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='ChIP_exo_Onecut1_day6-GSM2098378/alignments.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='ChIP_exo_Onecut1_day6-GSM2098378/peakXus/', 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='ChIP_exo_Onecut1_day6-GSM2098378/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='ChIP_exo_Onecut1_day6-GSM2098378/peakXus/', 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='ChIP_exo_Onecut1_day6-GSM2098378/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='ChIP_exo_Onecut1_day6-GSM2098378/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 ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 2.97709512711 s Creating peak regions... Creating peak regions took 31.5789170265 s Estimating background... Estimating background took 11.6409060955 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 2.35591483116 s Creating peak regions... Creating peak regions took 28.1631388664 s Estimating background... Estimating background took 11.3114061356 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 1.91768312454 s Creating peak regions... Creating peak regions took 27.4566078186 s Estimating background... Estimating background took 10.482156992 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 2.05695390701 s Creating peak regions... Creating peak regions took 28.0354177952 s Estimating background... Estimating background took 11.0245900154 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 2.30253505707 s Creating peak regions... Creating peak regions took 32.4814860821 s Estimating background... Estimating background took 11.738106966 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 2.04077315331 s Creating peak regions... Creating peak regions took 28.9023430347 s Estimating background... Estimating background took 9.66225814819 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 2.19670295715 s Creating peak regions... Creating peak regions took 28.4834301472 s Estimating background... Estimating background took 9.57178401947 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 1.75174403191 s Creating peak regions... Creating peak regions took 23.0033590794 s Estimating background... Estimating background took 8.60696697235 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 1.71817493439 s Creating peak regions... Creating peak regions took 23.2333960533 s Estimating background... Estimating background took 8.93490099907 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 1.50985193253 s Creating peak regions... Creating peak regions took 15.9808330536 s Estimating background... Estimating background took 6.16577601433 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 3.99059391022 s Creating peak regions... Creating peak regions took 56.8680589199 s Estimating background... Estimating background took 17.1198251247 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.069580078125 s Creating peak regions... Creating peak regions took 0.281759023666 s Estimating background... Estimating background took 0.342614889145 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0728590488434 s Creating peak regions... Creating peak regions took 0.245489120483 s Estimating background... Estimating background took 0.329206943512 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.073851108551 s Creating peak regions... Creating peak regions took 0.228682041168 s Estimating background... Estimating background took 0.352982997894 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0500588417053 s Creating peak regions... Creating peak regions took 0.250639915466 s Estimating background... Estimating background took 0.351639986038 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 4.24389505386 s Creating peak regions... Creating peak regions took 49.6550700665 s Estimating background... Estimating background took 18.3860220909 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 3.19695281982 s Creating peak regions... Creating peak regions took 43.7922708988 s Estimating background... Estimating background took 14.6947181225 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 2.84445905685 s Creating peak regions... Creating peak regions took 40.5752639771 s Estimating background... Estimating background took 13.939800024 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0959239006042 s Creating peak regions... Creating peak regions took 0.186632156372 s Estimating background... Estimating background took 0.307525873184 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0515298843384 s Creating peak regions... Creating peak regions took 0.0187339782715 s Estimating background... Estimating background took 0.335535049438 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0469732284546 s Creating peak regions... Creating peak regions took 0.00257682800293 s Estimating background... Estimating background took 0.352090835571 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 3.05247282982 s Creating peak regions... Creating peak regions took 36.0160179138 s Estimating background... Estimating background took 14.0933871269 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0800440311432 s Creating peak regions... Creating peak regions took 0.297233104706 s Estimating background... Estimating background took 0.374213933945 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0463569164276 s Creating peak regions... Creating peak regions took 0.67004108429 s Estimating background... Estimating background took 0.361512899399 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 2.66406083107 s Creating peak regions... Creating peak regions took 40.2225949764 s Estimating background... Estimating background took 13.7279160023 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 2.16133403778 s Creating peak regions... Creating peak regions took 34.8646030426 s Estimating background... Estimating background