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='RbKO_crypts_Myc-GSM1606985/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='RbKO_crypts_Myc-GSM1606985/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='RbKO_crypts_Myc-GSM1606985/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='RbKO_crypts_Myc-GSM1606985/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 RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 13.6699969769 s Creating peak regions... Creating peak regions took 51.9154288769 s Estimating background... Estimating background took 142.288537979 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 13.4884941578 s Creating peak regions... Creating peak regions took 51.0331530571 s Estimating background... Estimating background took 119.639564991 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 13.2670879364 s Creating peak regions... Creating peak regions took 50.4649820328 s Estimating background... Estimating background took 122.151080132 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 11.277328968 s Creating peak regions... Creating peak regions took 48.9209899902 s Estimating background... Estimating background took 120.380882025 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 15.2067670822 s Creating peak regions... Creating peak regions took 58.1664779186 s Estimating background... Estimating background took 122.891957998 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 11.3388049603 s Creating peak regions... Creating peak regions took 45.7627651691 s Estimating background... Estimating background took 103.937148094 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 11.754144907 s Creating peak regions... Creating peak regions took 58.0938398838 s Estimating background... Estimating background took 109.842213869 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 9.96836709976 s Creating peak regions... Creating peak regions took 43.375054121 s Estimating background... Estimating background took 95.6132760048 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 10.8394489288 s Creating peak regions... Creating peak regions took 43.7929830551 s Estimating background... Estimating background took 91.2190749645 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 6.12137103081 s Creating peak regions... Creating peak regions took 25.4317579269 s Estimating background... Estimating background took 68.1162030697 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 20.642375946 s Creating peak regions... Creating peak regions took 95.0886001587 s Estimating background... Estimating background took 208.891093016 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.490139961243 s Creating peak regions... Creating peak regions took 1.18261504173 s Estimating background... Estimating background took 0.374871015549 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0635008811951 s Creating peak regions... Creating peak regions took 0.396070957184 s Estimating background... Estimating background took 0.374608039856 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.062667131424 s Creating peak regions... Creating peak regions took 0.250622034073 s Estimating background... Estimating background took 0.373726129532 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0624060630798 s Creating peak regions... Creating peak regions took 0.335155963898 s Estimating background... Estimating background took 0.388419866562 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 25.1157839298 s Creating peak regions... Creating peak regions took 88.5150279999 s Estimating background... Estimating background took 185.106927872 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 18.2374920845 s Creating peak regions... Creating peak regions took 78.269051075 s Estimating background... Estimating background took 185.646305084 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 20.4520561695 s Creating peak regions... Creating peak regions took 80.6712431908 s Estimating background... Estimating background took 163.019315958 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 1.5866689682 s Creating peak regions... Creating peak regions took 0.843989849091 s Estimating background... Estimating background took 0.505364894867 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0567638874054 s Creating peak regions... Creating peak regions took 0.0321431159973 s Estimating background... Estimating background took 0.413505792618 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0653040409088 s Creating peak regions... Creating peak regions took 0.0065610408783 s Estimating background... Estimating background took 0.411130905151 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 20.3337240219 s Creating peak regions... Creating peak regions took 65.5890758038 s Estimating background... Estimating background took 177.800643921 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 1.20989394188 s Creating peak regions... Creating peak regions took 0.467387914658 s Estimating background... Estimating background took 0.384454965591 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0794658660889 s Creating peak regions... Creating peak regions took 0.283616065979 s Estimating background... Estimating background took 0.375964164734 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0511591434479 s Creating peak regions... Creating peak regions took 0.273699998856 s Estimating background... Estimating background took 0.392668008804 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0618071556091 s Creating peak regions... Creating peak regions took 1.19557404518 s Estimating background... Estimating background took 0.371386051178 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 16.5356199741 s Creating peak regions... Creating peak regions took 81.4361109734 s Estimating background... Estimating background took 154.078699112 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 13.6468279362 s Creating peak