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-Rep2-GSM1689022.35mers.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-Rep2-GSM1689022-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-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 1.29164409637 s Creating peak regions... Creating peak regions took 42.1399550438 s Estimating background... Estimating background took 3.00460195541 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 1.18494105339 s Creating peak regions... Creating peak regions took 37.7614359856 s Estimating background... Estimating background took 0.629999160767 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 1.30046081543 s Creating peak regions... Creating peak regions took 37.163973093 s Estimating background... Estimating background took 0.535603046417 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 1.089854002 s Creating peak regions... Creating peak regions took 39.1634850502 s Estimating background... Estimating background took 0.431219816208 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 1.17037796974 s Creating peak regions... Creating peak regions took 38.6375131607 s Estimating background... Estimating background took 0.446793794632 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.989145994186 s Creating peak regions... Creating peak regions took 32.0341808796 s Estimating background... Estimating background took 0.429118156433 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.988473892212 s Creating peak regions... Creating peak regions took 30.3583929539 s Estimating background... Estimating background took 0.44854092598 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.967700958252 s Creating peak regions... Creating peak regions took 29.4045290947 s Estimating background... Estimating background took 0.546045064926 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.882719039917 s Creating peak regions... Creating peak regions took 28.0485348701 s Estimating background... Estimating background took 0.461159944534 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.708873033524 s Creating peak regions... Creating peak regions took 19.1441688538 s Estimating background... Estimating background took 0.460255861282 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 2.46219992638 s Creating peak regions... Creating peak regions took 61.1602940559 s Estimating background... Estimating background took 0.778656005859 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0607240200043 s Creating peak regions... Creating peak regions took 0.218619823456 s Estimating background... Estimating background took 0.243645906448 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0300619602203 s Creating peak regions... Creating peak regions took 0.268883943558 s Estimating background... Estimating background took 0.268013000488 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0344979763031 s Creating peak regions... Creating peak regions took 0.20285487175 s Estimating background... Estimating background took 0.264930963516 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0265638828278 s Creating peak regions... Creating peak regions took 0.184576034546 s Estimating background... Estimating background took 0.243782997131 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 2.20682191849 s Creating peak regions... Creating peak regions took 54.7855510712 s Estimating background... Estimating background took 4.44078397751 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 1.21778893471 s Creating peak regions... Creating peak regions took 49.3624389172 s Estimating background... Estimating background took 0.596807003021 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 1.36009097099 s Creating peak regions... Creating peak regions took 46.8517570496 s Estimating background... Estimating background took 0.565429925919 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0541958808899 s Creating peak regions... Creating peak regions took 0.0714070796967 s Estimating background... Estimating background took 0.245074987411 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 1.36453986168 s Creating peak regions... Creating peak regions took 47.1524651051 s Estimating background... Estimating background took 0.570496082306 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 1.36777496338 s Creating peak regions... Creating peak regions took 46.2687411308 s Estimating background... Estimating background took 0.576731920242 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 1.45950913429 s Creating peak regions... Creating peak regions took 45.1936609745 s Estimating background... Estimating background took 0.590563058853 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 1.28739595413 s Creating peak regions... Creating peak regions took 40.1236710548 s Estimating background... Estimating background took 0.569988012314 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 1.41919803619 s Creating peak regions... Creating peak regions took 37.4513809681 s Estimating background... Estimating background took 0.586613893509 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0572950839996 s Creating peak regions... Creating peak regions took 0.0335350036621 s Estimating background... Estimating background took 0.251893997192 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0304791927338 s Creating peak regions... Creating peak regions took 0.0565550327301 s Estimating background... Estimating background took 0.25607585907 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0337340831757 s Creating peak regions... Creating peak regions took 0.033411026001 s Estimating background... Estimating background took 0.258399963379 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0334410667419 s Creating peak regions... Creating peak regions took 0.046492099762 s Estimating background... Estimating background took 0.247370004654 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0312919616699 s Creating peak regions... Creating peak regions took 0.0589780807495 s Estimating background... Estimating background took 0.259379863739 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0280330181122 s Creating peak regions... Creating peak regions took 0.0283060073853 s Estimating background... Estimating background took 0.261204004288 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0335590839386 s Creating peak regions... Creating peak regions took 0.0304741859436 s Estimating background... Estimating background took 0.250478029251 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0314629077911 s Creating peak regions... Creating peak regions took 0.0324048995972 s Estimating background... Estimating background took 0.262835979462 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0337738990784 s Creating peak regions... Creating peak regions took 0.0456740856171 s Estimating background... Estimating background took 0.262477874756 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0331559181213 s Creating peak regions... Creating peak regions took 0.0819869041443 s Estimating background... Estimating background took 0.238561868668 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0284469127655 s Creating peak regions... Creating peak regions took 0.0248219966888 s Estimating background... Estimating background took 0.247473955154 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.035208940506 s Creating peak regions... Creating peak regions took 0.0665709972382 s Estimating background... Estimating background took 0.248297929764 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0274369716644 s Creating peak regions... Creating peak regions took 0.0258429050446 s Estimating background... Estimating background took 0.260307788849 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0839829444885 s Creating peak regions... Creating peak regions took 0.0437450408936 s Estimating background... Estimating background took 0.298939228058 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0344700813293 s Creating peak regions... Creating peak regions took 0.0392518043518 s Estimating background... Estimating background took 0.260168075562 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0496261119843 s Creating peak regions... Creating peak regions took 0.0668478012085 s Estimating background... Estimating background took 0.259611129761 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0351738929749 s Creating peak regions... Creating peak regions took 0.0763409137726 s Estimating background... Estimating background took 0.257716178894 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0328907966614 s Creating peak regions... Creating peak regions took 0.0366740226746 s Estimating background... Estimating background took 0.258780956268 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.036630153656 s Creating peak regions... Creating peak regions took 0.0328221321106 s Estimating background... Estimating background took 0.256540060043 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.054141998291 s Creating peak regions... Creating peak regions took 0.190921068192 s Estimating background... Estimating background took 0.256705999374 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.675634860992 s Creating peak regions... Creating peak regions took 50.9838199615 s Estimating background... Estimating background took 0.254297971725 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0458118915558 s Creating peak regions... Creating peak regions took 0.424499988556 s Estimating background... Estimating background took 0.251153945923 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Reading data took 0.0339698791504 s Creating peak regions... Creating peak regions took 25.7953388691 s Estimating background... Estimating background took 0.255412101746 s Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689022.35mers.unique.bam Reading in data...