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/mm10.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/mm10/female.mm10.chrom.sizes', e4='PeakXus', fastq='TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.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='TAL1_G1E-ER4_3h_Rep3-GSM1689031/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)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/mm10.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes', e4='PeakXus', fastq='TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.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='TAL1_G1E-ER4_3h_Rep3-GSM1689031/', 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_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.730381011963 s Creating peak regions... Creating peak regions took 31.6025109291 s Estimating background... Estimating background took 0.335790872574 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.646041870117 s Creating peak regions... Creating peak regions took 28.0218751431 s Estimating background... Estimating background took 0.43451499939 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.841038942337 s Creating peak regions... Creating peak regions took 28.3239011765 s Estimating background... Estimating background took 0.321255922318 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.663217067719 s Creating peak regions... Creating peak regions took 26.8033051491 s Estimating background... Estimating background took 0.319093942642 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.70752286911 s Creating peak regions... Creating peak regions took 28.4875450134 s Estimating background... Estimating background took 0.328528165817 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.536664962769 s Creating peak regions... Creating peak regions took 22.3726520538 s Estimating background... Estimating background took 0.318894147873 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.648699998856 s Creating peak regions... Creating peak regions took 21.2494399548 s Estimating background... Estimating background took 0.318143844604 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.51162815094 s Creating peak regions... Creating peak regions took 20.1064970493 s Estimating background... Estimating background took 0.297191143036 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.465639829636 s Creating peak regions... Creating peak regions took 19.216490984 s Estimating background... Estimating background took 0.317400932312 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.297692060471 s Creating peak regions... Creating peak regions took 13.2585978508 s Estimating background... Estimating background took 0.311332941055 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 1.3797519207 s Creating peak regions... Creating peak regions took 43.3828771114 s Estimating background... Estimating background took 0.575857162476 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0876979827881 s Creating peak regions... Creating peak regions took 0.18199801445 s Estimating background... Estimating background took 0.235100984573 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0536479949951 s Creating peak regions... Creating peak regions took 0.328783988953 s Estimating background... Estimating background took 0.241897106171 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0546600818634 s Creating peak regions... Creating peak regions took 0.239944934845 s Estimating background... Estimating background took 0.248840808868 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0414438247681 s Creating peak regions... Creating peak regions took 0.283994913101 s Estimating background... Estimating background took 0.253087043762 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 1.4530711174 s Creating peak regions... Creating peak regions took 48.3807680607 s Estimating background... Estimating background took 0.479422092438 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.998630046844 s Creating peak regions... Creating peak regions took 36.388479948 s Estimating background... Estimating background took 0.373890161514 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 1.1185529232 s Creating peak regions... Creating peak regions took 34.1445310116 s Estimating background... Estimating background took 0.347014904022 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.143198013306 s Creating peak regions... Creating peak regions took 0.0866310596466 s Estimating background... Estimating background took 0.254338026047 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0291478633881 s Creating peak regions... Creating peak regions took 0.0180180072784 s Estimating background... Estimating background took 0.264032840729 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 1.04894399643 s Creating peak regions... Creating peak regions took 33.3763449192 s Estimating background... Estimating background took 4.03855490685 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0316550731659 s Creating peak regions... Creating peak regions took 0.254642009735 s Estimating background... Estimating background took 0.278184175491 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.856295108795 s Creating peak regions... Creating peak regions took 32.9351849556 s Estimating background... Estimating background took 0.503643035889 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.842820882797 s Creating peak regions... Creating peak regions took 31.11413908 s Estimating background... Estimating background took 0.644219875336 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.958135843277 s Creating peak regions... Creating peak regions took 31.4586338997 s Estimating background... Estimating background took 0.405763149261 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.704030036926 s Creating peak regions... Creating peak regions took 28.9909992218 s Estimating background... Estimating background took 0.521088838577 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.112236976624 s Creating peak regions... Creating peak regions took 0.0427951812744 s Estimating background... Estimating background took 0.313934803009 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0359659194946 s Creating peak regions... Creating peak regions took 0.0689580440521 s Estimating background... Estimating background took 0.3344810009 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0387370586395 s Creating peak regions... Creating peak regions took 0.0551328659058 s Estimating background... Estimating background took 0.336006879807 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0488538742065 s Creating peak regions... Creating peak regions took 0.0716049671173 s Estimating background... Estimating background took 0.328385829926 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0544040203094 s Creating peak regions... Creating peak regions took 0.0270700454712 s Estimating background... Estimating background took 0.319509029388 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0546069145203 s Creating peak regions... Creating peak regions took 0.0351829528809 s Estimating background... Estimating background took 0.334019184113 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.033842086792 s Creating peak regions... Creating peak regions took 0.0414519309998 s Estimating background... Estimating background took 0.331113100052 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0541570186615 s Creating peak regions... Creating peak regions took 0.0440139770508 s Estimating background... Estimating background took 0.331041812897 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0542070865631 s Creating peak regions... Creating peak regions took 0.0583610534668 s Estimating background... Estimating background took 0.342499017715 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.054664850235 s Creating peak regions... Creating peak regions took 0.0383770465851 s Estimating background... Estimating background took 0.32745718956 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0409710407257 s Creating peak regions... Creating peak regions took 0.0768120288849 s Estimating background... Estimating background took 0.319557905197 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.035304069519 s Creating peak regions... Creating peak regions took 0.0445051193237 s Estimating background... Estimating background took 0.331664800644 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.054398059845 s Creating peak regions... Creating peak regions took 0.0371079444885 s Estimating background... Estimating background took 0.330873966217 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.105655908585 s Creating peak regions... Creating peak regions took 0.0379750728607 s Estimating background... Estimating background took 0.316112041473 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0536189079285 s Creating peak regions... Creating peak regions took 0.0450859069824 s Estimating background... Estimating background took 0.319135189056 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0670738220215 s Creating peak regions... Creating peak regions took 0.0852279663086 s Estimating background... Estimating background took 0.318941116333 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0350449085236 s Creating peak regions... Creating peak regions took 0.0774118900299 s Estimating background... Estimating background took 0.320338010788 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0338490009308 s Creating peak regions... Creating peak regions took 0.03466796875 s Estimating background... Estimating background took 0.325128793716 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0559470653534 s Creating peak regions... Creating peak regions took 0.0393419265747 s Estimating background... Estimating background took 0.32945895195 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0736148357391 s Creating peak regions... Creating peak regions took 0.212916851044 s Estimating background... Estimating background took 0.325903892517 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.473562955856 s Creating peak regions... Creating peak regions took 42.753704071 s Estimating background... Estimating background took 0.316449165344 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0457499027252 s Creating peak regions... Creating peak regions took 0.355829954147 s Estimating background... Estimating background took 0.314621925354 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Reading data took 0.0552318096161 s Creating peak regions... Creating peak regions took 18.1118559837 s Estimating background... Estimating background took 0.326743841171 s Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep3-GSM1689031/aligned.36mers.unique.bam Reading in data...