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-Rep4-GSM1689023.35mers.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-Rep4-GSM1689023-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-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 1.05452990532 s Creating peak regions... Creating peak regions took 44.387556076 s Estimating background... Estimating background took 0.617125988007 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 1.22612190247 s Creating peak regions... Creating peak regions took 38.2713470459 s Estimating background... Estimating background took 3.24261403084 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 1.31111693382 s Creating peak regions... Creating peak regions took 37.1662390232 s Estimating background... Estimating background took 0.835175991058 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 1.13393712044 s Creating peak regions... Creating peak regions took 38.0231978893 s Estimating background... Estimating background took 0.743252038956 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 1.29291701317 s Creating peak regions... Creating peak regions took 39.1556560993 s Estimating background... Estimating background took 0.647019147873 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 1.09026098251 s Creating peak regions... Creating peak regions took 32.6298649311 s Estimating background... Estimating background took 0.668881893158 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 1.0000910759 s Creating peak regions... Creating peak regions took 30.8854589462 s Estimating background... Estimating background took 0.672276973724 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.973754167557 s Creating peak regions... Creating peak regions took 29.6568670273 s Estimating background... Estimating background took 3.28286099434 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.74706697464 s Creating peak regions... Creating peak regions took 27.9119961262 s Estimating background... Estimating background took 0.526710033417 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.649252176285 s Creating peak regions... Creating peak regions took 19.3687160015 s Estimating background... Estimating background took 0.55150604248 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 2.20947790146 s Creating peak regions... Creating peak regions took 62.4357590675 s Estimating background... Estimating background took 5.05437302589 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0416769981384 s Creating peak regions... Creating peak regions took 0.163870096207 s Estimating background... Estimating background took 0.227313995361 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0508449077606 s Creating peak regions... Creating peak regions took 0.235811948776 s Estimating background... Estimating background took 0.218822002411 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.048357963562 s Creating peak regions... Creating peak regions took 0.197234869003 s Estimating background... Estimating background took 0.201411962509 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.037899017334 s Creating peak regions... Creating peak regions took 0.227399110794 s Estimating background... Estimating background took 0.22328209877 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 2.04587316513 s Creating peak regions... Creating peak regions took 57.7832510471 s Estimating background... Estimating background took 4.42485713959 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 1.27478790283 s Creating peak regions... Creating peak regions took 50.0292351246 s Estimating background... Estimating background took 3.96217799187 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 1.26865005493 s Creating peak regions... Creating peak regions took 48.7390389442 s Estimating background... Estimating background took 3.95252895355 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0388751029968 s Creating peak regions... Creating peak regions took 0.0737798213959 s Estimating background... Estimating background took 0.26057600975 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0335168838501 s Creating peak regions... Creating peak regions took 0.0169961452484 s Estimating background... Estimating background took 0.260902881622 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 1.38287591934 s Creating peak regions... Creating peak regions took 48.1364908218 s Estimating background... Estimating background took 0.925582885742 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.029326915741 s Creating peak regions... Creating peak regions took 0.444520950317 s Estimating background... Estimating background took 0.258490800858 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 1.43148589134 s Creating peak regions... Creating peak regions took 47.2286710739 s Estimating background... Estimating background took 0.808132886887 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 1.52267599106 s Creating peak regions... Creating peak regions took 44.9652910233 s Estimating background... Estimating background took 0.781275033951 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 1.33065700531 s Creating peak regions... Creating peak regions took 40.8464272022 s Estimating background... Estimating background took 4.0232758522 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 1.29373216629 s Creating peak regions... Creating peak regions took 38.9832251072 s Estimating background... Estimating background took 0.792665958405 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0983550548553 s Creating peak regions... Creating peak regions took 0.0527510643005 s Estimating background... Estimating background took 0.273412942886 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.03400182724 s Creating peak regions... Creating peak regions took 0.0600490570068 s Estimating background... Estimating background took 0.283998012543 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0359418392181 s Creating peak regions... Creating peak regions took 0.0321471691132 s Estimating background... Estimating background took 0.27340388298 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0335428714752 s Creating peak regions... Creating peak regions took 0.0503380298615 s Estimating background... Estimating background took 0.285575151443 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0367469787598 s Creating peak regions... Creating peak regions took 0.072674036026 s Estimating background... Estimating background took 0.283582925797 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.036957025528 s Creating peak regions... Creating peak regions took 0.0492670536041 s Estimating background... Estimating background took 0.284132957458 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0359680652618 s Creating peak regions... Creating peak regions took 0.0329911708832 s Estimating background... Estimating background took 0.263925790787 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0316450595856 s Creating peak regions... Creating peak regions took 0.0364789962769 s Estimating background... Estimating background took 0.282265901566 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0374631881714 s Creating peak regions... Creating peak regions took 0.0398910045624 s Estimating background... Estimating background took 0.283120155334 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0373809337616 s Creating peak regions... Creating peak regions took 0.105048894882 s Estimating background... Estimating background took 0.277248859406 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0361640453339 s Creating peak regions... Creating peak regions took 0.0362730026245 s Estimating background... Estimating background took 0.266616106033 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0375578403473 s Creating peak regions... Creating peak regions took 0.102164983749 s Estimating background... Estimating background took 0.287369966507 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0375502109528 s Creating peak regions... Creating peak regions took 0.0423190593719 s Estimating background... Estimating background took 0.290285110474 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0376989841461 s Creating peak regions... Creating peak regions took 0.0404369831085 s Estimating background... Estimating background took 0.290657043457 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.104845046997 s Creating peak regions... Creating peak regions took 0.0617680549622 s Estimating background... Estimating background took 0.334789037704 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0402829647064 s Creating peak regions... Creating peak regions took 0.053230047226 s Estimating background... Estimating background took 0.278301954269 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0526900291443 s Creating peak regions... Creating peak regions took 0.0721809864044 s Estimating background... Estimating background took 0.319398880005 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0378179550171 s Creating peak regions... Creating peak regions took 0.0874030590057 s Estimating background... Estimating background took 0.271546125412 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0341811180115 s Creating peak regions... Creating peak regions took 0.0380189418793 s Estimating background... Estimating background took 0.283982038498 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0614011287689 s Creating peak regions... Creating peak regions took 0.195006132126 s Estimating background... Estimating background took 0.304790973663 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.741443872452 s Creating peak regions... Creating peak regions took 54.1714129448 s Estimating background... Estimating background took 0.442328214645 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0667231082916 s Creating peak regions... Creating peak regions took 0.313867092133 s Estimating background... Estimating background took 0.272555112839 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Reading data took 0.0325949192047 s Creating peak regions... Creating peak regions took 21.7319848537 s Estimating background... Estimating background took 0.294834852219 s Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep4-GSM1689023.35mers.unique.bam Reading in data...