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/Thiomacs_GSM537986_H3K4me1_ChIP-seq_mm9_ht3_q10.log Version: Initializing class Log_Buffer $Revision: 2530 $ Info: * Output directory : wig/ Info: * Naming files as : Thiomacs_GSM537986_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/chr14.part.interval.gz Info: out/chr15.part.interval.gz Info: out/chr16.part.interval.gz Info: out/chr17.part.interval.gz Info: out/chr18.part.interval.gz Info: out/chr19.part.interval.gz Info: out/chr1.part.interval.gz Info: out/chr2.part.interval.gz Info: out/chr3.part.interval.gz Info: out/chr4.part.interval.gz Info: out/chr5.part.interval.gz Info: out/chr6.part.interval.gz Info: out/chr7.part.interval.gz Info: out/chr8.part.interval.gz Info: out/chr9.part.interval.gz Info: out/chrM.part.interval.gz Info: out/chrX.part.interval.gz Info: out/chrY.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: 304937 Info: Reads filtered by duplicate: 8238 Version: Initializing class PeakStats $Revision: 2532 $ Version: Initializing class Histogram $Revision: 2530 $ Version: Initializing class WigwriterBuffered $Revision: 2530 $ Info: writing to : wig/Thiomacs_GSM537986_H3K4me1_ChIP-seq_mm9_ht3_q10_triangle_standard_chr10.wig.gz Info: Running Peak Processor Info: Current chromosome : chr11 Info: Reads used: 359352 Info: Reads filtered by duplicate: 10256 Info: Running Peak Processor Info: Current chromosome : chr12 Info: Reads used: 241024 Info: Reads filtered by duplicate: 9106 Info: Running Peak Processor Info: Current chromosome : chr13 Info: Reads used: 259642 Info: Reads filtered by duplicate: 9173 Info: Running Peak Processor Info: Current chromosome : chr14 Info: Reads used: 238837 Info: Reads filtered by duplicate: 6211 Info: Running Peak Processor Info: Current chromosome : chr15 Info: Reads used: 238973 Info: Reads filtered by duplicate: 6345 Info: Running Peak Processor Info: Current chromosome : chr16 Info: Reads used: 211066 Info: Reads filtered by duplicate: 5652 Info: Running Peak Processor Info: Current chromosome : chr17 Info: Reads used: 235731 Info: Reads filtered by duplicate: 6237 Info: Running Peak Processor Info: Current chromosome : chr18 Info: Reads used: 174170 Info: Reads filtered by duplicate: 4748 Info: Running Peak Processor Info: Current chromosome : chr19 Info: Reads used: 166788 Info: Reads filtered by duplicate: 4539 Info: Running Peak Processor Info: Current chromosome : chr1 Info: Reads used: 403132 Info: Reads filtered by duplicate: 10622 Info: Running Peak Processor Info: Current chromosome : chr2 Info: Reads used: 441783 Info: Reads filtered by duplicate: 111257 Info: Running Peak Processor Info: Current chromosome : chr3 Info: Reads used: 315409 Info: Reads filtered by duplicate: 8398 Info: Running Peak Processor Info: Current chromosome : chr4 Info: Reads used: 342487 Info: Reads filtered by duplicate: 9629 Info: Running Peak Processor Info: Current chromosome : chr5 Info: Reads used: 337887 Info: Reads filtered by duplicate: 8692 Info: Running Peak Processor Info: Current chromosome : chr6 Info: Reads used: 324219 Info: Reads filtered by duplicate: 11537 Info: Running Peak Processor Info: Current chromosome : chr7 Info: Reads used: 322697 Info: Reads filtered by duplicate: 8020 Info: Running Peak Processor Info: Current chromosome : chr8 Info: Reads used: 277496 Info: Reads filtered by duplicate: 7275 Info: Running Peak Processor Info: Current chromosome : chr9 Info: Reads used: 313743 Info: Reads filtered by duplicate: 157109 Info: Running Peak Processor Info: Current chromosome : chrM Info: Reads used: 50 Info: Reads filtered by duplicate: 1 Info: Running Peak Processor Info: Current chromosome : chrX Info: Reads used: 157231 Info: Reads filtered by duplicate: 5051 Info: Running Peak Processor Info: Current chromosome : chrY Info: Reads used: 8779 Info: Reads filtered by duplicate: 914 Info: Wrote to:wig/Thiomacs_GSM537986_H3K4me1_ChIP-seq_mm9_ht3_q10_triangle_standard.wig.gz