCCCCCCCCHCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCEEEEEEEECCCHHCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCEHHHHHHHHHHCCCEEEEEECCEEEEEEEEECCCCCCCCCCCCEEEECCCCEEEECCHHHEEECCCCCCCCCCCCCCEEEECCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCEEEEEEEECCCCCCEEECCHHHHEHHHCCCCCEEEEEEECCCCCCCCCCCCHHHHHCHHEEEECCCCCEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCCEEEEEEEECHHHHCCCCCECCCCCCHHHHCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCEEEECCCCCCCCCCEEEEEECCCCCCCCCCCCEEEEEEEEEEEECHCCCCHHHHCCCCCCCCCCCCCEEEEECCCCEEEECCCCHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCHEEHHHHHHHHECCEEEEEECCCEEEEEEEEECCCCCCCCCCCCEEEEECCEEEECCCCCCEEECCCCCCCCCCCCCCEEECCCCCCCCCCHHHEEEEEECCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCECCCCHHHCCCCEEEECCCCCEEEEECCCCCCCCCHEEEECCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCCEEEEEEECCCCCCCCCCCCCCCCCCCEEEEECC
predict: major vote:
CCCCCCCCCCHHHHCCCCCCCCCCCCCCHHHHHHCCCCCCCEEEECCCCCCCCCCCEEEEECCCCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHCCCCCCCCCCCCCEEEEECCCCEEEECCCHHHHHHHCCCCHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEHHHHHHHHCCCEEEEEEECCEEEEEEEEECCCCCCCCCCCCEEEECCCEEEEECCCCCEEECCCCCCCCCCCCCCEEEECCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCEEEEEEEECCCCCCEEHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCEEECCCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEEECCCCEEEEEEECCCCCCCCCCCCCCCCCCCEEEECCC
* predict: successful (+) prediction at output/6G44A.ss3rule2
* predict: returned code is 0 (0 = success, non-zero = failure)

4 of 5] processing of /home/max/16jF_secnet_ubuntu/input/5YH1A.fasta
* script: /home/max/16jF_secnet_ubuntu/bin/run_psiblast.py3 /home/max/16jF_secnet_ubuntu/input/5YH1A.fasta
* script: psiblast is set to use 8 CPU cores
* command: /home/max/16jF_secnet_ubuntu/3rd_software/unix/ncbi-blast-2.6.0+/bin/psiblast -db /home/max/16jF_secnet_ubuntu/3rd_databases/blast/uniref90.fasta -query /home/max/16jF_secnet_ubuntu/input/5YH1A.fasta -inclusion_ethresh 0.001 -evalue 10 -save_pssm_after_last_round -out_ascii_pssm /home/max/16jF_secnet_ubuntu/features/psiblast/5YH1A.mtx -num_iterations 2 -num_threads 8 -save_each_pssm > /dev/null 2>&1
* script: /home/max/16jF_secnet_ubuntu/bin/run_hmm.py3 /home/max/16jF_secnet_ubuntu/input/5YH1A.fasta
* command: bash /home/max/16jF_secnet_ubuntu/3rd_software/generic/process_hmm.bash -i /home/max/16jF_secnet_ubuntu/input/5YH1A.fasta
* hhm: number of detected CPU cores is 8
* hhm: 8 CPU cores will be used
* hhm: input fasta is /home/max/16jF_secnet_ubuntu/input/5YH1A.fasta
* hhm: /home/max/16jF_secnet_ubuntu/3rd_software/unix/hh/hh/buildali2.pl /home/max/16jF_secnet_ubuntu/features/temp/5YH1A_10887/5YH1A.seq -cpu 8 -noss 1>/home/max/16jF_secnet_ubuntu/features/temp/5YH1A_10887/5YH1A_alignment.output 2>/home/max/16jF_secnet_ubuntu/features/temp/5YH1A_10887/5YH1A_alignment.error
* hhm: /home/max/16jF_secnet_ubuntu/3rd_software/unix/hh/hh/hhmake -i /home/max/16jF_secnet_ubuntu/features/temp/5YH1A_10887/5YH1A.a3m -o /home/max/16jF_secnet_ubuntu/features/hhm/5YH1A.hhm1 1>/home/max/16jF_secnet_ubuntu/features/temp/5YH1A_10887/5YH1A_hhmake.output 2>/home/max/16jF_secnet_ubuntu/features/temp/5YH1A_10887/5YH1A_hhmake.error
* hhm: success
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 8 -i /home/max/16jF_secnet_ubuntu/input/5YH1A.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 8 labels: H, E, C, T, G, S, B, I
* predict: label definition: 8 original DSSP labels unchanged (C, S, B, T, I, G, H, E)
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/8label
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/8label/CV1/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/8label/CV2/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/8label/CV3/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/8label/CV4/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/8label/CV5/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/8label/CV6/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/8label/CV7/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/8label/CV8/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/8label/CV9/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/8label/CV10/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/5YH1A.fasta
* predict: base name of entry is 5YH1A
* predict: parsed sequence from the input file is:
PGSHMAEVKRKIEEELDRRAQPSDVGFLVKSEVLEALKPKIMKAAFMIRRAIFEGRPIILRHHADTDGYTAGVALETAIIPLIEKVAPDPEARWHLFKRRPSRAPFYELEDVLKDIIFMMEDHMRFGDELPLVVIVDNGGTTEDIPAYKRLKAYGVKIVVIDHHDPRDWISEDKAKVDEYVDVHVNPHHVKRGYYELTAGMLATEVARYINPEVEDRIKHLPAIAGTGDRSKAPEFYQYLEYAKEKGLDEEDLKKIAEVIDHEAFYWKFMDGRGIIEEILLITGNLQRHRMLVEGIYPEVKEKQEKVLKAVLPHVKSVVLPNGIRFNTIDVELYAPKFEYPSPGKLSGIIHDHFKEQYGEDSPILTLAYGPDFAVVRASDGMAKYNFDLNKIVKILAEKLPDAGVEGGGHSYAGSIKFFEGKRKEVLEAFAKEVLKLKAGE
* predict: prediction file will be output/5YH1A.ss8
predict: predicted secondary structure for 10 models
CCHHHHHHHHHHHHHHHHHHCCCCCCGGGTCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSSHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCTSCCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEECCCCCGTGHHHHHHHHHHTCCEEEEESSCCCCCCCTGGCEECTTCCEEECTTTTTSSCHHHHHHHHHHHHHHHHCTTHHHHHTTSCEEEEEECCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGTEEEEECTTSCEEEEEEHHHHTTTCCCCCHHHHHHHHHHHHHHHHCSSSCEEEEEEETTEEEEEECSCCCTTCCCHHHHHHHHHHHCTTSCEEECCCSTEEEEEECTTCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCGCCCCGGGCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSSHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCTSSCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEEECCCCGTGHHHHHHHHHTTCCEEEEESCCCCGGCCTTCCEECTTCCEEECTTGTTSCHHHHHHHHHHHHHHHHHCTGGHHHHTTCHEEEEEECCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHTCTSCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGEEEEECTTSCEEEEEEHHHHCTTCCCCCHHHHHHHHHHHHHHHHCTTCCEEEEEEETSEEEEEECTSCCTTTCCHHHHHHHHHHHCTTCEEEECCCSSEEEEEEETTCHHHHHHHHHHHHHHHHCCC
CCHHHHHHHHHHHHHHHHHCCCCGCGGGGTCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSSHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCSSCCCCHHHHHHHHHHHHHHHHHHTCCCEEEEEECCTCCTTGHHHHHHHHHTTCCEEEEECCCCCSCCCTTCCEECTTCCCECCTTCCCTTGHHHHHHHHHHHHHHHHCTTGHHHHTTHHHEEEECCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHTCTCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGEEEEECTTSCEEEEEEHHHHCTTCCCCCHHHHHHHHHHHHHHHHCTTCCEEEEEECTSEEEEEECSCCCTTCCCHHHHHHHHHHHCTTSCEEECCCSEEEEEEECTTCHHHHHHHHHHHHHHHHCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSSHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCSSCCCCHHHHHHHHHHHHHHHHHHTSCCCEEEEECCCCCTGGHHHHHHHHHTTCSEEEEESCCCCGCCCTTCEEECTTCCEECCGGGTTSTCHHHHHHHHHHHHHHHHCGGGGGGGTTSHHEEEEECCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHTCTSCHHHHHHHHHHHHHHHHHHHHHHHHHHGTTEEEEECTTSCEEEEEEHHHHTTTCCCCCHHHHHHHHHHHHHHHHCSSSCEEEEEECTTEEEEEECSCHHTTTCCHHHHHHHHHHHCTTCEEEECCCSTTCEEEECTTCHHHHHHHHHHHHHHHHCCC
