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predict.example.log.txt
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predict.example.log.txt
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>> python promotech.py -g -t 0.5
2020-08-10 16:00:11.042238: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'libnvinfer.so.6'; dlerror: libnvinfer.so.6: cannot open shared object file: No such file or directory
2020-08-10 16:00:11.043297: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'libnvinfer_plugin.so.6'; dlerror: libnvinfer_plugin.so.6: cannot open shared object file: No such file or directory
2020-08-10 16:00:11.043489: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:30] Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.
PROMOTECH
MODE : COMMAND-LINE
ML MODEL : 40NT SEQUENCE
INPUT TYPE : RF-HOT
INPUT : None
TEST SAMPLES : None
LOADING MACHINE LEARNING MODEL AT: models/RF-HOT.model WITH SIZE: 3,770.57 MB
GridSearchCV(cv=10,
estimator=RandomForestClassifier(class_weight={0: 0.5512173740112261,
1: 5.381156147232458},
min_samples_leaf=5, verbose=2),
iid=False,
param_grid={'max_features': ['log2'], 'n_estimators': [2000]},
refit='average_precision',
scoring=['average_precision', 'precision', 'recall'], verbose=2)
TIME ELAPSED FROM START (HOUR:MIN:SEC): 00:00:11
LOADING FORWARD STRAND SEQUENCES CONVERTED TO HOT-ENCODED SEQUENCES: results/RF-HOT.data WITH SIZE: 5,938.73 MB
LOADING FORWARD STRAND SEQUENCES CONVERTED TO HOT-ENCODED SEQUENCES AT: results/RF-HOT-INV.data WITH SIZE: 5,938.73 MB
FORWARD STRAND SEQS: (4639634, 160)
INVERSE STRAND SEQS: (4639634, 160)
ML-MODEL:
GridSearchCV(cv=10,
estimator=RandomForestClassifier(class_weight={0: 0.5512173740112261,
1: 5.381156147232458},
min_samples_leaf=5, verbose=2),
iid=False,
param_grid={'max_features': ['log2'], 'n_estimators': [2000]},
refit='average_precision',
scoring=['average_precision', 'precision', 'recall'], verbose=2)
TIME ELAPSED FROM START (HOUR:MIN:SEC): 00:00:40
GENERATING PREDICTIONS FOR FORWARD STRAND SEQUENCES WITH SHAPE: (4639634, 160)
[Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers.
[Parallel(n_jobs=1)]: Done 1 out of 1 | elapsed: 1.1s remaining: 0.0s
[Parallel(n_jobs=1)]: Done 2000 out of 2000 | elapsed: 29.0min finished
TIME ELAPSED FROM START (HOUR:MIN:SEC): 00:29:44
GENERATING PREDICTIONS FOR INVERSE STRAND SEQUENCES WITH SHAPE: (4639634, 160)
[Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers.
[Parallel(n_jobs=1)]: Done 1 out of 1 | elapsed: 1.0s remaining: 0.0s
[Parallel(n_jobs=1)]: Done 2000 out of 2000 | elapsed: 28.9min finished
TIME ELAPSED FROM START (HOUR:MIN:SEC): 00:58:45
PREDICTIONS GENERATED SUCCESSFULLY
FORWARD SEQUENCE SAMPLE:
SEQ:
1000010000100001000100010001001010000001000100100001010010000010000101000010100010000010010001000100001010001000000110000001010000010010000100100001010000010100
PREDICTION: 0.2877
INVERSE SEQUENCE SAMPLE:
SEQ: 0010100000101000010010000100100000101000000110000001000101000010001000100100000100010100001010000100000100101000010010001000000101001000100010001000010000100001
PREDICTION: 0.2722
FORWARD STRAND PREDICTIONS ABOVE THRESHOLD: 27,600 and BELOW: 4,612,034 FROM TOTAL 4,639,634
INVERSE STRAND PREDICTIONS ABOVE THRESHOLD: 27,402 and BELOW: 4,612,232 FROM TOTAL 4,639,634
GENERATING DETECTED PROMOTERS' BED FILE BASED ON THRESHOLD: 0.500 FOR CHROM: NC_000913.2. # SEQS: 4639634 # INV SEQS: 4639634. # SEQS ABOVE THRES: 27600 # INV SEQS ABOVE THRES: 27402
SAVING BED FILE WITH SHAPE (55002, 6) TO results/genome_predictions.csv. SAMPLE:
chrom start end score strand sequence
0 NC_000913.2 73 112 0.64976 + TGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTG
1 NC_000913.2 97 136 0.53367 - GTTAAAGTATTTAGTGACCTAAGTCAATAAAATTTTAATT
2 NC_000913.2 108 147 0.59078 + TATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCA
3 NC_000913.2 121 160 0.55026 - TGTCTGTGCGCTATGCCTATATTGGTTAAAGTATTTAGTG
4 NC_000913.2 122 161 0.53101 - CTGTCTGTGCGCTATGCCTATATTGGTTAAAGTATTTAGT
TIME ELAPSED FROM START (HOUR:MIN:SEC): 01:05:27