****************************** RCOpt version 1.01 *****************************
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* Copyright 2014 Hamed S. Najafabadi .........................................*
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Received parameters:
Input file containing the randomForest results: ./out/KLF13.IDR0.05.filt.narrowPeak/results.RF_out.txt
The filter for ZFPs: 
Input file containing the ZF weights: None
Input file containing the sequences: ./tmp/KLF13.IDR0.05.filt.narrowPeak/all.fa
Enrichment fold expected for each ZF (negative means PWMs should not be normalized): 50
Optimization mode (1: optimized AUC; 2: optimize AUC x Similarity; 3: until convergence): 3
The experiment name: 
Output file: ./out/KLF13.IDR0.05.filt.narrowPeak/results

Opening the randomForest output file...
EOL candidate no. 1 was approved.
Reading RF results...
3 motifs were read.

Opening the FASTA file...
EOL candidate no. 1 was approved.
Reading the sequences...
7806 sequences were read, including 3903 positive and 3903 negatives.

Generating PWMs...
Optimizing PWMs...
Writing to output...

Job finished successfully.