CCHHHHHHHHHHHHHHHHHHCCCCCCCHHCCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSSHHHHHHHHHHHHHHHHHHHHHCSCTTCCEEEEEECCCSSCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEECCCCCGGGHHHHHHHHHTTCCEEEEESCCCCGCCCTTCCCCCTTCCEECCTGGCTTCCHHHHHHHHHHHHHHHHCTTHHHHHTTHHHHEEEECCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGEEEEECTTSCEEEEEEHHHHCTTCCCCCHHHHHHHHHHHHHHHHCSTSCEEEEEEETTEEEEEECHHHHTTCCCHHHHHHHHHHHCTTCCEEECCCSSCEEEEECTTGHHHHHHHHHHHHHHHHCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCGGGGCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSSHHHHHHHHHHHHHHHHHHHHHCCCTTCEEEEEEECCTSCCTTCHHHHHHHHHHHHHHHHHHTCCCCEEEEEECCCCGGGHHHHHHHHHHTCCEEEEESCCCCSCCCTTCCEECTTCCEECCTTGCCCCGHHHHHHHHHHHHHHHHCHHHHHHHTTSCEEEEEECCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGEEEEECTTSCEEEEEEHHHHGTTCCCCCHHHHHHHHHHHHHHHHCSTCCEEEEEECTTEEEEEECSCHHTTCCCHHHHHHHHHHHCTTCEEEEEECTTEEEEEECTTCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCGGGGCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSSHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCTSSCCCCHHHHHHHHHHHHHHHHHHTCCCEEEEEEECTCCGGGHHHHHHHHHTTCSEEEEECCCCCGCCCTCCCEECTTCCEEECTTGTTTTCHHHHHHHHHHHHHHHHCTTHHHHHHTSHEEEEEECCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHTCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGEEEEECTTSCEEEEEEHHHHCTTCCCCCHHHHHHHHHHHHHHHHCSSSCEEEEEEETSEEEEEECTTHHTTTCCHHHHHHHHHHHCTTCCEECECCTTTEEEEEETTCHHHHHHHHHHHHHHHHCCC
CCHHHHHHHHHHHHHHHHHCCCGCCCHGGCCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSSHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCTSSCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEECCTCCGGGHHHHHHHHHTTCCEEEEECCCCCGCCCTTCCEECTTCCEEECTTGTTTTCHHHHHHHHHHHHHHHHCTHHHHHGGGSCEEEEEECCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGTEEEEEETTSCEEEEEEHHHHCTTCCCCCHHHHHHHHHHHHHHHHCTSSCEEEEEECTSEEEEEECSCCCTTTCCHHHHHHHHHHHCTTCEEEEECCSTCEEEEECTTCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCGGGTSHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSSHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCTSCCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEEECCCCGGGHHHHHHHHHHTCSEEEEESCCCCSCCCTTCCEECTTCCEECCGTGTTTTCHHHHHHHHHHHHHHHHCTTHHHHHHTSCEEEEEECCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGEEEEEETTSCEEEEEECGGTCTTCCCCCHHHHHHHHHHHHHHHHCSSSCEEEEEEETTEEEEEECTTHHTTTCCHHHHHHHHHHHCTTTEECCCSCSSEEEEEECTTCHHHHHHHHHHHHHHHHCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCGGGCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSSHHHHHHHHHHHHHHHHHHHHHCCCTTGCEEEEEECCCSSCCCCHHHHHHHHHHHHHHHHHHTCCCEEEEEECCCCCGGGHHHHHHHHHHTCCEEEEESSCCCGGCCTTGCECCTTCCEEECTTTTTSTHHHHHHHHHHHHHHHHHCHHHHHHHTTHHHHHHHHTCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHTCSCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGEEEEECTTSCEEEEEECHGHCTTCCCCCHHHHHHHHHHHHHHHHCSCCCEEEEEEETSEEEEEECSCCCCTTCCHHHHHHHHHHHCTTCCECCCCCSSEEEEEECTTCHHHHHHHHHHHHHHHHCCC
predict: major vote:
CCHHHHHHHHHHHHHHHHHCCCCCCCGGGGCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSSHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCTSSCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEECCCCCGGGHHHHHHHHHTTCCEEEEESCCCCGCCCTTCCEECTTCCEECCTTGTTTTCHHHHHHHHHHHHHHHHCTTHHHHHTTSHEEEEEECCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHTCTSCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGEEEEECTTSCEEEEEEHHHHCTTCCCCCHHHHHHHHHHHHHHHHCSSSCEEEEEEETSEEEEEECSCCCTTTCCHHHHHHHHHHHCTTCCEEECCCSTEEEEEECTTCHHHHHHHHHHHHHHHHCCC
* predict: successful (+) prediction at output/5YH1A.ss8
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 5 -i /home/max/16jF_secnet_ubuntu/input/5YH1A.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 5 labels: H, E, C, T, G
* predict: label definition: (C, S, B) -> C, (H, I) -> H, (E) -> E, (T) -> T, (G) -> G
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/5label_practical
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV1/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV2/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV3/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV4/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV5/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV6/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV7/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV8/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV9/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV10/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/5YH1A.fasta
* predict: base name of entry is 5YH1A
* predict: parsed sequence from the input file is:
PGSHMAEVKRKIEEELDRRAQPSDVGFLVKSEVLEALKPKIMKAAFMIRRAIFEGRPIILRHHADTDGYTAGVALETAIIPLIEKVAPDPEARWHLFKRRPSRAPFYELEDVLKDIIFMMEDHMRFGDELPLVVIVDNGGTTEDIPAYKRLKAYGVKIVVIDHHDPRDWISEDKAKVDEYVDVHVNPHHVKRGYYELTAGMLATEVARYINPEVEDRIKHLPAIAGTGDRSKAPEFYQYLEYAKEKGLDEEDLKKIAEVIDHEAFYWKFMDGRGIIEEILLITGNLQRHRMLVEGIYPEVKEKQEKVLKAVLPHVKSVVLPNGIRFNTIDVELYAPKFEYPSPGKLSGIIHDHFKEQYGEDSPILTLAYGPDFAVVRASDGMAKYNFDLNKIVKILAEKLPDAGVEGGGHSYAGSIKFFEGKRKEVLEAFAKEVLKLKAGE
* predict: prediction file will be output/5YH1A.ss5
predict: predicted secondary structure for 10 models
CCCHHHHHHHHHHHHHHHHCCCCCCCHCCCCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEEECCCCGGGHHHHHHHHHTTCCEEEEECCCCCCCCCTCCCCCCTTCCCCCCTTCCCCCCHHHHHHHHHHHHHHHHCTHHHHHHHTHHHHHHHCCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGEEEEEETTCCEEEEEEHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCTCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCTTCCECCCCCCTTTEEEECTTCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCHHCCCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCTCCGGGHHHHHHHHHTTCCEEEECCCCCCCCCCTCCCCCCTTCCEECCTTCCCCCCHHHHHHHHHHHHHHHHCTTHHHHHTTCCEEEEECCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGTEEEEECTTCCEEEEEEGGGCCTTCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCTTCCHHHHHHHHHHHCTTCCEEEECCCTEEEEEECTTCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCHHHHTCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEEECCCCGGGHHHHHHHHHTTCCEEEEECCCCCHHCCTCCCEECTTCCEECCTTCCCCCCHHHHHHHHHHHHHHHHCGTHHHHHHTCCHEEEEECCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGEEEEEETTCCEEEEEEHHHHGGGCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCTCCCHHHHHHHHHHHCTTCEEEEECCCCECCEEECTTCHHHHHHHHHHHHHHHHCCC
