INPUT PARAMETERS: Namespace(B2=None, N4=1000, N6=1000, S4=1, UMIs=None, adapters1=None, b3=0.05, blacklist='/home/users/marinovg/genomes/blacklists/mm10/mm10.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes', e4='PeakXus', fastq='TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.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='TAL1-G1E-ER4-0h-Rep1-GSM1689024-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 TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.647483825684 s Creating peak regions... Creating peak regions took 41.9178888798 s Estimating background... Estimating background took 0.207072019577 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.653394937515 s Creating peak regions... Creating peak regions took 38.1703560352 s Estimating background... Estimating background took 0.186518907547 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.574495077133 s Creating peak regions... Creating peak regions took 39.0250329971 s Estimating background... Estimating background took 0.22104716301 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.641655921936 s Creating peak regions... Creating peak regions took 37.2013049126 s Estimating background... Estimating background took 0.235353946686 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.687323093414 s Creating peak regions... Creating peak regions took 38.45561409 s Estimating background... Estimating background took 0.215934991837 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.588569164276 s Creating peak regions... Creating peak regions took 32.0451309681 s Estimating background... Estimating background took 0.206457853317 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.54966211319 s Creating peak regions... Creating peak regions took 30.3164219856 s Estimating background... Estimating background took 0.204291820526 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.519417047501 s Creating peak regions... Creating peak regions took 29.1023159027 s Estimating background... Estimating background took 0.195669174194 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.553312063217 s Creating peak regions... Creating peak regions took 27.8988420963 s Estimating background... Estimating background took 0.198070049286 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.373085975647 s Creating peak regions... Creating peak regions took 18.9509980679 s Estimating background... Estimating background took 0.18160200119 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 1.35429000854 s Creating peak regions... Creating peak regions took 60.7277061939 s Estimating background... Estimating background took 0.381496906281 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0220589637756 s Creating peak regions... Creating peak regions took 0.20464682579 s Estimating background... Estimating background took 0.199749946594 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 1.19818520546 s Creating peak regions... Creating peak regions took 56.2765440941 s Estimating background... Estimating background took 0.373685836792 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.975762844086 s Creating peak regions... Creating peak regions took 49.4344670773 s Estimating background... Estimating background took 0.22691988945 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.822323083878 s Creating peak regions... Creating peak regions took 48.1075410843 s Estimating background... Estimating background took 0.233994960785 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0390620231628 s Creating peak regions... Creating peak regions took 0.0578880310059 s Estimating background... Estimating background took 0.207036972046 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.847351074219 s Creating peak regions... Creating peak regions took 46.9878408909 s Estimating background... Estimating background took 0.221431016922 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0217320919037 s Creating peak regions... Creating peak regions took 0.486093044281 s Estimating background... Estimating background took 0.224833965302 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.854841947556 s Creating peak regions... Creating peak regions took 46.218624115 s Estimating background... Estimating background took 0.232414007187 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.958950996399 s Creating peak regions... Creating peak regions took 45.0079100132 s Estimating background... Estimating background took 0.220533847809 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.713673114777 s Creating peak regions... Creating peak regions took 39.6988940239 s Estimating background... Estimating background took 0.232012987137 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.804692983627 s Creating peak regions... Creating peak regions took 38.6306159496 s Estimating background... Estimating background took 0.363072156906 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0447158813477 s Creating peak regions... Creating peak regions took 0.025426864624 s Estimating background... Estimating background took 0.231268167496 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0303478240967 s Creating peak regions... Creating peak regions took 0.0644359588623 s Estimating background... Estimating background took 0.215711832047 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0255968570709 s Creating peak regions... Creating peak regions took 0.0258731842041 s Estimating background... Estimating background took 0.234802007675 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0299379825592 s Creating peak regions... Creating peak regions took 0.0504038333893 s Estimating background... Estimating background took 0.235121011734 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0293619632721 s Creating peak regions... Creating peak regions took 0.0505640506744 s Estimating background... Estimating background took 0.228062868118 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.027379989624 s Creating peak regions... Creating peak regions took 0.0523340702057 s Estimating background... Estimating background took 0.231333017349 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0235710144043 s Creating peak regions... Creating peak regions took 0.0413630008698 s Estimating background... Estimating background took 0.233747005463 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0296800136566 s Creating peak regions... Creating peak regions took 0.0959138870239 s Estimating background... Estimating background took 0.232264041901 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0248839855194 s Creating peak regions... Creating peak regions took 0.0558829307556 s Estimating background... Estimating background took 0.232918977737 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0475099086761 s Creating peak regions... Creating peak regions took 0.0364089012146 s Estimating background... Estimating background took 0.233544111252 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0308220386505 s Creating peak regions... Creating peak regions took 0.0386099815369 s Estimating background... Estimating background took 0.233328104019 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0341458320618 s Creating peak regions... Creating peak regions took 0.0387890338898 s Estimating background... Estimating background took 0.234163999557 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0309238433838 s Creating peak regions... Creating peak regions took 0.0830571651459 s Estimating background... Estimating background took 0.234174966812 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0247001647949 s Creating peak regions... Creating peak regions took 0.0307450294495 s Estimating background... Estimating background took 0.23321890831 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0385069847107 s Creating peak regions... Creating peak regions took 0.178915023804 s Estimating background... Estimating background took 0.234554052353 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.428292036057 s Creating peak regions... Creating peak regions took 52.1729500294 s Estimating background... Estimating background took 0.251070022583 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0391550064087 s Creating peak regions... Creating peak regions took 0.403761148453 s Estimating background... Estimating background took 0.20156288147 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Reading data took 0.0251820087433 s Creating peak regions... Creating peak regions took 25.3941938877 s Estimating background... Estimating background took 0.243330955505 s Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-0h-Rep1-GSM1689024.35mers.unique.bam Reading in data...