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parse.example.log.txt
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parse.example.log.txt
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>> clear && python promotech.py -pg -m RF-HOT -f examples/genome/ECOLI_2.fasta
2020-08-10 15:18:49.907717: 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 15:18:49.908428: 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 15:18:49.908607: 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 : FASTA FILE
INPUT TYPE : RF-HOT
INPUT : ['examples/genome/ECOLI_2.fasta']
TEST SAMPLES : None
CREATING OUTPUT FOLDER: results
PRINTING CONTENT
1. GENOME: NC_000913.2 - LENGTH: 4639675
JOINING ALL CHROMS AND SEQS INTO A SINGLE FOR TETRA-NUCLEOTIDE SLIDING WINDOW
JOINED GENOME: NC_000913.2 - LENGTH: 4,639,675
GENERATING PROMOTER SEQUENCES WITH WINDOW-SIZE: 40 AND STEP: 1. EXPECTED SAMPLES: 4,639,634
100% (4639634 of 4639634) |###########################################################################################################################################################################| Elapsed Time: 0:00:10 Time: 0:00:10
TIME ELAPSED FROM START (HOUR:MIN:SEC): 00:00:13
CUTTED 40 NT SEQUENCES GENERATED SUCCESSFULLY. # OF SAMPLES: 4,639,634 = (4639634,).
SAMPLE #1: AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTG
SAMPLE #2: GCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGT
CONVERTING 4639634 CUTTED 40 NT SEQUENCES TO RF-HOT SEQUENCES USING MAPPING VALUES
[{'A': array([1., 0., 0., 0.])}, {'G': array([0., 1., 0., 0.])}, {'C': array([0., 0., 1., 0.])}, {'T': array([0., 0., 0., 1.])}]
CONVERTING DATA
99% (4639434 of 4639634) |########################################################################################################################################################################## | Elapsed Time: 0:14:41 ETA: 0:00:00
HOT ENCODED SEQUENCES GENERATED SUCCESSFULLY.
A G C T A ... T A G C T
0 1 0 0 0 0 ... 1 0 1 0 0
1 0 1 0 0 0 ... 0 0 0 0 1
2 0 0 1 0 0 ... 1 0 1 0 0
3 0 0 0 1 0 ... 0 0 1 0 0
4 0 0 0 1 0 ... 0 1 0 0 0
[5 rows x 160 columns]
TIME ELAPSED FROM START (HOUR:MIN:SEC): 00:16:37
RF-HOT SEQUENCES GENERATED SUCCESSFULLY. OUTPUT DATAFRAME SHAPE: (4639634, 160)
SAMPLE:
A G C T A ... T A G C T
0 1 0 0 0 0 ... 1 0 1 0 0
1 0 1 0 0 0 ... 0 0 0 0 1
2 0 0 1 0 0 ... 1 0 1 0 0
3 0 0 0 1 0 ... 0 0 1 0 0
4 0 0 0 1 0 ... 0 1 0 0 0
[5 rows x 160 columns]
SAVING FORWARD STRAND HOT-ENCODED SEQUENCES TO BINARY FILE USING JOBLIB TO: results/RF-HOT.data
TIME ELAPSED FROM START (HOUR:MIN:SEC): 00:17:32
FILE SAVED SUCCESSFULLY AT:
results/RF-HOT.data
GENERATING INVERSE STRAND SEQUENCES.
100% (4639634 of 4639634) |###########################################################################################################################################################################| Elapsed Time: 0:00:24 Time: 0:00:24
INVERSE STRAND SEQUENCES GENERATED SUCCESSFULLY. # OF SAMPLES: 4,639,634.
SAMPLE:
ORIGINAL : AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTG
INVERSE : CACAGAGACATATTGCCCGTTGCAGTCAGAATGAAAAGCT
TIME ELAPSED FROM START (HOUR:MIN:SEC): 00:17:59
CONVERTING 4639634 INVERSE STRAND 40 NT SEQUENCES TO RF-HOT SEQUENCES USING MAPPING VALUES
[{'A': array([1., 0., 0., 0.])}, {'G': array([0., 1., 0., 0.])}, {'C': array([0., 0., 1., 0.])}, {'T': array([0., 0., 0., 1.])}]
CONVERTING INVERSE DATA
99% (4639235 of 4639634) |########################################################################################################################################################################## | Elapsed Time: 0:14:46 ETA: 0:00:00
HOT ENCODED SEQUENCES GENERATED SUCCESSFULLY.
A G C T A ... T A G C T
0 0 0 1 0 1 ... 0 0 0 0 1
1 1 0 0 0 0 ... 0 0 0 1 0
2 0 0 1 0 1 ... 0 0 1 0 0
3 0 0 1 0 0 ... 0 1 0 0 0
4 0 0 0 1 0 ... 0 1 0 0 0
[5 rows x 160 columns]
TIME ELAPSED FROM START (HOUR:MIN:SEC): 00:35:42