CHHHHHHHHHHHHHHHHHHCCCCCCCHHHTCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEEECCCCGGGHHHHHHHHHTTCCEEEECCCCCCCCCCTCCCCCCTTCCCCCCTTCCCCCCHHHHHHHHHHHHHHHHCTTHHHHHTTCCEEEEECCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGTTEEEEECTTCCEEEEEEHHHHCTCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECTTEEEEEECCCCCCTCCCHHHHHHHHHHHCTTCEEEECCCCCCCEEEECTTCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCHHHHTCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEECCCCCGGGHHHHHHHHHTTCCEEEEECCCCCCCCCTTCCEECTTCCEECCTTCCCCCCCHHHHHHHHHHHHHHHCTTHHHHHHTCHHHHHHCCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGEEEEEETTCCEEEEEEHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCTCCCHHHHHHHHHHHCTTCEEEECCCCTTEEEEECTTCHHHHHHHHHHHHHHHHCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCHGCCCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCGGGHHHHHHHHHTTCCEEEECCCCCCCCCCTCCCEECTTCCCCCCGGCCCCCCCCHHHHHHHHHHHHHHCTTHHGHGGTHHHHHEEECCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGTEEEEECTTCCEEEEEECGGCTTTCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECTTEEEEEECCCCCCTCCCHHHHHHHHHHHCTTCEEEECCCCTCCEEEECTTCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCHHHTCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEECCCCCGTGHHHHHHHHHTTCCEEEEECCCCCCCCCTCCCEECTTCCCECCTTTCCCCCCHHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGEEEEEETTCCEEEEEEHHHHCTTCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECTTEEEEEECCCCCCTCCCHHHHHHHHHHHCTTCCEEECCCCCCCCEEECTTCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCHHHHTCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCTCCCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEECCCCCGGGHHHHHHHHHTTCCEEEEECCCCCCCCCCCCCCCCTTCCCCCCTTCTCCCCHHHHHHHHHHHHHHHHCTTHHHHHGTCCEEEEECCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGEEEEECTTCCEEEEEEHHHHTTTCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCHHHTCCCHHHHHHHHHHHCTTCCEECCCCCTCEEEEECTTCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCHHHTCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHTCCCEEEEEEECCCCGGGHHHHHHHHHTTCCEEEEECCCCCCHCCTCCCEECTTCCCCCCTTHCCCCCHHHHHHHHHHHHHHHHCTTHHHHHTTCHEEEEECCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGCEEEECTTCCEEEEEECGGCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCTCCCHHHHHHHHHHHCTTCEEEECCCCCCEEEEECTTCHHHHHHHHHHHHHHHHCCC
CCHHHHHHHHHHHHHHHHHCCGGGCHHHHTCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEECCCCCTGGHHHHHHHHHTTCCEEEEECCCCCCCCCTCCEEECTTCCEECCCTGCCCCCHHHHHHHHHHHHHHHHCHHHHHHHTHHHHHHHHHCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGEEEEECTTCCEEEEEECGGTGTTCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCTCCCHHHHHHHHHHHCTTCCEEEECCCCCCCEEECTTCHHHHHHHHHHHHHHHCCCC
predict: major vote:
CCHHHHHHHHHHHHHHHHHCCCCCCCHHHTCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEECCCCCGGGHHHHHHHHHTTCCEEEEECCCCCCCCCTCCCEECTTCCCCCCTTCCCCCCHHHHHHHHHHHHHHHHCTTHHHHHHTCHHEEEECCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGEEEEECTTCCEEEEEEHHHHCTTCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCTCCCHHHHHHHHHHHCTTCCEEECCCCCCCEEEECTTCHHHHHHHHHHHHHHHCCCC
* predict: successful (+) prediction at output/5YH1A.ss5
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 4 -i /home/max/16jF_secnet_ubuntu/input/5YH1A.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 4 labels: H, E, C, T
* predict: label definition: (C, S, B, G) -> C, (H, I) -> H, (E) -> E, (T) -> T
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/4label_practical
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV1/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV2/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV3/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV4/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV5/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV6/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV7/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV8/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV9/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV10/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/5YH1A.fasta
* predict: base name of entry is 5YH1A
* predict: parsed sequence from the input file is:
PGSHMAEVKRKIEEELDRRAQPSDVGFLVKSEVLEALKPKIMKAAFMIRRAIFEGRPIILRHHADTDGYTAGVALETAIIPLIEKVAPDPEARWHLFKRRPSRAPFYELEDVLKDIIFMMEDHMRFGDELPLVVIVDNGGTTEDIPAYKRLKAYGVKIVVIDHHDPRDWISEDKAKVDEYVDVHVNPHHVKRGYYELTAGMLATEVARYINPEVEDRIKHLPAIAGTGDRSKAPEFYQYLEYAKEKGLDEEDLKKIAEVIDHEAFYWKFMDGRGIIEEILLITGNLQRHRMLVEGIYPEVKEKQEKVLKAVLPHVKSVVLPNGIRFNTIDVELYAPKFEYPSPGKLSGIIHDHFKEQYGEDSPILTLAYGPDFAVVRASDGMAKYNFDLNKIVKILAEKLPDAGVEGGGHSYAGSIKFFEGKRKEVLEAFAKEVLKLKAGE
* predict: prediction file will be output/5YH1A.ss4
predict: predicted secondary structure for 10 models
CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEEECCCCCCCHHHHHHHHHTTCCEEEEECCCCCCCCCCCCCCCCTTCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCTTHHHHHHTCHHHEECCCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECTTCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCTCCCHHHHHHHHHHHCTTCEEECCCCTTTCCEEECTTCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHTTCCEEEECCCCCCCCCCCCCCCCCTTCCCECCCCCCCCCCHHHHHHHHHHHHHHHHCTTCHHHCTTCCEEEECCCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCTEEEEECTTCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCTTCCEECCCCCCCCEEEEETTCHHHHHHHHHHHHHHCCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEECCCCCCCCHHHHHHHHHTTCCEEEEECCCCCCCCCCCCCCCCTTCCEEECCCCCCCCCHHHHHHHHHHHHHHHHCTTCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECTTCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCTTCCEEEECCTTTCEEEECTTCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHCHHHHHHHHHTTCCEEEECCCCCCCCCCCCCCECCTTCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCTTCCCHHTTCHHHHHHCCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHTCTCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCTEEEEECTTCCEEEEEECHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCTTCEEECCCCCCCCEEEECTTCHHHHHHHHHHHHHHCCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCTCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHTTCCEEEECCCCCCCCCCCCCCEECTTCCCECCCCCCCCCCHHHHHHHHHHHHHHHHCHHHHHHHHTCHHEEEEECCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECTTCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECTCEEEEEECCCCCCCCCCHHHHHHHHHHHCTTCCEEECCCCCCEEEEECTTCHHHHHHHHHHHHHHHHCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEEECCCCCCCHHHHHHHHHTTCCEEEECCCCCCCCCCCCCCCCCTTCCEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHTTCHHHHEHCCