Info: Log File: wig/iPS_mef_H3K4me1_ChIP-seq_mm9_ht3_q10.log Info: * Output directory : wig/ Info: * Naming files as : iPS_mef_H3K4me1_ChIP-seq_mm9_ht3_q10 Info: * MC simulation : Off Info: * Chr name prepend : none Info: * Min. reported pk ht : 3 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/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: 136639 Info: Reads filtered by duplicate: 5903 Version: Initializing class PeakStats $Revision: 2532 $ Version: Initializing class Histogram $Revision: 2530 $ Version: Initializing class WigwriterBuffered $Revision: 2530 $ Info: writing to : wig/iPS_mef_H3K4me1_ChIP-seq_mm9_ht3_q10_triangle_standard_chr10.wig.gz Info: Running Peak Processor Info: Current chromosome : chr11 Info: Reads used: 207240 Info: Reads filtered by duplicate: 8335 Info: Running Peak Processor Info: Current chromosome : chr12 Info: Reads used: 109805 Info: Reads filtered by duplicate: 4308 Info: Running Peak Processor Info: Current chromosome : chr13 Info: Reads used: 109052 Info: Reads filtered by duplicate: 4763 Info: Running Peak Processor Info: Current chromosome : chr13_random Info: Reads used: 250 Info: Reads filtered by duplicate: 2 Info: Running Peak Processor Info: Current chromosome : chr14 Info: Reads used: 99793 Info: Reads filtered by duplicate: 4498 Info: Running Peak Processor Info: Current chromosome : chr15 Info: Reads used: 117735 Info: Reads filtered by duplicate: 4925 Info: Running Peak Processor Info: Current chromosome : chr16 Info: Reads used: 86943 Info: Reads filtered by duplicate: 3522 Info: Running Peak Processor Info: Current chromosome : chr17 Info: Reads used: 132714 Info: Reads filtered by duplicate: 5208 Info: Running Peak Processor Info: Current chromosome : chr17_random Info: Reads used: 434 Info: Reads filtered by duplicate: 11 Info: Running Peak Processor Info: Current chromosome : chr18 Info: Reads used: 81341 Info: Reads filtered by duplicate: 3717 Info: Running Peak Processor Info: Current chromosome : chr19 Info: Reads used: 79266 Info: Reads filtered by duplicate: 3108 Info: Running Peak Processor Info: Current chromosome : chr1 Info: Reads used: 162106 Info: Reads filtered by duplicate: 6540 Info: Running Peak Processor Info: Current chromosome : chr1_random Info: Reads used: 881 Info: Reads filtered by duplicate: 46 Info: Running Peak Processor Info: Current chromosome : chr2 Info: Reads used: 206014 Info: Reads filtered by duplicate: 15673 Info: Running Peak Processor Info: Current chromosome : chr3 Info: Reads used: 113797 Info: Reads filtered by duplicate: 4851 Info: Running Peak Processor Info: Current chromosome : chr3_random Info: Reads used: 8 Info: Running Peak Processor Info: Current chromosome : chr4 Info: Reads used: 198889 Info: Reads filtered by duplicate: 7487 Info: Running Peak Processor Info: Current chromosome : chr4_random Info: Reads used: 156 Info: Reads filtered by duplicate: 4 Info: Running Peak Processor Info: Current chromosome : chr5 Info: Reads used: 185832 Info: Reads filtered by duplicate: 7593 Info: Running Peak Processor Info: Current chromosome : chr5_random Info: Reads used: 41 Info: Running Peak Processor Info: Current chromosome : chr6 Info: Reads used: 134277 Info: Reads filtered by duplicate: 5531 Info: Running Peak Processor Info: Current chromosome : chr7 Info: Reads used: 169628 Info: Reads filtered by duplicate: 6985 Info: Running Peak Processor Info: Current chromosome : chr7_random Info: Reads used: 39 Info: Running Peak Processor Info: Current chromosome : chr8 Info: Reads used: 149173 Info: Reads filtered by duplicate: 5973 Info: Running Peak Processor Info: Current chromosome : chr8_random Info: Reads used: 549 Info: Reads filtered by duplicate: 9 Info: Running Peak Processor Info: Current chromosome : chr9 Info: Reads used: 150383 Info: Reads filtered by duplicate: 11441 Info: Running Peak Processor Info: Current chromosome : chr9_random Info: Reads used: 470 Info: Reads filtered by duplicate: 25 Info: Running Peak Processor Info: Current chromosome : chrM Info: Reads used: 178 Info: Reads filtered by duplicate: 7 Info: Running Peak Processor Info: Current chromosome : chrUn_random Info: Reads used: 2753 Info: Reads filtered by duplicate: 1391 Info: Running Peak Processor Info: Current chromosome : chrX Info: Reads used: 43199 Info: Reads filtered by duplicate: 1923 Info: Running Peak Processor Info: Current chromosome : chrX_random Info: Reads used: 199 Info: Reads filtered by duplicate: 3 Info: Running Peak Processor Info: Current chromosome : chrY Info: Reads used: 411 Info: Reads filtered by duplicate: 14 Info: Running Peak Processor Info: Current chromosome : chrY_random Info: Reads used: 5568 Info: Reads filtered by duplicate: 27 Info: Wrote to:wig/iPS_mef_H3K4me1_ChIP-seq_mm9_ht3_q10_triangle_standard.wig.gz