regions... Creating peak regions took 67.2089579105 s Estimating background... Estimating background took 126.017236948 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 18.2154819965 s Creating peak regions... Creating peak regions took 56.2868599892 s Estimating background... Estimating background took 120.718753815 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 14.3155810833 s Creating peak regions... Creating peak regions took 54.8185079098 s Estimating background... Estimating background took 121.328587055 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 1.19984507561 s Creating peak regions... Creating peak regions took 0.367676019669 s Estimating background... Estimating background took 0.993527173996 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.100301980972 s Creating peak regions... Creating peak regions took 0.0805850028992 s Estimating background... Estimating background took 0.537506818771 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0662181377411 s Creating peak regions... Creating peak regions took 0.0630030632019 s Estimating background... Estimating background took 0.445188045502 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0893840789795 s Creating peak regions... Creating peak regions took 0.0772631168365 s Estimating background... Estimating background took 0.455978155136 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.059672832489 s Creating peak regions... Creating peak regions took 0.0868580341339 s Estimating background... Estimating background took 0.451415061951 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.108188867569 s Creating peak regions... Creating peak regions took 0.0964469909668 s Estimating background... Estimating background took 0.458986997604 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.08828997612 s Creating peak regions... Creating peak regions took 0.0688271522522 s Estimating background... Estimating background took 0.467714071274 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0705671310425 s Creating peak regions... Creating peak regions took 0.0624268054962 s Estimating background... Estimating background took 0.559906959534 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0843021869659 s Creating peak regions... Creating peak regions took 0.0568690299988 s Estimating background... Estimating background took 0.454874038696 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0891649723053 s Creating peak regions... Creating peak regions took 0.0768690109253 s Estimating background... Estimating background took 0.444844007492 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0909280776978 s Creating peak regions... Creating peak regions took 0.13254404068 s Estimating background... Estimating background took 0.458867073059 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0638339519501 s Creating peak regions... Creating peak regions took 0.076621055603 s Estimating background... Estimating background took 0.458138942719 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0609800815582 s Creating peak regions... Creating peak regions took 0.0438342094421 s Estimating background... Estimating background took 0.4516248703 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.178158998489 s Creating peak regions... Creating peak regions took 0.07972407341 s Estimating background... Estimating background took 0.666600942612 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0948810577393 s Creating peak regions... Creating peak regions took 0.0865869522095 s Estimating background... Estimating background took 0.460969924927 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0878489017487 s Creating peak regions... Creating peak regions took 0.0811851024628 s Estimating background... Estimating background took 0.446105957031 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 1.10785412788 s Creating peak regions... Creating peak regions took 0.0334877967834 s Estimating background... Estimating background took 0.861838102341 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.119540929794 s Creating peak regions... Creating peak regions took 0.0530910491943 s Estimating background... Estimating background took 0.544440984726 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.33744096756 s Creating peak regions... Creating peak regions took 0.0360260009766 s Estimating background... Estimating background took 0.661112070084 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.122576951981 s Creating peak regions... Creating peak regions took 0.101325035095 s Estimating background... Estimating background took 0.562747001648 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.0939960479736 s Creating peak regions... Creating peak regions took 0.0658359527588 s Estimating background... Estimating background took 0.458863973618 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.145030021667 s Creating peak regions... Creating peak regions took 0.0504679679871 s Estimating background... Estimating background took 0.556167125702 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.435125112534 s Creating peak regions... Creating peak regions took 0.20778298378 s Estimating background... Estimating background took 1.61119198799 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 14.4819271564 s Creating peak regions... Creating peak regions took 63.2549750805 s Estimating background... Estimating background took 103.647491932 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 2.4695250988 s Creating peak regions... Creating peak regions took 0.749614953995 s Estimating background... Estimating background took 0.617383003235 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Reading data took 0.240444898605 s Creating peak regions... Creating peak regions took 28.3600971699 s Estimating background... Estimating background took 0.945279121399 s Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_Myc-GSM1606985/aligned.36mers.unique.bam Reading in data...