INFO  @ Wed, 25 Apr 2012 18:45:33: 
# ARGUMENTS LIST:
# name = results
# format = BAM
# ChIP-seq file = treatment.bam
# control file = control.bam
# effective genome size = 3.08e+09
# band width = 200
# model fold = 10,30
# pvalue cutoff = 1.00e-05
# Small dataset will be scaled towards larger dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
 
INFO  @ Wed, 25 Apr 2012 18:45:33: #1 read tag files... 
INFO  @ Wed, 25 Apr 2012 18:45:33: #1 read treatment tags... 
INFO  @ Wed, 25 Apr 2012 18:45:33: tag size: 27 
INFO  @ Wed, 25 Apr 2012 18:45:41:  1000000 
INFO  @ Wed, 25 Apr 2012 18:45:49:  2000000 
INFO  @ Wed, 25 Apr 2012 18:45:57:  3000000 
INFO  @ Wed, 25 Apr 2012 18:45:57: #1.2 read input tags... 
INFO  @ Wed, 25 Apr 2012 18:46:05:  1000000 
INFO  @ Wed, 25 Apr 2012 18:46:13:  2000000 
INFO  @ Wed, 25 Apr 2012 18:46:17: #1 tag size is determined as 28 bps 
INFO  @ Wed, 25 Apr 2012 18:46:17: #1 tag size = 28 
INFO  @ Wed, 25 Apr 2012 18:46:17: #1  total tags in treatment: 3014699 
INFO  @ Wed, 25 Apr 2012 18:46:17: #1 calculate max duplicate tags in single position based on binomal distribution... 
INFO  @ Wed, 25 Apr 2012 18:46:18: #1  max_dup_tags based on binomal = 1 
INFO  @ Wed, 25 Apr 2012 18:46:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Wed, 25 Apr 2012 18:46:19: #1  tags after filtering in treatment: 2805356 
INFO  @ Wed, 25 Apr 2012 18:46:19: #1  Redundant rate of treatment: 0.07 
INFO  @ Wed, 25 Apr 2012 18:46:19: #1  total tags in control: 2442445 
INFO  @ Wed, 25 Apr 2012 18:46:19: #1  for control, calculate max duplicate tags in single position based on binomal distribution... 
INFO  @ Wed, 25 Apr 2012 18:46:19: #1  max_dup_tags based on binomal = 1 
INFO  @ Wed, 25 Apr 2012 18:46:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Wed, 25 Apr 2012 18:46:20: #1  tags after filtering in control: 2173631 
INFO  @ Wed, 25 Apr 2012 18:46:20: #1  Redundant rate of control: 0.11 
INFO  @ Wed, 25 Apr 2012 18:46:20: #1 finished! 
INFO  @ Wed, 25 Apr 2012 18:46:20: #2 Build Peak Model... 
DEBUG @ Wed, 25 Apr 2012 18:46:20: Chromosome: chr1 
DEBUG @ Wed, 25 Apr 2012 18:46:39: Number of unique tags on + strand: 1567635 
DEBUG @ Wed, 25 Apr 2012 18:46:39: Number of peaks in + strand: 229844 
DEBUG @ Wed, 25 Apr 2012 18:46:57: Number of unique tags on - strand: 1237721 
DEBUG @ Wed, 25 Apr 2012 18:46:57: Number of peaks in - strand: 213237 
DEBUG @ Wed, 25 Apr 2012 18:46:57: Number of paired peaks: 74164 
INFO  @ Wed, 25 Apr 2012 18:46:57: #2 number of paired peaks: 74164 
DEBUG @ Wed, 25 Apr 2012 18:46:57: Use 1000 pairs to build the model. 
INFO  @ Wed, 25 Apr 2012 18:46:58: #2 finished! 