took 11.9932951927 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 2.76638889313 s Creating peak regions... Creating peak regions took 33.7785789967 s Estimating background... Estimating background took 13.2445957661 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 2.57826495171 s Creating peak regions... Creating peak regions took 32.3462212086 s Estimating background... Estimating background took 11.8282101154 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0863389968872 s Creating peak regions... Creating peak regions took 0.130712985992 s Estimating background... Estimating background took 0.531751155853 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0756659507751 s Creating peak regions... Creating peak regions took 0.0676290988922 s Estimating background... Estimating background took 0.316348075867 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0715029239655 s Creating peak regions... Creating peak regions took 0.0310781002045 s Estimating background... Estimating background took 0.327606916428 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0527579784393 s Creating peak regions... Creating peak regions took 0.0430920124054 s Estimating background... Estimating background took 0.319751024246 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0735421180725 s Creating peak regions... Creating peak regions took 0.0726399421692 s Estimating background... Estimating background took 0.319779872894 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0717570781708 s Creating peak regions... Creating peak regions took 0.060781955719 s Estimating background... Estimating background took 0.332193851471 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0522749423981 s Creating peak regions... Creating peak regions took 0.0286650657654 s Estimating background... Estimating background took 0.326740980148 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0694160461426 s Creating peak regions... Creating peak regions took 0.0387849807739 s Estimating background... Estimating background took 0.323880195618 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0731670856476 s Creating peak regions... Creating peak regions took 0.0583209991455 s Estimating background... Estimating background took 0.340854167938 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0721759796143 s Creating peak regions... Creating peak regions took 0.0426270961761 s Estimating background... Estimating background took 0.324557065964 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0721471309662 s Creating peak regions... Creating peak regions took 0.0986289978027 s Estimating background... Estimating background took 0.336642026901 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0713620185852 s Creating peak regions... Creating peak regions took 0.0356750488281 s Estimating background... Estimating background took 0.34335398674 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0712189674377 s Creating peak regions... Creating peak regions took 0.0309150218964 s Estimating background... Estimating background took 0.339800834656 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0790910720825 s Creating peak regions... Creating peak regions took 0.0869598388672 s Estimating background... Estimating background took 0.335339069366 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.072340965271 s Creating peak regions... Creating peak regions took 0.0508990287781 s Estimating background... Estimating background took 0.342108011246 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.071900844574 s Creating peak regions... Creating peak regions took 0.0387418270111 s Estimating background... Estimating background took 0.337739944458 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.16762304306 s Creating peak regions... Creating peak regions took 0.0597660541534 s Estimating background... Estimating background took 0.325968980789 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0770781040192 s Creating peak regions... Creating peak regions took 0.066410779953 s Estimating background... Estimating background took 0.329349040985 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0661199092865 s Creating peak regions... Creating peak regions took 0.053288936615 s Estimating background... Estimating background took 0.32848405838 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0752549171448 s Creating peak regions... Creating peak regions took 0.113379955292 s Estimating background... Estimating background took 0.327513217926 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0716941356659 s Creating peak regions... Creating peak regions took 0.0378170013428 s Estimating background... Estimating background took 0.341568946838 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0785961151123 s Creating peak regions... Creating peak regions took 0.0492820739746 s Estimating background... Estimating background took 0.32781791687 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0846228599548 s Creating peak regions... Creating peak regions took 0.153029918671 s Estimating background... Estimating background took 0.533093929291 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 1.4907579422 s Creating peak regions... Creating peak regions took 39.0763180256 s Estimating background... Estimating background took 7.14756798744 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.0565412044525 s Creating peak regions... Creating peak regions took 0.254982948303 s Estimating background... Estimating background took 0.322410821915 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Reading data took 0.132045984268 s Creating peak regions... Creating peak regions took 19.1299200058 s Estimating background... Estimating background took 0.325532913208 s Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day6-GSM2098378/aligned.36mers.unique.bam Reading in data...