Version: Vancouver Short Read Analysis Package 4.0.13 Version: Initializing class FindPeaks $Revision: 2084 $ Version: Initializing class Parameters $Revision: 2225 $ Info: Log File: /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30.log Version: Initializing class Log_Buffer $Revision: 1643 $ Info: * Output directory : /projects/NBL/wig_files_transcriptome/ Info: * Naming files as : HS1799bam2wigJune2010Q30 Info: * MC simulation : Off Info: * Chr name prepend : none Info: * Min. reported pk ht : 0 Info: * Min. cov. allowed : 0.0010 Info: * Minimum ht to process: Off Info: * Lander-Waterman FDR : Off Info: * Output Sequence : Off Info: * Control files in use : Off Info: * Compare files in use : Off Info: * Auto-threshold : Off Info: * Filter on PET flags : Off Info: * Maximum PET frag size: 1000 Info: * Aligner : sam Info: * PET/native mode : On Info: * One file per chr. : On Info: * Sub-peaks : Off Info: * Trim : Off Info: * Saturation Analysis : Off Info: * Wig step size : 1 Info: * Histogram length : 30 Info: * Histogram precision : 1 Info: * Peaks File Header : On Info: * Min readahead window : Off Info: * Bedgraph/Wigfile : wig file Info: * R mode : Off Info: * Filter Duplicates : Off Info: * Filter quality min. : On (30) Info: * Input Files : Info: /projects/olenam/NBL_targets_genomes_variants/BAM_files/transcriptome/HS1799.bam Version: Initializing class PeakWriter $Revision: 1498 $ Version: Initializing class Generic_AlignRead_Iterator $Revision: 1600 $ Version: Initializing class SAMIterator $Revision: 936 $ Info: Running Peak Processor Version: Initializing class PeakDataSet Peak Locator $Revision: 2226 $ Version: Initializing class PeakStore $Revision: 1335 $ Version: Initializing class MapStore $Revision: 1335 $ Info: Current chromosome : 10 Info: Reads used: 3977831 Info: Reads filtered by iterator: 491700 Version: Initializing class PeakStats $Revision: 1335 $ Version: Initializing class Histogram $Revision: 1197 $ Version: Initializing class WigwriterBuffered $Revision: 2195 $ Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_10.wig.gz Info: Running Peak Processor Info: Current chromosome : 11 Info: Reads used: 10513714 Info: Reads filtered by iterator: 1582392 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_11.wig.gz Info: Running Peak Processor Info: Current chromosome : 12 Info: Reads used: 8558881 Info: Reads filtered by iterator: 2750823 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_12.wig.gz Info: Running Peak Processor Info: Current chromosome : 13 Info: Reads used: 2843040 Info: Reads filtered by iterator: 3015203 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_13.wig.gz Info: Running Peak Processor Info: Current chromosome : 14 Info: Reads used: 6649070 Info: Reads filtered by iterator: 3806474 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_14.wig.gz Info: Running Peak Processor Info: Current chromosome : 15 Info: Reads used: 4819063 Info: Reads filtered by iterator: 4673289 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_15.wig.gz Info: Running Peak Processor Info: Current chromosome : 16 Info: Reads used: 6475895 Info: Reads filtered by iterator: 6186237 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_16.wig.gz Info: Running Peak Processor Info: Current chromosome : 17 Info: Reads used: 13318874 Info: Reads filtered by iterator: 7841261 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_17.wig.gz Info: Running Peak Processor Info: Current chromosome : 18 Info: Reads used: 2109745 Info: Reads filtered by iterator: 8071305 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_18.wig.gz Info: Running Peak Processor Info: Current chromosome : 19 Info: Reads used: 8867502 Info: Reads filtered by iterator: 9116761 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_19.wig.gz Info: Running Peak Processor Info: Current chromosome : 1 Info: Reads used: 15008154 Info: Reads filtered by iterator: 11234166 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_1.wig.gz Info: Running Peak Processor Info: Current chromosome : 20 Info: Reads used: 4688011 Info: Reads filtered by iterator: 11650041 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_20.wig.gz Info: Running Peak Processor Info: Current chromosome : 21 Info: Reads used: 1444566 Info: Reads filtered by iterator: 11816967 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_21.wig.gz Info: Running Peak Processor Info: Current chromosome : 22 Info: Reads used: 4256459 Info: Reads filtered by iterator: 12413937 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_22.wig.gz Info: Running Peak Processor Info: Current chromosome : 2 Info: Reads used: 11005312 Info: Reads filtered by iterator: 13885605 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_2.wig.gz Info: Running Peak Processor Info: Current chromosome : 3 Info: Reads used: 6710380 Info: Reads filtered by iterator: 14639511 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_3.wig.gz Info: Running Peak Processor Info: Current chromosome : 4 Info: Reads used: 5768605 Info: Reads filtered by iterator: 15249870 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_4.wig.gz Info: Running Peak Processor Info: Current chromosome : 5 Info: Reads used: 7579631 Info: Reads filtered by iterator: 16469329 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_5.wig.gz Info: Running Peak Processor Info: Current chromosome : 6 Info: Reads used: 7196316 Info: Reads filtered by iterator: 17482703 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_6.wig.gz Info: Running Peak Processor Info: Current chromosome : 7 Info: Reads used: 8381937 Info: Reads filtered by iterator: 19182066 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_7.wig.gz Info: Running Peak Processor Info: Current chromosome : 8 Info: Reads used: 5229893 Info: Reads filtered by iterator: 19814796 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_8.wig.gz Info: Running Peak Processor Info: Current chromosome : 9 Info: Reads used: 6250774 Info: Reads filtered by iterator: 20885290 Info: writing to : /projects/NBL/wig_files_transcriptome/HS1799bam2wigJune2010Q30_mode_3_standard_9.wig.gz Info: Running Peak Processor Info: Current chromosome : M