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='exo_IRF4_rep1-GSM2259188/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='exo_IRF4_rep1-GSM2259188/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 exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 3.9876768589 s Creating peak regions... Creating peak regions took 35.5060720444 s Estimating background... Estimating background took 19.7278399467 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 3.9811630249 s Creating peak regions... Creating peak regions took 35.9930639267 s Estimating background... Estimating background took 20.3798091412 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 3.64548301697 s Creating peak regions... Creating peak regions took 37.4596619606 s Estimating background... Estimating background took 15.7302589417 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 4.12689900398 s Creating peak regions... Creating peak regions took 39.3522589207 s Estimating background... Estimating background took 18.6991391182 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 3.36261606216 s Creating peak regions... Creating peak regions took 34.9170379639 s Estimating background... Estimating background took 14.9526760578 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 3.4023680687 s Creating peak regions... Creating peak regions took 35.5426511765 s Estimating background... Estimating background took 16.0365929604 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 3.35070514679 s Creating peak regions... Creating peak regions took 27.627712965 s Estimating background... Estimating background took 14.8538749218 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 2.69434404373 s Creating peak regions... Creating peak regions took 24.6403980255 s Estimating background... Estimating background took 12.9027919769 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 2.64219117165 s Creating peak regions... Creating peak regions took 27.005259037 s Estimating background... Estimating background took 11.8245120049 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 2.21194410324 s Creating peak regions... Creating peak regions took 18.6588561535 s Estimating background... Estimating background took 9.79232287407 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 5.25386309624 s Creating peak regions... Creating peak regions took 55.4588069916 s Estimating background... Estimating background took 27.7159438133 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.132941007614 s Creating peak regions... Creating peak regions took 0.609023809433 s Estimating background... Estimating background took 0.354851961136 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0653841495514 s Creating peak regions... Creating peak regions took 0.389726161957 s Estimating background... Estimating background took 0.352360963821 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0550029277802 s Creating peak regions... Creating peak regions took 0.241893053055 s Estimating background... Estimating background took 0.398069143295 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0579619407654 s Creating peak regions... Creating peak regions took 0.338999032974 s Estimating background... Estimating background took 0.335448026657 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 8.03220391273 s Creating peak regions... Creating peak regions took 59.1489861012 s Estimating background... Estimating background took 28.3549828529 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 4.39833498001 s Creating peak regions... Creating peak regions took 41.5769860744 s Estimating background... Estimating background took 20.6636857986 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 4.25686907768 s Creating peak regions... Creating peak regions took 41.1231138706 s Estimating background... Estimating background took 19.8641819954 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.198461055756 s Creating peak regions... Creating peak regions took 0.273741006851 s Estimating background... Estimating background took 0.320547819138 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0485019683838 s Creating peak regions... Creating peak regions took 0.0193531513214 s Estimating background... Estimating background took 0.326858043671 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.048623085022 s Creating peak regions... Creating peak regions took 0.00281381607056 s Estimating background... Estimating background took 0.322644948959 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 4.52745604515 s Creating peak regions... Creating peak regions took 42.6096680164 s Estimating background... Estimating background took 19.5350048542 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.205415010452 s Creating peak regions... Creating peak regions took 0.321635007858 s Estimating background... Estimating background took 0.386655807495 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0448169708252 s Creating peak regions... Creating peak regions took 1.01162409782 s Estimating background... Estimating background took 0.373987197876 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 4.80460000038 s Creating peak regions... Creating peak regions took 45.3711929321 s Estimating background... Estimating background took 21.3598749638 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 4.45585179329 s Creating peak regions... Creating peak regions took 46.9126319885 s Estimating background... Estimating background took 20.2001781464 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 3.24567294121 s Creating peak regions... Creating peak regions took 37.556926012 s Estimating background... Estimating background took 14.8662939072 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 3.95424509048 s Creating peak regions... Creating peak regions took 32.5053100586 s Estimating background... Estimating background took 20.3059489727 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.197274923325 s Creating peak regions... Creating peak regions took 0.219928026199 s Estimating background... Estimating background took 0.325968980789 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0874030590057 s Creating peak regions... Creating peak regions took 0.0964090824127 s Estimating background... Estimating background took 0.324284791946 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0752720832825 s Creating peak regions... Creating peak regions took 0.0368640422821 s Estimating background... Estimating background took 0.328885793686 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0523161888123 s Creating peak regions... Creating peak regions took 0.0452768802643 s Estimating background... Estimating background took 0.370567798615 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0762691497803 s Creating peak regions... Creating peak regions took 0.0721061229706 s Estimating background... Estimating background took 0.330874919891 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0537838935852 s Creating peak regions... Creating peak regions took 0.0757870674133 s Estimating background... Estimating background took 0.330810070038 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.052787065506 s Creating peak regions... Creating peak regions took 0.0312631130219 s Estimating background... Estimating background took 0.333281040192 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0762691497803 s Creating peak regions... Creating peak regions took 0.0425841808319 s Estimating background... Estimating background took 0.333542108536 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0753209590912 s Creating peak regions... Creating peak regions took 0.0422790050507 s Estimating background... Estimating background took 0.330112934113 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.076220035553 s Creating peak regions... Creating peak regions took 0.0517699718475 s Estimating background... Estimating background took 0.329171180725 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0714991092682 s Creating peak regions... Creating peak regions took 0.114777088165 s Estimating background... Estimating background took 0.328940153122 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0520620346069 s Creating peak regions... Creating peak regions took 0.0386559963226 s Estimating background... Estimating background took 0.330410957336 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0512459278107 s Creating peak regions... Creating peak regions took 0.0317780971527 s Estimating background... Estimating background took 0.336744070053 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0812599658966 s Creating peak regions... Creating peak regions took 0.0612609386444 s Estimating background... Estimating background took 0.337363004684 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0723841190338 s Creating peak regions... Creating peak regions took 0.04652094841 s Estimating background... Estimating background took 0.350284099579 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0550758838654 s Creating peak regions... Creating peak regions took 0.0410351753235 s Estimating background... Estimating background took 0.340966939926 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.456688165665 s Creating peak regions... Creating peak regions took 0.0321891307831 s Estimating background... Estimating background took 0.543797016144 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0749189853668 s Creating peak regions... Creating peak regions took 0.0547001361847 s Estimating background... Estimating background took 0.328804016113 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.121504068375 s Creating peak regions... Creating peak regions took 0.0441689491272 s Estimating background... Estimating background took 0.430407047272 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0695469379425 s Creating peak regions... Creating peak regions took 0.0967350006104 s Estimating background... Estimating background took 0.338960886002 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0525860786438 s Creating peak regions... Creating peak regions took 0.0385100841522 s Estimating background... Estimating background took 0.329925060272 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0622069835663 s Creating peak regions... Creating peak regions took 0.0547149181366 s Estimating background... Estimating background took 0.329694986343 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.123631000519 s Creating peak regions... Creating peak regions took 0.161101102829 s Estimating background... Estimating background took 0.740248918533 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 3.78838515282 s Creating peak regions... Creating peak regions took 40.9987230301 s Estimating background... Estimating background took 13.0230870247 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0827350616455 s Creating peak regions... Creating peak regions took 0.384469985962 s Estimating background... Estimating background took 0.327129125595 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Reading data took 0.0835149288177 s Creating peak regions... Creating peak regions took 18.7378668785 s Estimating background... Estimating background took 0.330383062363 s Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep1-GSM2259188/aligned.36mers.unique.bam Reading in data...