Version: Vancouver Short Read Analysis Package 4.0.16-dev.interval Version: Initializing class FindPeaks $Revision: 3126 $ Version: Initializing class Parameters $Revision: 3117 $ Info: Log File: wig/ES_129JAEC57bl6_H3K4me1_ChIP-seq_mm9_ht3_q10.log Version: Initializing class Log_Buffer $Revision: 2530 $ Info: * Output directory : wig/ Info: * Naming files as : ES_129JAEC57bl6_H3K4me1_ChIP-seq_mm9_ht3_q10 Info: * MC simulation : Off Info: * Chr name prepend : none Info: * Min. reported pk ht : 5 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: Off Info: * Aligner : interval Info: * Triangle dist. : 100 low Info: * Triangle dist. : 200 median Info: * Triangle dist. : 300 high Info: * One file per chr. : Off 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: * Wig File Headers : On Info: * Min readahead window : Off Info: * Bedgraph/Wigfile : wig file Info: * R mode : Off Info: * Filter Duplicates : On Info: * Filter quality min. : On (10) Info: * Input Files : Info: out/chr10.part.interval.gz Info: out/chr11.part.interval.gz Info: out/chr12.part.interval.gz Info: out/chr13.part.interval.gz Info: out/chr13_random.part.interval.gz Info: out/chr14.part.interval.gz Info: out/chr15.part.interval.gz Info: out/chr16.part.interval.gz Info: out/chr16_random.part.interval.gz Info: out/chr17.part.interval.gz Info: out/chr17_random.part.interval.gz Info: out/chr18.part.interval.gz Info: out/chr19.part.interval.gz Info: out/chr1.part.interval.gz Info: out/chr1_random.part.interval.gz Info: out/chr2.part.interval.gz Info: out/chr3.part.interval.gz Info: out/chr3_random.part.interval.gz Info: out/chr4.part.interval.gz Info: out/chr4_random.part.interval.gz Info: out/chr5.part.interval.gz Info: out/chr5_random.part.interval.gz Info: out/chr6.part.interval.gz Info: out/chr7.part.interval.gz Info: out/chr7_random.part.interval.gz Info: out/chr8.part.interval.gz Info: out/chr8_random.part.interval.gz Info: out/chr9.part.interval.gz Info: out/chr9_random.part.interval.gz Info: out/chrM.part.interval.gz Info: out/chrUn_random.part.interval.gz Info: out/chrX.part.interval.gz Info: out/chrX_random.part.interval.gz Info: out/chrY.part.interval.gz Info: out/chrY_random.part.interval.gz Version: Initializing class PeakWriter $Revision: 2532 $ Info: Running Peak Processor Version: Initializing class Generic_AlignRead_Iterator $Revision: 3118 $ Version: Initializing class BedIterator $Revision: 2933 $ Version: Initializing class PeakDataSet Peak Locator $Revision: 2785 $ Version: Initializing class PeakStore $Revision: 2739 $ Version: Initializing class MapStore $Revision: 2738 $ Info: Current chromosome : chr10 Info: Reads used: 599235 Info: Reads filtered by duplicate: 42674 Version: Initializing class PeakStats $Revision: 2532 $ Version: Initializing class Histogram $Revision: 2530 $ Version: Initializing class WigwriterBuffered $Revision: 2530 $ Info: writing to : wig/ES_129JAEC57bl6_H3K4me1_ChIP-seq_mm9_ht3_q10_triangle_standard_chr10.wig.gz Info: Running Peak Processor Info: Current chromosome : chr11 Info: Reads used: 811353 Info: Reads filtered by duplicate: 59958 Info: Running Peak Processor Info: Current chromosome : chr12 Info: Reads used: 493798 Info: Reads filtered by duplicate: 36454 Info: Running Peak Processor Info: Current chromosome : chr13 Info: Reads used: 518009 Info: Reads filtered by duplicate: 39341 Info: Running Peak Processor Info: Current chromosome : chr13_random Info: Reads used: 1267 Info: Reads filtered by duplicate: 35 Info: Running Peak Processor Info: Current chromosome : chr14 Info: Reads used: 476879 Info: Reads filtered by duplicate: 31805 Info: Running Peak Processor Info: Current chromosome : chr15 Info: