INPUT PARAMETERS: Namespace(B2=None, N4=1000, N6=1000, S4=1, UMIs=None, adapters1=None, b3=0.05, blacklist='/oak/stanford/groups/akundaje/marinovg/genomes/blacklists/hg38.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes', e4='PeakXus', fastq='ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam', genome2=None, k4=4, l3=5, l6='PeakXus', l_l3=60, m4=10, m5=20, m6=100, matrixhits=None, maxw7=50, minw7=4, ml4=17, ms4=-8, n3=1, n4=1, o5=1, outdir='ZNF169-rep2-SRR5197066/peakXus/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)Testing that input files exist...done! Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.67203092575 s Creating peak regions... Creating peak regions took 75.8196499348 s Estimating background... Estimating background took 39.6633541584 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.01868510246 s Creating peak regions... Creating peak regions took 37.9090781212 s Estimating background... Estimating background took 15.6967759132 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.05458593369 s Creating peak regions... Creating peak regions took 39.7137000561 s Estimating background... Estimating background took 15.4983658791 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... INPUT PARAMETERS: Namespace(B2=None, N4=1000, N6=1000, S4=1, UMIs=None, adapters1=None, b3=0.05, blacklist='/oak/stanford/groups/akundaje/marinovg/genomes/blacklists/hg38.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38-male.chrom.sizes', e4='PeakXus', fastq='ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam', genome2=None, k4=4, l3=5, l6='PeakXus', l_l3=60, m4=10, m5=20, m6=100, matrixhits=None, maxw7=50, minw7=4, ml4=17, ms4=-8, n3=1, n4=1, o5=1, outdir='ZNF169-rep2-SRR5197066/peakXus/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)Testing that input files exist...done! Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.12314200401 s Creating peak regions... Creating peak regions took 69.4526629448 s Estimating background... Estimating background took 36.3757090569 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.50653910637 s Creating peak regions... Creating peak regions took 34.8615159988 s Estimating background... Estimating background took 14.5566830635 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.49753093719 s Creating peak regions... Creating peak regions took 36.3597381115 s Estimating background... Estimating background took 15.5105121136 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.63878107071 s Creating peak regions... Creating peak regions took 36.1574890614 s Estimating background... Estimating background took 16.0675418377 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51533102989 s Creating peak regions... Creating peak regions took 33.4436609745 s Estimating background... Estimating background took 17.0869910717 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.02310109138 s Creating peak regions... Creating peak regions took 28.3449409008 s Estimating background... Estimating background took 10.3137850761 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.79055190086 s Creating peak regions... Creating peak regions took 28.7289760113 s Estimating background... Estimating background took 11.4221119881 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.61847186089 s Creating peak regions... Creating peak regions took 23.8884370327 s Estimating background... Estimating background took 9.75791192055 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.91241598129 s Creating peak regions... Creating peak regions took 23.0899710655 s Estimating background... Estimating background took 12.7694010735 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40893101692 s Creating peak regions... Creating peak regions took 21.4330990314 s Estimating background... Estimating background took 8.11692619324 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.27852296829 s Creating peak regions... Creating peak regions took 15.9440860748 s Estimating background... Estimating background took 8.08062195778 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.30939602852 s Creating peak regions... Creating peak regions took 65.3692901134 s Estimating background... Estimating background took 25.0874891281 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.54785704613 s Creating peak regions... Creating peak regions took 18.6440179348 s Estimating background... Estimating background took 8.73297595978 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.770922899246 s Creating peak regions... Creating peak regions took 12.485669136 s Estimating background... Estimating background took 4.76054215431 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.00208187103 s Creating peak regions... Creating peak regions took 14.6554501057 s Estimating background... Estimating background took 7.45630407333 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.71313500404 s Creating peak regions... Creating peak regions took 50.8384511471 s Estimating background... Estimating background took 19.774107933 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.15465593338 s Creating peak regions... Creating peak regions took 54.2251319885 s Estimating background... Estimating background took 15.9851310253 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.39085388184 s Creating peak regions... Creating peak regions took 51.5694580078 s Estimating background... Estimating background took 19.1937170029 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.65561795235 s Creating peak regions... Creating peak regions took 47.3832118511 s Estimating background... Estimating background took 22.3109760284 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.32863497734 s Creating peak regions... Creating peak regions took 43.9435420036 s Estimating background... Estimating background took 19.1290969849 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85518598557 s Creating peak regions... Creating peak regions took 39.6440391541 s Estimating background... Estimating background took 14.1836338043 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.40064406395 s Creating peak regions... Creating peak regions took 37.0062658787 s Estimating background... Estimating background took 13.5378148556 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0948710441589 s Creating peak regions... Creating peak regions took 0.160862207413 s Estimating background... Estimating background took 0.655507087708 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.28878307343 s Creating peak regions... Creating peak regions took 40.4709119797 s Estimating background... Estimating background took 19.5681221485 s Processing ZNF169-rep2-SRR5197066.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.136945009232 s Creating peak regions... Creating peak regions took 13.8005042076 s Estimating background... Estimating background took 0.584256887436 s