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='Total_input_293T_sampled-SRR5197033.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='Total_input_293T_sampled-SRR5197033/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 Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 15.8636600971 s Creating peak regions... Creating peak regions took 92.4206809998 s Estimating background... Estimating background took 250.07766819 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.0361301899 s Creating peak regions... Creating peak regions took 47.922606945 s Estimating background... Estimating background took 103.0814991 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.93503403664 s Creating peak regions... Creating peak regions took 47.841012001 s Estimating background... Estimating background took 101.861397982 s Processing Total_input_293T_sampled-SRR5197033.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='Total_input_293T_sampled-SRR5197033.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='Total_input_293T_sampled-SRR5197033/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 Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 15.2593688965 s Creating peak regions... Creating peak regions took 88.8506829739 s Estimating background... Estimating background took 244.978469133 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.63091111183 s Creating peak regions... Creating peak regions took 44.8724119663 s Estimating background... Estimating background took 98.9471681118 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.5586540699 s Creating peak regions... Creating peak regions took 44.1972699165 s Estimating background... Estimating background took 97.8410480022 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.68578100204 s Creating peak regions... Creating peak regions took 45.0389831066 s Estimating background... Estimating background took 100.1109519 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.23116612434 s Creating peak regions... Creating peak regions took 38.1475229263 s Estimating background... Estimating background took 96.0251731873 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.03189086914 s Creating peak regions... Creating peak regions took 34.2782280445 s Estimating background... Estimating background took 62.2714660168 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.97465801239 s Creating peak regions... Creating peak regions took 32.3945448399 s Estimating background... Estimating background took 67.6402320862 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.84138798714 s Creating peak regions... Creating peak regions took 29.8103728294 s Estimating background... Estimating background took 66.3177928925 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.57071495056 s Creating peak regions... Creating peak regions took 29.9809689522 s Estimating background... Estimating background took 86.9132120609 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.32087802887 s Creating peak regions... Creating peak regions took 27.7284557819 s Estimating background... Estimating background took 50.0068881512 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.38470506668 s Creating peak regions... Creating peak regions took 22.6914420128 s Estimating background... Estimating background took 61.0304090977 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 12.9889669418 s Creating peak regions... Creating peak regions took 81.9906320572 s Estimating background... Estimating background took 166.868473053 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.0797150135 s Creating peak regions... Creating peak regions took 24.8980541229 s Estimating background... Estimating background took 54.7973182201 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.20608878136 s Creating peak regions... Creating peak regions took 15.1378519535 s Estimating background... Estimating background took 28.0595638752 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.96607708931 s Creating peak regions... Creating peak regions took 17.2124371529 s Estimating background... Estimating background took 51.1957559586 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.85152482986 s Creating peak regions... Creating peak regions took 60.0235891342 s Estimating background... Estimating background took 123.924431086 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.27654480934 s Creating peak regions... Creating peak regions took 59.1074960232 s Estimating background... Estimating background took 94.435336113 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.72139120102 s Creating peak regions... Creating peak regions took 59.2176170349 s Estimating background... Estimating background took 119.355879068 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 10.426651001 s Creating peak regions... Creating peak regions took 59.2708630562 s Estimating background... Estimating background took 132.984667063 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.69000315666 s Creating peak regions... Creating peak regions took 54.2449040413 s Estimating background... Estimating background took 117.04194212 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.08869504929 s Creating peak regions... Creating peak regions took 47.9122450352 s Estimating background... Estimating background took 84.3685069084 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.84665894508 s Creating peak regions... Creating peak regions took 43.8830339909 s Estimating background... Estimating background took 80.4719130993 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.333286046982 s Creating peak regions... Creating peak regions took 0.433154821396 s Estimating background... Estimating background took 1.00608110428 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.96990013123 s Creating peak regions... Creating peak regions took 51.7415421009 s Estimating background... Estimating background took 124.303792953 s Processing Total_input_293T_sampled-SRR5197033.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.640791893005 s Creating peak regions... Creating peak regions took 15.6868710518 s Estimating background... Estimating background took 1.43960905075 s