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='ZNF680-SRR5197212.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='ZNF680-SRR5197212/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 ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.18524193764 s Creating peak regions... Creating peak regions took 76.0356419086 s Estimating background... Estimating background took 33.961014986 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28496813774 s Creating peak regions... Creating peak regions took 38.9935519695 s Estimating background... Estimating background took 13.9151070118 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.22171807289 s Creating peak regions... Creating peak regions took 38.8135361671 s Estimating background... Estimating background took 13.2574689388 s Processing ZNF680-SRR5197212.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='ZNF680-SRR5197212.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='ZNF680-SRR5197212/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 ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.09743189812 s Creating peak regions... Creating peak regions took 77.4885659218 s Estimating background... Estimating background took 37.2818329334 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.70912694931 s Creating peak regions... Creating peak regions took 44.6119310856 s Estimating background... Estimating background took 14.9168879986 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.47834801674 s Creating peak regions... Creating peak regions took 40.9610660076 s Estimating background... Estimating background took 14.5501701832 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.72678089142 s Creating peak regions... Creating peak regions took 42.9769558907 s Estimating background... Estimating background took 15.572042942 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23559308052 s Creating peak regions... Creating peak regions took 39.8052859306 s Estimating background... Estimating background took 14.7949299812 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.72637081146 s Creating peak regions... Creating peak regions took 31.7312018871 s Estimating background... Estimating background took 10.2883229256 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.68113303185 s Creating peak regions... Creating peak regions took 29.3872420788 s Estimating background... Estimating background took 11.1033859253 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.74425697327 s Creating peak regions... Creating peak regions took 29.339523077 s Estimating background... Estimating background took 11.238615036 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.13124489784 s Creating peak regions... Creating peak regions took 28.6873669624 s Estimating background... Estimating background took 13.3374910355 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.29341506958 s Creating peak regions... Creating peak regions took 24.6126451492 s Estimating background... Estimating background took 7.65896606445 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.52565789223 s Creating peak regions... Creating peak regions took 19.5458900928 s Estimating background... Estimating background took 10.1439208984 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.33140897751 s Creating peak regions... Creating peak regions took 81.5743300915 s Estimating background... Estimating background took 25.9059669971 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40900206566 s Creating peak regions... Creating peak regions took 21.0020740032 s Estimating background... Estimating background took 8.87504315376 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.843935966492 s Creating peak regions... Creating peak regions took 13.5980489254 s Estimating background... Estimating background took 4.62877392769 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.27613091469 s Creating peak regions... Creating peak regions took 15.4777460098 s Estimating background... Estimating background took 9.02176117897 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.54622197151 s Creating peak regions... Creating peak regions took 60.5083701611 s Estimating background... Estimating background took 20.8448829651 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.84889101982 s Creating peak regions... Creating peak regions took 57.9788720608 s Estimating background... Estimating background took 16.3721010685 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.13150382042 s Creating peak regions... Creating peak regions took 55.6315770149 s Estimating background... Estimating background took 18.5169489384 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.45999193192 s Creating peak regions... Creating peak regions took 57.5226790905 s Estimating background... Estimating background took 22.3515977859 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.18596720695 s Creating peak regions... Creating peak regions took 48.9441380501 s Estimating background... Estimating background took 18.272974968 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.61356306076 s Creating peak regions... Creating peak regions took 46.817535162 s Estimating background... Estimating background took 13.9271819592 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.10950899124 s Creating peak regions... Creating peak regions took 43.0033397675 s Estimating background... Estimating background took 12.7703750134 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0808081626892 s Creating peak regions... Creating peak regions took 0.187925100327 s Estimating background... Estimating background took 0.567920923233 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.74885606766 s Creating peak regions... Creating peak regions took 49.3369588852 s Estimating background... Estimating background took 14.4341671467 s Processing ZNF680-SRR5197212.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.182723999023 s Creating peak regions... Creating peak regions took 15.2889750004 s Estimating background... Estimating background took 0.457119941711 s