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-ER4-3h-Rep2-GSM1689031.35mers.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-ER4-3h-Rep2-GSM1689031-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-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.869251966476 s Creating peak regions... Creating peak regions took 43.8955688477 s Estimating background... Estimating background took 0.304244995117 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.678479909897 s Creating peak regions... Creating peak regions took 38.039908886 s Estimating background... Estimating background took 0.538972854614 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.700526952744 s Creating peak regions... Creating peak regions took 36.9272699356 s Estimating background... Estimating background took 0.421749830246 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.657113075256 s Creating peak regions... Creating peak regions took 37.566783905 s Estimating background... Estimating background took 0.307492017746 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.705942153931 s Creating peak regions... Creating peak regions took 39.0619988441 s Estimating background... Estimating background took 0.297474145889 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.571269989014 s Creating peak regions... Creating peak regions took 31.747838974 s Estimating background... Estimating background took 0.30437207222 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.549201965332 s Creating peak regions... Creating peak regions took 29.4177510738 s Estimating background... Estimating background took 0.306129932404 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.552109956741 s Creating peak regions... Creating peak regions took 29.4730029106 s Estimating background... Estimating background took 0.394907951355 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.520489931107 s Creating peak regions... Creating peak regions took 28.2661929131 s Estimating background... Estimating background took 0.333779811859 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.38846206665 s Creating peak regions... Creating peak regions took 19.2718229294 s Estimating background... Estimating background took 0.307992935181 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 1.46361017227 s Creating peak regions... Creating peak regions took 61.4961149693 s Estimating background... Estimating background took 0.703486919403 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0839960575104 s Creating peak regions... Creating peak regions took 0.194600105286 s Estimating background... Estimating background took 0.203884840012 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.03191614151 s Creating peak regions... Creating peak regions took 0.316018104553 s Estimating background... Estimating background took 0.228860139847 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0374422073364 s Creating peak regions... Creating peak regions took 0.20876789093 s Estimating background... Estimating background took 0.210294008255 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0276839733124 s Creating peak regions... Creating peak regions took 0.271891832352 s Estimating background... Estimating background took 0.218347787857 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 1.27471780777 s Creating peak regions... Creating peak regions took 57.2153220177 s Estimating background... Estimating background took 0.537098884583 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.860916852951 s Creating peak regions... Creating peak regions took 48.3930590153 s Estimating background... Estimating background took 0.470772027969 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.852806806564 s Creating peak regions... Creating peak regions took 49.1025919914 s Estimating background... Estimating background took 0.430938005447 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0700879096985 s Creating peak regions... Creating peak regions took 0.0803468227386 s Estimating background... Estimating background took 0.220333099365 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0278868675232 s Creating peak regions... Creating peak regions took 0.0200929641724 s Estimating background... Estimating background took 0.231942176819 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.875504016876 s Creating peak regions... Creating peak regions took 47.4191191196 s Estimating background... Estimating background took 0.438122987747 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.027801990509 s Creating peak regions... Creating peak regions took 0.875366926193 s Estimating background... Estimating background took 0.23237991333 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.856355905533 s Creating peak regions... Creating peak regions took 45.5658969879 s Estimating background... Estimating background took 0.451138973236 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 1.09872102737 s Creating peak regions... Creating peak regions took 45.525796175 s Estimating background... Estimating background took 4.51627016068 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.588515996933 s Creating peak regions... Creating peak regions took 40.2080118656 s Estimating background... Estimating background took 0.528618097305 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.78310418129 s Creating peak regions... Creating peak regions took 38.6807088852 s Estimating background... Estimating background took 0.601376056671 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0727260112762 s Creating peak regions... Creating peak regions took 0.0406589508057 s Estimating background... Estimating background took 0.267153978348 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0345089435577 s Creating peak regions... Creating peak regions took 0.063854932785 s Estimating background... Estimating background took 0.270345211029 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0280380249023 s Creating peak regions... Creating peak regions took 0.0474581718445 s Estimating background... Estimating background took 0.273430109024 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0351798534393 s Creating peak regions... Creating peak regions took 0.0734391212463 s Estimating background... Estimating background took 0.252922058105 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0328629016876 s Creating peak regions... Creating peak regions took 0.024806022644 s Estimating background... Estimating background took 0.274536848068 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0344829559326 s Creating peak regions... Creating peak regions took 0.0325260162354 s Estimating background... Estimating background took 0.278294086456 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0300929546356 s Creating peak regions... Creating peak regions took 0.0466628074646 s Estimating background... Estimating background took 0.278140068054 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0348908901215 s Creating peak regions... Creating peak regions took 0.0412220954895 s Estimating background... Estimating background took 0.277786970139 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0349130630493 s Creating peak regions... Creating peak regions took 0.0565259456635 s Estimating background... Estimating background took 0.273372173309 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.035266160965 s Creating peak regions... Creating peak regions took 0.0360698699951 s Estimating background... Estimating background took 0.274173974991 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0339570045471 s Creating peak regions... Creating peak regions took 0.0845739841461 s Estimating background... Estimating background took 0.27746295929 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0342371463776 s Creating peak regions... Creating peak regions took 0.0470330715179 s Estimating background... Estimating background took 0.327764987946 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0330290794373 s Creating peak regions... Creating peak regions took 0.034303188324 s Estimating background... Estimating background took 0.276273012161 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0713441371918 s Creating peak regions... Creating peak regions took 0.0427629947662 s Estimating background... Estimating background took 0.278268098831 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0369119644165 s Creating peak regions... Creating peak regions took 0.0438840389252 s Estimating background... Estimating background took 0.276460886002 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0438868999481 s Creating peak regions... Creating peak regions took 0.0979220867157 s Estimating background... Estimating background took 0.313039064407 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0354461669922 s Creating peak regions... Creating peak regions took 0.0912621021271 s Estimating background... Estimating background took 0.276910066605 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0349941253662 s Creating peak regions... Creating peak regions took 0.0397350788116 s Estimating background... Estimating background took 0.268372058868 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0358190536499 s Creating peak regions... Creating peak regions took 0.0389831066132 s Estimating background... Estimating background took 0.270658016205 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0473008155823 s Creating peak regions... Creating peak regions took 0.211238145828 s Estimating background... Estimating background took 0.306752920151 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.403152942657 s Creating peak regions... Creating peak regions took 53.5457279682 s Estimating background... Estimating background took 0.289957046509 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0531380176544 s Creating peak regions... Creating peak regions took 0.313286066055 s Estimating background... Estimating background took 0.275789022446 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Reading data took 0.0351312160492 s Creating peak regions... Creating peak regions took 25.9637460709 s Estimating background... Estimating background took 0.281946182251 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689031.35mers.unique.bam Reading in data...