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECTTCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCTTCEEEEECCCTEEEEEECTTCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEEECCCCCCCHHHHHHHHHTTCCEEEECCCCCCCCCCCCCCCCCTTCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCTTCCHHHHTCHHEEEECCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHTCCCHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECTTCCEEEEEECHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCTTCCECCCCCCCCCEEEECTTCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHTCCCCEEEEECCCCCCCCHHHHHHHHHTTCCEEEEECCCCHHHCCTCCCEECTTCCCCCCCCCCTCCCHHHHHHHHHHHHHHHHCTTCHHHHTHHHHHHHHCCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCTEEEEECTTCCEEEEEECCHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCTTCCCCCCCCCCCCEEEECTTCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHTTCCEEEEECCCCCCCCCTCCCECCTTCCCECCCCCCCCCCCHHHHHHHHHHHHHHHCTTCCCCCTTCHHHHHHHCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECTTCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECTCEEEEEECCCCCCCCCCHHHHHHHHHHHCTTCCEEEECCCTCEEEEECTTCHHHHHHHHHHHHHHHHCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHTTCCEEEECCCCCCCCCCTCCCCCCTTCCCCCCCCCCTCCCHHHHHHHHHHHHHHHHCTCCHHHCTTCCHHHEECCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCTEEEEECTTCCEEEEEECHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCTTCEEECCCCCCCCEEEECTTCHHHHHHHHHHHHHHHCCCC
predict: major vote:
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCTTCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHTTCCEEEECCCCCCCCCCCCCCCCCTTCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCTTCHHHHTTCHHHEEECCCCCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECTTCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCTTCCEECCCCCCCCEEEECTTCHHHHHHHHHHHHHHHCCCC
* predict: successful (+) prediction at output/5YH1A.ss4
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 3 -r 1 -i /home/max/16jF_secnet_ubuntu/input/5YH1A.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 3 labels of Rule #1: H, E, C
* predict: label definition: (C, S, T) -> C, (H, I, G) -> H, (E, B) -> E
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV1/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV2/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV3/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV4/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV5/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV6/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV7/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV8/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV9/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV10/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/5YH1A.fasta
* predict: base name of entry is 5YH1A
* predict: parsed sequence from the input file is:
PGSHMAEVKRKIEEELDRRAQPSDVGFLVKSEVLEALKPKIMKAAFMIRRAIFEGRPIILRHHADTDGYTAGVALETAIIPLIEKVAPDPEARWHLFKRRPSRAPFYELEDVLKDIIFMMEDHMRFGDELPLVVIVDNGGTTEDIPAYKRLKAYGVKIVVIDHHDPRDWISEDKAKVDEYVDVHVNPHHVKRGYYELTAGMLATEVARYINPEVEDRIKHLPAIAGTGDRSKAPEFYQYLEYAKEKGLDEEDLKKIAEVIDHEAFYWKFMDGRGIIEEILLITGNLQRHRMLVEGIYPEVKEKQEKVLKAVLPHVKSVVLPNGIRFNTIDVELYAPKFEYPSPGKLSGIIHDHFKEQYGEDSPILTLAYGPDFAVVRASDGMAKYNFDLNKIVKILAEKLPDAGVEGGGHSYAGSIKFFEGKRKEVLEAFAKEVLKLKAGE
* predict: prediction file will be output/5YH1A.ss3rule1
predict: predicted secondary structure for 10 models
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEECCCCCEEEEEEHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCEEEECCCCCEEEEEECCCCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCHHHHCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCECCCCCCECCCCCCCCCHHHHHHHHHHHHHHHHHCHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEECCCCCEEEEEEHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCCEEEECCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCEEEEECCCCCHCCCCCCCEECCCCCEECCCCCCCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHCHHEEEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEECCCCCEEEEEEHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCEEEECCCCCCCCEEECCCCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEEECCCCEEEEEEHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCCEECCCCCCCEEEEEECCCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEECCCCEEEEEEHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCEEEECCCCCEEEEEECCCCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCEECCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHCHHHHHHHCCCHEEEEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEECCCCEEEEEEHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCEEEEECCCHHHHHHHHHHHHHHHHCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCECCCCCCEECCCCCCCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEECCCCEEEEEEHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCC
CCCHHHHHHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCEECCCCCCECCCCHCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEECCCCCEEEEEECHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCCEECCCCCCEEEEEECCCCHHHHHHHHHHHHHHHCCCC
CCCHHHHHHHHHHHHHHHHCCHHHCHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEECCCCCEEEEEECHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCEEEECCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCC
CCCHHHHHHHHHHHHHHHHCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHHHHCCCCEEEEECCCCCHCCCCCCCEECCCCCCECCCCCCCCCCHHHHHHHHHHHHHHHHCHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEECCCCCEEEEEEHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCC
predict: major vote:
CCHHHHHHHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCEECCCCCCECCCCCCCCCCHHHHHHHHHHHHHHHHCHHHHHHHHCCHHEEEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEECCCCCEEEEEEHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCEEEECCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCC
* predict: successful (+) prediction at output/5YH1A.ss3rule1
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 3 -r 2 -i /home/max/16jF_secnet_ubuntu/input/5YH1A.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 3 labels of Rule #2: H, E, C
* predict: label definition: (C, S, B, T, I, G) -> C, (H) -> H, (E) -> E
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV1/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV2/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV3/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV4/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV5/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV6/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV7/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV8/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV9/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV10/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/5YH1A.fasta
