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/hg38.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes', e4='PeakXus', fastq='ZNF431-SRR5197137.hg20-male.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='ZNF431-SRR5197137/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 ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.93319201469 s Creating peak regions... Creating peak regions took 78.2593281269 s Estimating background... Estimating background took 38.816434145 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.5736579895 s Creating peak regions... Creating peak regions took 40.2619690895 s Estimating background... Estimating background took 15.4080779552 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53175210953 s Creating peak regions... Creating peak regions took 40.2966151237 s Estimating background... Estimating background took 15.2930250168 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... 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/hg38.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38-male.chrom.sizes', e4='PeakXus', fastq='ZNF431-SRR5197137.hg20-male.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='ZNF431-SRR5197137/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 ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.13561892509 s Creating peak regions... Creating peak regions took 76.6331529617 s Estimating background... Estimating background took 40.3069820404 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.68048501015 s Creating peak regions... Creating peak regions took 38.9024729729 s Estimating background... Estimating background took 15.0581059456 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.71695899963 s Creating peak regions... Creating peak regions took 41.0732209682 s Estimating background... Estimating background took 16.3814918995 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.78689599037 s Creating peak regions... Creating peak regions took 40.6115970612 s Estimating background... Estimating background took 16.3254032135 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.29783296585 s Creating peak regions... Creating peak regions took 36.133893013 s Estimating background... Estimating background took 15.8009400368 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.86230993271 s Creating peak regions... Creating peak regions took 32.1150848866 s Estimating background... Estimating background took 10.5791189671 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.87655091286 s Creating peak regions... Creating peak regions took 31.0148141384 s Estimating background... Estimating background took 11.3913750648 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.56877303123 s Creating peak regions... Creating peak regions took 26.3665738106 s Estimating background... Estimating background took 11.4232039452 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.19275999069 s Creating peak regions... Creating peak regions took 26.0911478996 s Estimating background... Estimating background took 15.2581210136 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.39545607567 s Creating peak regions... Creating peak regions took 25.5523879528 s Estimating background... Estimating background took 8.20622396469 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.53816080093 s Creating peak regions... Creating peak regions took 17.4529080391 s Estimating background... Estimating background took 9.55373501778 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.36114907265 s Creating peak regions... Creating peak regions took 77.3769609928 s Estimating background... Estimating background took 26.5285851955 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.47391200066 s Creating peak regions... Creating peak regions took 19.4936599731 s Estimating background... Estimating background took 9.03885293007 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.917526960373 s Creating peak regions... Creating peak regions took 14.4474821091 s Estimating background... Estimating background took 5.28709888458 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.16236805916 s Creating peak regions... Creating peak regions took 16.206403017 s Estimating background... Estimating background took 9.69633197784 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.61832714081 s Creating peak regions... Creating peak regions took 61.6157748699 s Estimating background... Estimating background took 18.8560600281 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39238405228 s Creating peak regions... Creating peak regions took 55.9202771187 s Estimating background... Estimating background took 15.7083699703 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.5302259922 s Creating peak regions... Creating peak regions took 57.9655520916 s Estimating background... Estimating background took 18.6552271843 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.56535482407 s Creating peak regions... Creating peak regions took 51.6225011349 s Estimating background... Estimating background took 23.1239318848 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.54892301559 s Creating peak regions... Creating peak regions took 48.3265337944 s Estimating background... Estimating background took 19.8240909576 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.70069885254 s Creating peak regions... Creating peak regions took 43.5603630543 s Estimating background... Estimating background took 14.2545819283 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.47147703171 s Creating peak regions... Creating peak regions took 40.3906040192 s Estimating background... Estimating background took 12.9704799652 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.098317861557 s Creating peak regions... Creating peak regions took 0.178378820419 s Estimating background... Estimating background took 0.748039007187 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.7508251667 s Creating peak regions... Creating peak regions took 41.3451697826 s Estimating background... Estimating background took 16.9186360836 s Processing ZNF431-SRR5197137.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.108293056488 s Creating peak regions... Creating peak regions took 13.5234229565 s Estimating background... Estimating background took 0.56454205513 s