DEBUG @ Wed, 25 Apr 2012 18:46:58: #2  Summary Model: 
DEBUG @ Wed, 25 Apr 2012 18:46:58: #2   min_tags: 1 
DEBUG @ Wed, 25 Apr 2012 18:46:58: #2   d: 163 
DEBUG @ Wed, 25 Apr 2012 18:46:58: #2   scan_window: 326 
INFO  @ Wed, 25 Apr 2012 18:46:58: #2 predicted fragment length is 163 bps 
INFO  @ Wed, 25 Apr 2012 18:46:58: #2.2 Generate R script for model : results_model.r 
INFO  @ Wed, 25 Apr 2012 18:46:58: #3 Call peaks... 
INFO  @ Wed, 25 Apr 2012 18:46:58: #3 shift treatment data 
DEBUG @ Wed, 25 Apr 2012 18:46:58: # 3 tag(s) extended outside of chromosome start are removed! 
INFO  @ Wed, 25 Apr 2012 18:46:58: #3 merge +/- strand of treatment data 
DEBUG @ Wed, 25 Apr 2012 18:46:59: #3 after shift and merging, tags: 2805356 
INFO  @ Wed, 25 Apr 2012 18:46:59: #3 call peak candidates 
DEBUG @ Wed, 25 Apr 2012 18:46:59: #3 search peak condidates... 
DEBUG @ Wed, 25 Apr 2012 18:46:59: #3 Chromosome chr1 
DEBUG @ Wed, 25 Apr 2012 18:48:01: #3 peak candidates: 127751 
DEBUG @ Wed, 25 Apr 2012 18:48:01: #3 Total number of candidates: 127751 
INFO  @ Wed, 25 Apr 2012 18:48:01: #3 shift control data 
INFO  @ Wed, 25 Apr 2012 18:48:01: #3 merge +/- strand of control data 
DEBUG @ Wed, 25 Apr 2012 18:48:02: # 2 tag(s) extended outside of chromosome start are removed! 
DEBUG @ Wed, 25 Apr 2012 18:48:02: #3 after shift and merging, tags: 2173631 
INFO  @ Wed, 25 Apr 2012 18:48:02: #3 call negative peak candidates 
DEBUG @ Wed, 25 Apr 2012 18:48:02: #3 search peak condidates... 
DEBUG @ Wed, 25 Apr 2012 18:48:02: #3 Chromosome chr1 
DEBUG @ Wed, 25 Apr 2012 18:48:59: #3 peak candidates: 148786 
DEBUG @ Wed, 25 Apr 2012 18:48:59: #3 Total number of candidates: 148786 
INFO  @ Wed, 25 Apr 2012 18:48:59: #3 use control data to filter peak candidates... 
DEBUG @ Wed, 25 Apr 2012 18:48:59: #3 Chromosome chr1 
DEBUG @ Wed, 25 Apr 2012 18:49:32: #3 peaks whose pvalue < cutoff: 1938 
INFO  @ Wed, 25 Apr 2012 18:49:32: #3 Finally, 1938 peaks are called! 
INFO  @ Wed, 25 Apr 2012 18:49:32: #3 find negative peaks by swapping treat and control 
DEBUG @ Wed, 25 Apr 2012 18:49:32: #3 Chromosome chr1 
DEBUG @ Wed, 25 Apr 2012 18:50:10: #3 peaks whose pvalue < cutoff: 881 
INFO  @ Wed, 25 Apr 2012 18:50:10: #3 Finally, 881 peaks are called! 
INFO  @ Wed, 25 Apr 2012 18:50:10: #4 Write output xls file... results_peaks.xls 
INFO  @ Wed, 25 Apr 2012 18:50:10: #4 Write peak bed file... results_peaks.bed 
INFO  @ Wed, 25 Apr 2012 18:50:10: #4 Write summits bed file... results_summits.bed 
INFO  @ Wed, 25 Apr 2012 18:50:10: #4 Write output xls file for negative peaks... results_negative_peaks.xls 
INFO  @ Wed, 25 Apr 2012 18:50:10: #5 Done! Check the output files! 