* predict: base name of entry is 5YH1A
* predict: parsed sequence from the input file is:
PGSHMAEVKRKIEEELDRRAQPSDVGFLVKSEVLEALKPKIMKAAFMIRRAIFEGRPIILRHHADTDGYTAGVALETAIIPLIEKVAPDPEARWHLFKRRPSRAPFYELEDVLKDIIFMMEDHMRFGDELPLVVIVDNGGTTEDIPAYKRLKAYGVKIVVIDHHDPRDWISEDKAKVDEYVDVHVNPHHVKRGYYELTAGMLATEVARYINPEVEDRIKHLPAIAGTGDRSKAPEFYQYLEYAKEKGLDEEDLKKIAEVIDHEAFYWKFMDGRGIIEEILLITGNLQRHRMLVEGIYPEVKEKQEKVLKAVLPHVKSVVLPNGIRFNTIDVELYAPKFEYPSPGKLSGIIHDHFKEQYGEDSPILTLAYGPDFAVVRASDGMAKYNFDLNKIVKILAEKLPDAGVEGGGHSYAGSIKFFEGKRKEVLEAFAKEVLKLKAGE
* predict: prediction file will be output/5YH1A.ss3rule2
predict: predicted secondary structure for 10 models
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCCEEECCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHCCCCCCCHHHEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCCEEECCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCHCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCCEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCHHEEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCCEECCCCCCCEEEEEECCCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCHCCCCCCCEEEECCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCEEEECCCCHHHHHHHHHHHHHHCCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHCCCCCCCCHEEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCCECCCCCCCCCCEEECCCCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHCHCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCEEEEECCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCEEEECCCCHHHHHHHHHHHHHHCCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHECCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCCEEEECCCCEEEEEECCCCHHHHHHHHHHHHHHHCCCC
CCCHHHHHHHHHHHHHHHHCCCCCCCCHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCEEEECCCCCCCEEEEECCCHHHHHHHHHHHHHHHCCCC
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCEEEECCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCC
predict: major vote:
CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCHHEEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCCEEECCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCC
* predict: successful (+) prediction at output/5YH1A.ss3rule2
* predict: returned code is 0 (0 = success, non-zero = failure)

5 of 5] processing of /home/max/16jF_secnet_ubuntu/input/5UB3B.fasta
* script: /home/max/16jF_secnet_ubuntu/bin/run_psiblast.py3 /home/max/16jF_secnet_ubuntu/input/5UB3B.fasta
* script: psiblast is set to use 8 CPU cores
* command: /home/max/16jF_secnet_ubuntu/3rd_software/unix/ncbi-blast-2.6.0+/bin/psiblast -db /home/max/16jF_secnet_ubuntu/3rd_databases/blast/uniref90.fasta -query /home/max/16jF_secnet_ubuntu/input/5UB3B.fasta -inclusion_ethresh 0.001 -evalue 10 -save_pssm_after_last_round -out_ascii_pssm /home/max/16jF_secnet_ubuntu/features/psiblast/5UB3B.mtx -num_iterations 2 -num_threads 8 -save_each_pssm > /dev/null 2>&1
* script: /home/max/16jF_secnet_ubuntu/bin/run_hmm.py3 /home/max/16jF_secnet_ubuntu/input/5UB3B.fasta
* command: bash /home/max/16jF_secnet_ubuntu/3rd_software/generic/process_hmm.bash -i /home/max/16jF_secnet_ubuntu/input/5UB3B.fasta
* hhm: number of detected CPU cores is 8
* hhm: 8 CPU cores will be used
* hhm: input fasta is /home/max/16jF_secnet_ubuntu/input/5UB3B.fasta
* hhm: /home/max/16jF_secnet_ubuntu/3rd_software/unix/hh/hh/buildali2.pl /home/max/16jF_secnet_ubuntu/features/temp/5UB3B_28911/5UB3B.seq -cpu 8 -noss 1>/home/max/16jF_secnet_ubuntu/features/temp/5UB3B_28911/5UB3B_alignment.output 2>/home/max/16jF_secnet_ubuntu/features/temp/5UB3B_28911/5UB3B_alignment.error
* hhm: /home/max/16jF_secnet_ubuntu/3rd_software/unix/hh/hh/hhmake -i /home/max/16jF_secnet_ubuntu/features/temp/5UB3B_28911/5UB3B.a3m -o /home/max/16jF_secnet_ubuntu/features/hhm/5UB3B.hhm1 1>/home/max/16jF_secnet_ubuntu/features/temp/5UB3B_28911/5UB3B_hhmake.output 2>/home/max/16jF_secnet_ubuntu/features/temp/5UB3B_28911/5UB3B_hhmake.error
* hhm: success
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 8 -i /home/max/16jF_secnet_ubuntu/input/5UB3B.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 8 labels: H, E, C, T, G, S, B, I
* predict: label definition: 8 original DSSP labels unchanged (C, S, B, T, I, G, H, E)
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/8label
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/8label/CV1/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/8label/CV2/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/8label/CV3/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/8label/CV4/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/8label/CV5/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/8label/CV6/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/8label/CV7/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/8label/CV8/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/8label/CV9/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/8label/CV10/model_config_weights_state_best_eps.hdf5 is 18.32 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/5UB3B.fasta
* predict: base name of entry is 5UB3B
* predict: parsed sequence from the input file is:
MSSVLVLGRISDDPASHYEQLKPLLDYVVPRMREVGIRRGEILMAPDARQMSSYLRRGRVDWVSETTGAAMLLEQRGSAHPLLMTERGGLRDFHTLFFVRRDSPIHSLSQLRGHTLALQNASSTSGYLLPMLELLRNGIACDVLLSADDTPARGSAGYLMVGSKLNVAAFVHKHLIDVGALSNVDWDDERHMPPVFKRDFRIVHRTAPVPRAVEMVRTGMDPAVEQRLRVVLLQAASDPKAGPALKRFFDTTGFRPLDPTSRRRLQELSAGVQRVRDHVE
* predict: prediction file will be output/5UB3B.ss8
predict: predicted secondary structure for 10 models
CCCEEEEEECCSCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEESSHHHHHHHHHTTSCSEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTSCCCSGGGGTTCEEEECCTTCTHHHHHHHHHHHHTTCCHGGCCCTTSCCCTTCEEEEEESCHHHHHHHHHTTSCSEEEEEHHHHHHHHHSCHHHHHTEEEEEECSCCCSEEEEECTTSCHHHHHHHHHHHHHHGTSHHHHHHHHHHHTCTTEEECCHHHHHHHHHHHHHHHHHHHHHC
CCCEEEEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEESSHHHHHHHHHTTSCSEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCSGGGGTTCEEEECCTTCHHHHHHHHHHHHHTTCCGHHHCCTTCCCCTTCCEEEEESCHHHHHHHHHTTSCSEEEEEHHHHHHHHTSCHHHHHHEEEEEECCCCCSCEEEEETTSCHHHHHHHHHHHHHHTTSHHHHHHHHHHHTCTTEEECCHHHHHHHHHHHHHHHHHHHHHC
CCCEEEEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEESSHHHHHHHHHTTSCSEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTSSCCSGGGGTTCEEEECCTTCHHHHHHHHHHHHHTTCCGGGHCCTTSCCCTTCCEEEEESCHHHHHHHHHTTSCSEEEEEHHHHHHHHHSCHHHHTTEEEEEECCCCCSCEEEEETTSCHHHHHHHHHHHHHHHTSHHHHHHHHHHHTCTTEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECSSHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEESSHHHHHHHHHTTSCSEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTSCCCSGGGGTTCEEEESCTTCTHHTHHHHHHHHHTTCCHHGCCCTTCCCCTTCEEEEEESCHHHHHHHHHTTSCSEEEEEHHHHHHHHTSCHHHHHTEEEEEEESCCCSEEEEEETTSCHHHHHHHHHHHHHGGTSHHHHHHHHHHHTCTCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEESSHHHHHHHHHTTSCSEEEEEHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCSGGGGTTCEEEECCTTCHHHHHHHHHHHHHTTCCHHHHCCTTCCCCTTCEEEEEESSHHHHHHHHHTTSCSEEEEEHHHHHHHHHSCHHHHHTEEEEEEECCCCSCEEEEETTSCHHHHHHHHHHHHHHGTSHHHHHHHHHHHTCTTEEECCHHHHHHHHHHHHHHHHHHHHHC
CCCEEEEEECCSCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEESSHHHHHHHHHTTSCSEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCSGGGGTTCEEEEECTTCTHHHHHHHHHHHHTTCCHHHHHCTTCCCCTTCEEEEEESCHHHHHHHHHTTSSSEEEEEHHHHHHHHHSCHHHHHTEEEEEECCCCCCCEEEEETTSCHHHHHHHHHHHHHHTTSHHHHHHHHHHHTCTCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEESSHHHHHHHHHTTSCSEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTSCCCSGGGGTTCEEEEECTTCHHHHHHHHHHHHHTTCCGGGCCCTTCCCCTTCCEEEEESCHHHHHHHHHTTSSSEEEECHHHHHHHHTSCHHHHHTEEEEEECSCCCSCEEEEETTSCHHHHHHHHHHHHHHHTSHHHHHHHHHHHTCTTCEECCHHHHHHHHHHHHHHHHHHHHHC
CCCCEEEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEESSHHHHHHHHHTTSCSEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTSSCCSGGGGTTCEEEESCTTCHHHHHHHHHHHHHTTCCGGGHCCTTCCCCTTCEEEEEESCHHHHHHHHHTTSCSEEEEEHHHHHHHHHSCHHHHTTEEEEEEECCCESCEEEEETTSCHHHHHHHHHHHHHHGTSHHHHHHHHHHHTCTTCEECCGGGHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEESSHHHHHHHHHTTSCSEEEEEHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTSCCCSGGGGTTCEEEEECTTCTTHHHHHHHHHHHTTCCGGGCCCTTSCCCTTCEEEEEESCHHHHHHHHHTTSCSEEEEEHHHHHHHHTSCHHHHHTEEEEEECCCCCSCEEEEETTSCHHHHHHHHHHHHHHGTSHHHHHHHHHHHTCTTEEECCHHHHHHHHHHHHHHHHHHHHHC
CCCCEEEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEESSHHHHHHHHHTTSCSEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCSGGGGTTCEEEECCTTCHHHHHHHHHHHHHTTCCGGGCCCTTCCCCTTCCEEEEESCHHHHHHHHHTTSCSEEEEEHHHHHHHHHSCHHHHHTEEEEEECCCCCSEEEEEETTSCHHHHHHHHHHHHHHGTSHHHHHHHHHHHTCTTEEECCHHHHHHHHHHHHHHHHHHHHCC
predict: major vote:
CCCEEEEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEESSHHHHHHHHHTTSCSEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTSCCCSGGGGTTCEEEECCTTCHHHHHHHHHHHHHTTCCGGGCCCTTCCCCTTCEEEEEESCHHHHHHHHHTTSCSEEEEEHHHHHHHHHSCHHHHHTEEEEEECCCCCSCEEEEETTSCHHHHHHHHHHHHHHGTSHHHHHHHHHHHTCTTEEECCHHHHHHHHHHHHHHHHHHHHCC
* predict: successful (+) prediction at output/5UB3B.ss8
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 5 -i /home/max/16jF_secnet_ubuntu/input/5UB3B.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 5 labels: H, E, C, T, G
* predict: label definition: (C, S, B) -> C, (H, I) -> H, (E) -> E, (T) -> T, (G) -> G
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/5label_practical
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV1/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV2/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV3/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV4/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV5/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV6/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV7/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV8/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV9/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/5label_practical/CV10/model_config_weights_state_best_eps.hdf5 is 18.26 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/5UB3B.fasta
* predict: base name of entry is 5UB3B
* predict: parsed sequence from the input file is:
MSSVLVLGRISDDPASHYEQLKPLLDYVVPRMREVGIRRGEILMAPDARQMSSYLRRGRVDWVSETTGAAMLLEQRGSAHPLLMTERGGLRDFHTLFFVRRDSPIHSLSQLRGHTLALQNASSTSGYLLPMLELLRNGIACDVLLSADDTPARGSAGYLMVGSKLNVAAFVHKHLIDVGALSNVDWDDERHMPPVFKRDFRIVHRTAPVPRAVEMVRTGMDPAVEQRLRVVLLQAASDPKAGPALKRFFDTTGFRPLDPTSRRRLQELSAGVQRVRDHVE
* predict: prediction file will be output/5UB3B.ss5
predict: predicted secondary structure for 10 models
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCGGGGTTCEEEECCTTCTHHHHHHHHHHHHTTCCCGGCCCTTCCCCCCCCEEEEECCHHHHHHHHHTTCCCEEEEEHHHHHHHHTCCHHHHHTEEEEEECCCCCCCEEEECTTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCTCEEECCHHHHHHHHHHHHHHHHHHHHHC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCGGGGTTCEEEECCTTCHHHHHHHHHHHHHTTCCGGGCCCTTCCCCTTCCEEEEECCHHHHHHHHHTTCCCEEEEEHHHHHHHHHCCHHHHTTEEEEEECCCCCCCEEEEETTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCGGGGTTCEEEEECTTCTHHHHHHHHHHHHTTCCHGHHCCTTCCCCTTCEEEEEECCHHHHHHHHHTTCCCEEEEEHHHHHHHHTCCHHHHHTEEEEEEECCCCCCEEEECTTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCTTEEECCHHHHHHHHHHHHHHHHHHHHHC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCGGGGTTCEEEECCTTCTHHHHHHHHHHHHTTCCHHHCCCTTCCCCTTCEEEEEECCHHHHHHHHHTTCCCEEEEEHHHHHHHHHCCHHHHHTEEEEEECCCCCCCEEEEETTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCCCCEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCGGGGTTCEEEEECTTCTHHHHHHHHHHHHTTCCGGGCCCTTCCCCTTCCEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHTCCHHHHHTEEEEEECCCCCCCEEEECTTCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHTCTCCEECCHHHHHHHHHHHHHHHHHHHHHC
CCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCGGGGTTCEEEECCTTCCHHHHHHHHHHHHTTCCCGGCCCTTCCCCTTCCEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHTCCHHHHHTEEEEEECCCCCCCEEEEETTCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHTCTCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHCCCEEEEEEEETTEEEEEEEEEEETTCCCCCGGGGTTCEEEEECTTCHHHHHHHHHHHHHTTCCCGGCCCTTCCCCTTCEEEEECCCHHHHHHHHHTTCCCEEEECHHHHHHHHTCCHHHHTTEEEEEECCCCCCCEEEEETTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCGGGGTTCEEEECCTTCHHHHHHHHHHHHHTTCCCHHCCCTTCCCCTCCEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHTCCHHHHHTEEEEEECCCCCCCEEEEETTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCTTEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCGGGGTTCEEEECCTTCCHHHHHHHHHHHHTTCCTHHCCCTTCCCCTTCCEEEEECCHHHHHHHHHTTCCCEEEEEHHHHHHHHTCCHHHHTTEEEEEECCCCCCCEEEECTTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCCCCEECCHHHHHHHHHHHHHHHHHHHHHC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCGGGGTTCEEEEECTTCTTHHHHHHHHHHHTTCCGGGCCCTTCCCCTCCCEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHCCHHHHHTEEEEEECCCCCCCEEEECTTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCCCCEECCHHHHHHHHHHHHHHHHHHHHCC
predict: major vote:
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCGGGGTTCEEEECCTTCTHHHHHHHHHHHHTTCCCGGCCCTTCCCCTTCCEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHTCCHHHHHTEEEEEECCCCCCCEEEECTTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
* predict: successful (+) prediction at output/5UB3B.ss5
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 4 -i /home/max/16jF_secnet_ubuntu/input/5UB3B.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 4 labels: H, E, C, T
* predict: label definition: (C, S, B, G) -> C, (H, I) -> H, (E) -> E, (T) -> T
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/4label_practical
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV1/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV2/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV3/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV4/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV5/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV6/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV7/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV8/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV9/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/4label_practical/CV10/model_config_weights_state_best_eps.hdf5 is 18.24 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/5UB3B.fasta
* predict: base name of entry is 5UB3B
* predict: parsed sequence from the input file is:
MSSVLVLGRISDDPASHYEQLKPLLDYVVPRMREVGIRRGEILMAPDARQMSSYLRRGRVDWVSETTGAAMLLEQRGSAHPLLMTERGGLRDFHTLFFVRRDSPIHSLSQLRGHTLALQNASSTSGYLLPMLELLRNGIACDVLLSADDTPARGSAGYLMVGSKLNVAAFVHKHLIDVGALSNVDWDDERHMPPVFKRDFRIVHRTAPVPRAVEMVRTGMDPAVEQRLRVVLLQAASDPKAGPALKRFFDTTGFRPLDPTSRRRLQELSAGVQRVRDHVE
* predict: prediction file will be output/5UB3B.ss4
predict: predicted secondary structure for 10 models
CCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCCCCCTTCEEEECCTTCCHHHHHHHHHHHHTTCCCCCCCCTTCCCCCCCCEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHTCCHHHHHTEEEEEECCCCCCCEEEECTTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTCEEEEEEEEEETTCCCCCCCCCTTCEEEECCTTCCHHHHHHHHHHHHTTCCCCCCCCTTCCCCTTCCEEEEECCHHHHHHHHHTTCCCEEEEEHHHHHHHHHCCHHHHHTEEEEEECCCCCCCCEEEETTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCTTCEECCHHHHHHHHHHHHHHHHHHHHCC
CCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCCCCCTTCEEEECCTTCCHHHHHHHHHHHHTTCCCCCCCCTTCCCCCTCCEEEEECCHHHHHHHHHTTCCCEEEECHHCHHHHHTCCHHHHHTEEEEEECCCCCCCEEEECTTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCTTCEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCCCCCTTCEEEECCTTCCHHHHHHHHHHHHTTCCCCCCCCTTCCCCCCCCEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHTCCHHHHHTEEEEEECCCCCCCEEEEETTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCCCCEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCCCCCTTCEEEECCTTCTTHHHHHHHHHHHTTCCCCCCCCCCCCCCCTCEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHCCHHHHHTEEEEEECCCCCCCEEEEETTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCCCCCTTCEEEECCTTCCHHHHHHHHHHHHTTCCCCCCCCTTCCCCTTCCEEEEECCHHHHHHHHHTTCCCEEEEEHHHHHHHHHCCHHHHHTEEEEEEECCCCCCEEEECTTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCCCEEECCHHHHHHHHHHHHHHHHHHHHHC
CCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHTCCEEEEEEEETTEEEEEEEEEEETTCCCCCCCCCTTCEEEECCTTCCHHHHHHHHHHHHTTCCCCCCCCTTCCCCTTCEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHTCCHHHHHHEEEEEECCCCCCCEEEEETTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCCCCCTTCEEEEECTTCCHHHHHHHHHHHHTTCCCCCCCCTTCCCCCCCEEEEEECCHHHHHHHHHTTCCCEEEEEHHHHHHHHTCCHHHHHTEEEEEEECCCCCCEEEEETTCCHHHHHHHHHHHHHHCTCHHHHHHHHHHHTCTCEEECCHHHHHHHHHHHHHHHHHHHHHC
CCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCCCCCTTCEEEECCTTCCHHHHHHHHHHHHTTCCCCCCCCTTCCCCCCCEEEEEECCHHHHHHHHHTTCCCEEEEEHHHHHHHHTCCHHHHHHEEEEEECCCCCCCEEEEETTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCCCCCTTCEEEECCTTCCHHHHHHHHHHHHTTCCCHCHCCTTCCCCCCCEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHCCHHHHHTEEEEEECCCCCCCEEEECTTCCHHHHHHHHHHHHHHCTCHHHHHHHHHHHTCCCCEECCHHHHHHHHHHHHHHHHHHHHHC
predict: major vote:
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHHHHCCEEEEEEEETTEEEEEEEEEEETTCCCCCCCCCTTCEEEECCTTCCHHHHHHHHHHHHTTCCCCCCCCTTCCCCCCCCEEEEECCHHHHHHHHHTTCCCEEEECHHHHHHHHTCCHHHHHTEEEEEECCCCCCCEEEEETTCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHTCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
* predict: successful (+) prediction at output/5UB3B.ss4
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 3 -r 1 -i /home/max/16jF_secnet_ubuntu/input/5UB3B.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 3 labels of Rule #1: H, E, C
* predict: label definition: (C, S, T) -> C, (H, I, G) -> H, (E, B) -> E
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV1/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV2/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV3/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV4/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV5/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV6/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV7/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV8/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV9/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/3label_rule1_harder/CV10/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/5UB3B.fasta
* predict: base name of entry is 5UB3B
* predict: parsed sequence from the input file is:
MSSVLVLGRISDDPASHYEQLKPLLDYVVPRMREVGIRRGEILMAPDARQMSSYLRRGRVDWVSETTGAAMLLEQRGSAHPLLMTERGGLRDFHTLFFVRRDSPIHSLSQLRGHTLALQNASSTSGYLLPMLELLRNGIACDVLLSADDTPARGSAGYLMVGSKLNVAAFVHKHLIDVGALSNVDWDDERHMPPVFKRDFRIVHRTAPVPRAVEMVRTGMDPAVEQRLRVVLLQAASDPKAGPALKRFFDTTGFRPLDPTSRRRLQELSAGVQRVRDHVE
* predict: prediction file will be output/5UB3B.ss3rule1
predict: predicted secondary structure for 10 models
