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-Rep1-GSM1689020.35mers.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-Rep1-GSM1689020-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-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 1.35156106949 s Creating peak regions... Creating peak regions took 42.3276150227 s Estimating background... Estimating background took 0.377788066864 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 1.0511238575 s Creating peak regions... Creating peak regions took 37.400398016 s Estimating background... Estimating background took 0.291378974915 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 1.25972104073 s Creating peak regions... Creating peak regions took 37.3724110126 s Estimating background... Estimating background took 0.331930160522 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 1.03785085678 s Creating peak regions... Creating peak regions took 37.5079729557 s Estimating background... Estimating background took 0.327306985855 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 1.12813806534 s Creating peak regions... Creating peak regions took 38.4851198196 s Estimating background... Estimating background took 0.290316820145 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.923029184341 s Creating peak regions... Creating peak regions took 32.2934110165 s Estimating background... Estimating background took 0.305926799774 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.905397176743 s Creating peak regions... Creating peak regions took 30.4727838039 s Estimating background... Estimating background took 0.332854986191 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.861783981323 s Creating peak regions... Creating peak regions took 29.3205878735 s Estimating background... Estimating background took 0.335464000702 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.790787935257 s Creating peak regions... Creating peak regions took 28.1447079182 s Estimating background... Estimating background took 0.18585395813 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.596946954727 s Creating peak regions... Creating peak regions took 18.9862020016 s Estimating background... Estimating background took 0.182298898697 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 2.26635694504 s Creating peak regions... Creating peak regions took 60.4485230446 s Estimating background... Estimating background took 0.454782009125 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0674738883972 s Creating peak regions... Creating peak regions took 0.144317865372 s Estimating background... Estimating background took 0.199795007706 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0292899608612 s Creating peak regions... Creating peak regions took 0.303025007248 s Estimating background... Estimating background took 0.198767900467 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.029865026474 s Creating peak regions... Creating peak regions took 0.21422791481 s Estimating background... Estimating background took 0.200829029083 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0269320011139 s Creating peak regions... Creating peak regions took 0.248315811157 s Estimating background... Estimating background took 0.201861143112 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 1.92137002945 s Creating peak regions... Creating peak regions took 56.2809438705 s Estimating background... Estimating background took 0.430935144424 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 1.42382192612 s Creating peak regions... Creating peak regions took 48.1450829506 s Estimating background... Estimating background took 0.331169843674 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 1.4165430069 s Creating peak regions... Creating peak regions took 49.0344669819 s Estimating background... Estimating background took 0.324432134628 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0584139823914 s Creating peak regions... Creating peak regions took 0.0669581890106 s Estimating background... Estimating background took 0.229789018631 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 1.36878013611 s Creating peak regions... Creating peak regions took 46.8632068634 s Estimating background... Estimating background took 0.347355127335 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.027293920517 s Creating peak regions... Creating peak regions took 0.710454940796 s Estimating background... Estimating background took 0.228526115417 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 1.37653803825 s Creating peak regions... Creating peak regions took 46.958523035 s Estimating background... Estimating background took 0.354552984238 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 1.22335410118 s Creating peak regions... Creating peak regions took 45.2961161137 s Estimating background... Estimating background took 0.372728824615 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 1.12564706802 s Creating peak regions... Creating peak regions took 40.2368679047 s Estimating background... Estimating background took 0.339694023132 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 1.26043891907 s Creating peak regions... Creating peak regions took 38.6087050438 s Estimating background... Estimating background took 0.319919109344 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0585839748383 s Creating peak regions... Creating peak regions took 0.027841091156 s Estimating background... Estimating background took 0.228056907654 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.039391040802 s Creating peak regions... Creating peak regions took 0.0592319965363 s Estimating background... Estimating background took 0.225784063339 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0292339324951 s Creating peak regions... Creating peak regions took 0.0477368831635 s Estimating background... Estimating background took 0.226565122604 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0295698642731 s Creating peak regions... Creating peak regions took 0.0517570972443 s Estimating background... Estimating background took 0.227679014206 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0369710922241 s Creating peak regions... Creating peak regions took 0.0110938549042 s Estimating background... Estimating background took 0.226801872253 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.030366897583 s Creating peak regions... Creating peak regions took 0.0443758964539 s Estimating background... Estimating background took 0.231293916702 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0285868644714 s Creating peak regions... Creating peak regions took 0.0268430709839 s Estimating background... Estimating background took 0.230916023254 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.032576084137 s Creating peak regions... Creating peak regions took 0.0623359680176 s Estimating background... Estimating background took 0.229587078094 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.034637928009 s Creating peak regions... Creating peak regions took 0.0453538894653 s Estimating background... Estimating background took 0.204690933228 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.033833026886 s Creating peak regions... Creating peak regions took 0.0332469940186 s Estimating background... Estimating background took 0.214382171631 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0885360240936 s Creating peak regions... Creating peak regions took 0.0401921272278 s Estimating background... Estimating background took 0.276848077774 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0366470813751 s Creating peak regions... Creating peak regions took 0.0411357879639 s Estimating background... Estimating background took 0.230072975159 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0477578639984 s Creating peak regions... Creating peak regions took 0.0484681129456 s Estimating background... Estimating background took 0.261100769043 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0381281375885 s Creating peak regions... Creating peak regions took 0.0824680328369 s Estimating background... Estimating background took 0.232248067856 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0380730628967 s Creating peak regions... Creating peak regions took 0.0390229225159 s Estimating background... Estimating background took 0.231706857681 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0405099391937 s Creating peak regions... Creating peak regions took 0.0351629257202 s Estimating background... Estimating background took 0.218599796295 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0500729084015 s Creating peak regions... Creating peak regions took 0.224447965622 s Estimating background... Estimating background took 0.263319969177 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.726529121399 s Creating peak regions... Creating peak regions took 52.7980530262 s Estimating background... Estimating background took 0.254276037216 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0548429489136 s Creating peak regions... Creating peak regions took 0.454571008682 s Estimating background... Estimating background took 0.230808973312 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Reading data took 0.0391829013824 s Creating peak regions... Creating peak regions took 24.1727781296 s Estimating background... Estimating background took 0.231117010117 s Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep1-GSM1689020.35mers.unique.bam Reading in data...