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_Rep2-GSM1689030/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_Rep2-GSM1689030/', 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_Rep2-GSM1689030/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_Rep2-GSM1689030/', 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_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.779696941376 s Creating peak regions... Creating peak regions took 29.1284558773 s Estimating background... Estimating background took 0.319493055344 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.762531042099 s Creating peak regions... Creating peak regions took 30.1212968826 s Estimating background... Estimating background took 0.430646896362 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.609699010849 s Creating peak regions... Creating peak regions took 25.670609951 s Estimating background... Estimating background took 0.31055188179 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.611572027206 s Creating peak regions... Creating peak regions took 25.319726944 s Estimating background... Estimating background took 0.294453144073 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.689368009567 s Creating peak regions... Creating peak regions took 26.2824368477 s Estimating background... Estimating background took 0.176846027374 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.49333190918 s Creating peak regions... Creating peak regions took 21.7237229347 s Estimating background... Estimating background took 0.307358026505 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.578685998917 s Creating peak regions... Creating peak regions took 20.9011828899 s Estimating background... Estimating background took 0.179269790649 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.715438127518 s Creating peak regions... Creating peak regions took 20.2424800396 s Estimating background... Estimating background took 0.175626039505 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.586834192276 s Creating peak regions... Creating peak regions took 19.4510550499 s Estimating background... Estimating background took 0.306931018829 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.549865961075 s Creating peak regions... Creating peak regions took 14.4762370586 s Estimating background... Estimating background took 0.321293115616 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 1.63127112389 s Creating peak regions... Creating peak regions took 48.2824292183 s Estimating background... Estimating background took 0.49801492691 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0532150268555 s Creating peak regions... Creating peak regions took 0.215909957886 s Estimating background... Estimating background took 0.272572994232 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0463721752167 s Creating peak regions... Creating peak regions took 0.261146783829 s Estimating background... Estimating background took 0.263446092606 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.045557975769 s Creating peak regions... Creating peak regions took 0.17574095726 s Estimating background... Estimating background took 0.266335010529 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 1.28562712669 s Creating peak regions... Creating peak regions took 41.3145298958 s Estimating background... Estimating background took 0.355332136154 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.751725196838 s Creating peak regions... Creating peak regions took 34.2435388565 s Estimating background... Estimating background took 0.248679876328 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 1.09816789627 s Creating peak regions... Creating peak regions took 33.0999929905 s Estimating background... Estimating background took 0.365110874176 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0397250652313 s Creating peak regions... Creating peak regions took 0.0511720180511 s Estimating background... Estimating background took 0.255148172379 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.82280087471 s Creating peak regions... Creating peak regions took 32.8938789368 s Estimating background... Estimating background took 4.15780997276 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0250940322876 s Creating peak regions... Creating peak regions took 0.190114974976 s Estimating background... Estimating background took 0.294595003128 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.881088972092 s Creating peak regions... Creating peak regions took 37.259827137 s Estimating background... Estimating background took 0.396755933762 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 1.02317500114 s Creating peak regions... Creating peak regions took 32.8241159916 s Estimating background... Estimating background took 0.399550914764 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.648224830627 s Creating peak regions... Creating peak regions took 28.2228419781 s Estimating background... Estimating background took 0.379160165787 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 1.0016708374 s Creating peak regions... Creating peak regions took 26.6612548828 s Estimating background... Estimating background took 0.514897108078 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.060389995575 s Creating peak regions... Creating peak regions took 0.0269341468811 s Estimating background... Estimating background took 0.291243076324 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0459959506989 s Creating peak regions... Creating peak regions took 0.053747177124 s Estimating background... Estimating background took 0.303124904633 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0320701599121 s Creating peak regions... Creating peak regions took 0.0378739833832 s Estimating background... Estimating background took 0.29265499115 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.044625043869 s Creating peak regions... Creating peak regions took 0.00445318222046 s Estimating background... Estimating background took 0.315333127975 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0351710319519 s Creating peak regions... Creating peak regions took 0.0335960388184 s Estimating background... Estimating background took 0.30580496788 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0282669067383 s Creating peak regions... Creating peak regions took 0.0202810764313 s Estimating background... Estimating background took 0.303219795227 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0325798988342 s Creating peak regions... Creating peak regions took 0.0299079418182 s Estimating background... Estimating background took 0.296270132065 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0350708961487 s Creating peak regions... Creating peak regions took 0.0615310668945 s Estimating background... Estimating background took 0.290870904922 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0553369522095 s Creating peak regions... Creating peak regions took 0.0337781906128 s Estimating background... Estimating background took 0.290156126022 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0479650497437 s Creating peak regions... Creating peak regions took 0.0426988601685 s Estimating background... Estimating background took 0.287037134171 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0577321052551 s Creating peak regions... Creating peak regions took 0.0744907855988 s Estimating background... Estimating background took 0.295243024826 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0476648807526 s Creating peak regions... Creating peak regions took 0.0850760936737 s Estimating background... Estimating background took 0.292206764221 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.045608997345 s Creating peak regions... Creating peak regions took 0.0150501728058 s Estimating background... Estimating background took 0.300950050354 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0285620689392 s Creating peak regions... Creating peak regions took 0.0285539627075 s Estimating background... Estimating background took 0.288505077362 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0635569095612 s Creating peak regions... Creating peak regions took 0.340375900269 s Estimating background... Estimating background took 0.28941988945 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.436878919601 s Creating peak regions... Creating peak regions took 37.8068611622 s Estimating background... Estimating background took 0.302183866501 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0663721561432 s Creating peak regions... Creating peak regions took 0.242514848709 s Estimating background... Estimating background took 0.285784006119 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Reading data took 0.0468721389771 s Creating peak regions... Creating peak regions took 17.8504419327 s Estimating background... Estimating background took 0.283560991287 s Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep2-GSM1689030/aligned.36mers.unique.bam Reading in data...