upload

 -------------------------------- PARAMETERS --------------------------------
 --inputPath          Path of training data set        : /home/egaytan/automatic-extraction-growth-conditions/predict-annot/input/
 --outputPath         Output path to place output files: /home/egaytan/automatic-extraction-growth-conditions/predict-annot/output/
---outputFileI        Output tagged file I             : annot-input_bg_outputI_v5.txt
---outputFileII       Output tagged file II            : annot-input_bg_outputII_v5
---outputFileII       Output tagged file III           : annot-input_bg_outputIII_v5
+--outputFileI        Output tagged file I             : annot-input_bg_outputI_v6
+--outputFileII       Output tagged file II            : annot-input_bg_outputII_v6
+--outputFileII       Output tagged file III           : annot-input_bg_outputIII_v6
 --modelPath          Path to read CRF model           : /home/egaytan/automatic-extraction-growth-conditions/CRF/models
 --modelName          Model name                       : model_Run3_v10_S1_False_S2_True_S3_False_S4_False_Run3_v10
 --infoPath           Path of GSE-GSM index file       : /home/egaytan/automatic-extraction-growth-conditions/predict-annot/mapping
@@ -15,16 +15,14 @@
 --S4                 Semantic features     : False
 -------------------------------- PROCESSING --------------------------------
 Reading CRF model...
-Reading CRF model done in: 0.009225s
+Reading CRF model done in: 0.009524s
 Processing corpus...
 Preprocessing file...annot-input_bg_v4.txt
 Sentences input data: 90688
 Predicting tags with model...
-Prediction done in: 27.733279s
+Prediction done in: 27.458162s
 Tagging file...
-GSE100233	GSM2675514	GPL18006-GPL18133-PMID:29186514	library_strategy.1	<Technique> ChIP-Seq </Technique>	Technique
-GSE100233	GSM2675514	GPL18006-GPL18133-PMID:29186514	growth_protocol_ch1.1	Cultures of Caulobacter -LRB- TLS1631-TLS1633 -RRB- were grown at 30oC in PYE and supplemented with antibiotics , as necessary , at appropriate concentrations . To deplete wild-type non-tagged ParB , exponential-phase cells were washed off xylose and re-introduced to PYE +0.2 % glucose for an additional <Supp> 5 hours </Supp> . After 4 hours , vanillate was added to induce the expression of flag-parB -LRB- WT -RRB- or flag-parB -LRB- G101S/R104A -RRB- for an hour . Cultures of Escherichia coli -LRB- TLS1637-TLS1650 -RRB- were grown at 30oC in LB and supplemented with antibiotics , as necessary , at appropriate concentrations . IPTG -LRB- 0.5 mM -RRB- was added to induce the production of T18-ParB -LRB- WT -RRB- or T18-ParB -LRB- G101S -RRB- . After an hour , formadehyde -LRB- 1 % final concentration -RRB- were added to fix cells for ChIP-seq . 	Supp
 Saving Ouput I...
 Saving Ouput II...
 Saving Ouput III...
-Pssing corpus done in: 258.328259s
+Passing corpus done in: 257.970281s

--------------------------------- PARAMETERS --------------------------------
---inputPath          Path of training data set        : /home/egaytan/automatic-extraction-growth-conditions/predict-annot/input/
---outputPath         Output path to place output files: /home/egaytan/automatic-extraction-growth-conditions/predict-annot/output/
---outputFileI        Output tagged file I             : annot-input_bg_outputI_v4.txt
---outputFileII       Output tagged file II            : annot-input_bg_outputII_v4
---modelPath          Path to read CRF model           : /home/egaytan/automatic-extraction-growth-conditions/CRF/models
---modelName          Model name                       : model_Run3_v10_S1_False_S2_True_S3_False_S4_False_Run3_v10
---infoPath           Path of GSE-GSM index file       : /home/egaytan/automatic-extraction-growth-conditions/predict-annot/mapping
---infoFile	        GSE-GSM index file               : bg_sentences_midx_v4.txt
---variant	        Run variant                      : 13
---S1                 General features                 : True
---S2                 Inner/Complete word features     : False
---S3                 Extended context features        : False
---S4                 Semantic features                : True
---filteringStopWords Filtering stop words             : False
---filterSymbols      Filtering punctuation marks      : False
-Filtering symbols ['.', ',', ':', ';', '?', '!', "'", '"', '<', '>', '(', ')', '-', '_', '/', '\\', '¿', '¡', '+', '{', '}', '[', ']', '*', '%', '$', '#', '&', '°', '`', '...']: False
--------------------------------- PROCESSING --------------------------------
-Reading CRF model...
-Reading CRF model done in: 0.009363s
-Processing corpus...
-Preprocessing file...annot-input_bg_v3.txt
-Sentences input data: 14716
-Predicting tags with model
-Prediction done in: 1.737334s
-Tagging file
-Preprocessing file...annot-input_bg_v4.txt
-Sentences input data: 90688
-Predicting tags with model
-Prediction done in: 26.434549s
-Tagging file
-Processing corpus done in: 58.304885s