Reads used: 497547 Info: Reads filtered by duplicate: 38664 Info: Running Peak Processor Info: Current chromosome : chr16 Info: Reads used: 394972 Info: Reads filtered by duplicate: 28285 Info: Running Peak Processor Info: Current chromosome : chr16_random Info: Reads used: 3 Info: Running Peak Processor Info: Current chromosome : chr17 Info: Reads used: 526614 Info: Reads filtered by duplicate: 37265 Info: Running Peak Processor Info: Current chromosome : chr17_random Info: Reads used: 1866 Info: Reads filtered by duplicate: 93 Info: Running Peak Processor Info: Current chromosome : chr18 Info: Reads used: 373896 Info: Reads filtered by duplicate: 28595 Info: Running Peak Processor Info: Current chromosome : chr19 Info: Reads used: 331057 Info: Reads filtered by duplicate: 23863 Info: Running Peak Processor Info: Current chromosome : chr1 Info: Reads used: 762447 Info: Reads filtered by duplicate: 52785 Info: Running Peak Processor Info: Current chromosome : chr1_random Info: Reads used: 4765 Info: Reads filtered by duplicate: 347 Info: Running Peak Processor Info: Current chromosome : chr2 Info: Reads used: 885598 Info: Reads filtered by duplicate: 181584 Info: Running Peak Processor Info: Current chromosome : chr3 Info: Reads used: 573235 Info: Reads filtered by duplicate: 39830 Info: Running Peak Processor Info: Current chromosome : chr3_random Info: Reads used: 68 Info: Reads filtered by duplicate: 4 Info: Running Peak Processor Info: Current chromosome : chr4 Info: Reads used: 818583 Info: Reads filtered by duplicate: 57538 Info: Running Peak Processor Info: Current chromosome : chr4_random Info: Reads used: 502 Info: Reads filtered by duplicate: 37 Info: Running Peak Processor Info: Current chromosome : chr5 Info: Reads used: 753460 Info: Reads filtered by duplicate: 53519 Info: Running Peak Processor Info: Current chromosome : chr5_random Info: Reads used: 306 Info: Reads filtered by duplicate: 4 Info: Running Peak Processor Info: Current chromosome : chr6 Info: Reads used: 619660 Info: Reads filtered by duplicate: 46987 Info: Running Peak Processor Info: Current chromosome : chr7 Info: Reads used: 712524 Info: Reads filtered by duplicate: 49422 Info: Running Peak Processor Info: Current chromosome : chr7_random Info: Reads used: 400 Info: Reads filtered by duplicate: 8 Info: Running Peak Processor Info: Current chromosome : chr8 Info: Reads used: 694797 Info: Reads filtered by duplicate: 50593 Info: Running Peak Processor Info: Current chromosome : chr8_random Info: Reads used: 4025 Info: Reads filtered by duplicate: 148 Info: Running Peak Processor Info: Current chromosome : chr9 Info: Reads used: 637577 Info: Reads filtered by duplicate: 214804 Info: Running Peak Processor Info: Current chromosome : chr9_random Info: Reads used: 1748 Info: Reads filtered by duplicate: 204 Info: Running Peak Processor Info: Current chromosome : chrM Info: Reads used: 2240 Info: Reads filtered by duplicate: 352 Info: Running Peak Processor Info: Current chromosome : chrUn_random Info: Reads used: 15384 Info: Reads filtered by duplicate: 25737 Info: Running Peak Processor Info: Current chromosome : chrX Info: Reads used: 251075 Info: Reads filtered by duplicate: 14920 Info: Running Peak Processor Info: Current chromosome : chrX_random Info: Reads used: 1328 Info: Reads filtered by duplicate: 50 Info: Running Peak Processor Info: Current chromosome : chrY Info: Reads used: 3334 Info: Reads filtered by duplicate: 549 Info: Running Peak Processor Info: Current chromosome : chrY_random Info: Reads used: 50159 Info: Reads filtered by duplicate: 465 Info: Wrote to:wig/ES_129JAEC57bl6_H3K4me1_ChIP-seq_mm9_ht3_q10_triangle_standard.wig.gz