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHCCCCCEEEECHHHHHHHHHHHCCEEEEEEEECCEEEEEEEEEEECCCCCCCHHHHCCCEEEECCCCCCHHHHHHHHHHHHCCCCHHHCCCCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCEEEEECHHHHHHHHCCHHHHHHEEEEEECCCCCCCEEEECCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCEEEEEEEEEEECCCCCCCHHHHCCCEEEECCCCCCHHHHHHHHHHHHCCCCHHHCCCCCCCCCCCCCEEEECCCHHHHHHHHHCCCCCEEEEEHHHHHHHHHCCHHHHHCEEEEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCEEEEEEEEEEECCCCCCCHHHHCCCEEEEECCCCCCCHHHHHHHHHHCCCCHHHCCCCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCEEEEEHHHHHHHHHCCHHHHHHEEEEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCEEEEEEEEEEECCCCCCCHHHHCCCEEEECCCCCCHHHHHHHHHHHHCCCCHHHCCCCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHCCCHHHHHHEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCEEEEEEEEEEECCCCCCCHHHHCCCEEEEECCCCCHHHHHHHHHHHHCCCCHHHHCCCCCCCCCCCEEEEEECCHHHHHHHHHCCCCCEEEEEHHHHHHHHHCCHHHHHCEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCEEEEEEEEEEECCCCCCCHHHHCCCEEEECCCCCCHHHHHHHHHHHHCCCCHHHHCCCCCCCCCCCCEEEECCCHHHHHHHHHCCCCCEEEEEHHHHHHHHHCCHHHHHHEEEEEECCCCCCCEEEECCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCEEEEEEEEEEECCCCCCCHHHHCCCEEEEECCCCCHHHHHHHHHHHHCCCCCHHCCCCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHCCHHHHHHEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCEEEEEEEEEEECCCCCCCHHHHCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEECCCHHHHHHHHHCCCCCEEEECHHHHHHHHHCCHHHHHHEEEEEEECCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCEEEEEEEEEEECCCCCCCHHHHCCCEEEECCCCCCHHHHHHHHHHHHCCCCHHHHCCCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCEEEEEHHHHHHHHHCCHHHHHHEEEEEECCCCCCCEEEECCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCEEEEEEEEEEECCCCCCCHHHHCCCEEEECCCCCCHHHHHHHHHHHHCCCCHHHHCCCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCEEEEEHHHHHHHHHCCHHHHHHEEEEEECCCCCCCEEEECCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
predict: major vote:
CCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCEEEEEEEEEEECCCCCCCHHHHCCCEEEECCCCCCHHHHHHHHHHHHCCCCHHHCCCCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCEEEEEHHHHHHHHHCCHHHHHHEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
* predict: successful (+) prediction at output/5UB3B.ss3rule1
* predict: returned code is 0 (0 = success, non-zero = failure)
* predict: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 of Version 1.16.4
* predict: application command: /home/max/16jF_secnet_ubuntu/bin/ss_nn_load_and_predict.py3 -l 3 -r 2 -i /home/max/16jF_secnet_ubuntu/input/5UB3B.fasta -o output/
* predict: kit directory: /home/max/16jF_secnet_ubuntu
* predict: python version: 3.5.2 |Anaconda 4.2.0 (64-bit)| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
* predict: labels for prediction: 3 labels of Rule #2: H, E, C
* predict: label definition: (C, S, B, T, I, G) -> C, (H) -> H, (E) -> E
Using Theano backend.
* theano: 0.8.2
* keras: 1.1.2
* neural network calculations will use 8 CPU cores
* predict: loading 10 model from /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier
* predict: loading model #1, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV1/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #2, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV2/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #3, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV3/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #4, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV4/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #5, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV5/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #6, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV6/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #7, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV7/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #8, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV8/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #9, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV9/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: loading model #10, /home/max/16jF_secnet_ubuntu/models/3label_rule2_easier/CV10/model_config_weights_state_best_eps.hdf5 is 18.22 MB
* predict: FASTA-formatted sequence file is /home/max/16jF_secnet_ubuntu/input/5UB3B.fasta
* predict: base name of entry is 5UB3B
* predict: parsed sequence from the input file is:
MSSVLVLGRISDDPASHYEQLKPLLDYVVPRMREVGIRRGEILMAPDARQMSSYLRRGRVDWVSETTGAAMLLEQRGSAHPLLMTERGGLRDFHTLFFVRRDSPIHSLSQLRGHTLALQNASSTSGYLLPMLELLRNGIACDVLLSADDTPARGSAGYLMVGSKLNVAAFVHKHLIDVGALSNVDWDDERHMPPVFKRDFRIVHRTAPVPRAVEMVRTGMDPAVEQRLRVVLLQAASDPKAGPALKRFFDTTGFRPLDPTSRRRLQELSAGVQRVRDHVE
* predict: prediction file will be output/5UB3B.ss3rule2
predict: predicted secondary structure for 10 models
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCCEEEEEEEEEECCCCCCCCCCCCCCEEEEECCCCCCHCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCEEEEEHHHHHHHHHCCHHHHHCEEEEEECCCCCCCEEEECCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHHCEEEEEEEEECCEEEEEEEEEEECCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEECCHHHHHHHHHCCCCCEEEEECHHHHHHHCCCHHHHHCEEEEEEECCCCCCCEEECCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCEEECCCCHHHHHHHHHHHHHHHHHHCC
CCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCEEEEEEEEEEECCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHCCHHHHHCEEEEEEECCECCCEEEECCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCEEEEEEEEEEECCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHCCCHHHHHCEEEEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCCEEEEEEEEEECCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCEEEEEHHHHHHHHCCCHHHHHCEEEEEECCCCCCCEEEEECCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCCEEEEEEEEEECCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHCCHHHHHCEEEEEECCCCCCCEEEECCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCEEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCEEEEEEEEEEECCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEECCHHHHHHHHHCCCCCEEEECCHHHHHHHHCCHHHHHCEEEEEECCCCCCCCEEECCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCEECCHHHHHHHHHHHHHHHHHHHHCC
CCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCEEEEEEEEEEECCCCCCCCCCCCCCEEEECCCCCCHHCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCEEEEEHHHHHHHHCCCHHHHHCEEEEEEECCCCCCEEEECCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCEECCHHHHHHHHHHHHHHHHHHHHCC
CCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCHHHHHHHHHCCCCCEEEECHHHHHHHHHHHCCEEEEEEEECCCEEEEEEEEEECCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEECCHHHHHHHHHCCCCCEEEEEHHHHHHHHCCCHHHHHCEEEEEEECCCCCCEEEECCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCEECCHHHHHHHHHHHHHHHHHHHHCC
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCCEEEEEEEEEECCCCCCCCCCCCCCEEEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCEEEEECHHHHHHHHCCHHHHHHEEEEEEECCCCCCEEEECCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCEECCHHHHHHHHHHHHHHHHHHHHCC
predict: major vote:
CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCEEEEEEEECCCEEEEEEEEEECCCCCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCEEEEEHHHHHHHHCCCHHHHHCEEEEEECCCCCCCEEEECCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCEECCHHHHHHHHHHHHHHHHHHHHCC
* predict: successful (+) prediction at output/5UB3B.ss3rule2
* predict: returned code is 0 (0 = success, non-zero = failure)

5 succeeded out of total of 5
<== ALL TASKS COMPLETED ==>