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='ZNF114-SRR5197055.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='ZNF114-SRR5197055/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 ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.47094702721 s Creating peak regions... Creating peak regions took 88.1362409592 s Estimating background... Estimating background took 107.71152401 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.78566789627 s Creating peak regions... Creating peak regions took 41.8181428909 s Estimating background... Estimating background took 33.8894708157 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.96056604385 s Creating peak regions... Creating peak regions took 39.9733140469 s Estimating background... Estimating background took 34.291353941 s Processing ZNF114-SRR5197055.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='ZNF114-SRR5197055.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='ZNF114-SRR5197055/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 ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.41990613937 s Creating peak regions... Creating peak regions took 71.4469530582 s Estimating background... Estimating background took 97.0253400803 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.26269507408 s Creating peak regions... Creating peak regions took 38.267343998 s Estimating background... Estimating background took 35.7298409939 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.54024100304 s Creating peak regions... Creating peak regions took 38.1700248718 s Estimating background... Estimating background took 38.4720649719 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.55561900139 s Creating peak regions... Creating peak regions took 38.3894760609 s Estimating background... Estimating background took 40.7648890018 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.05770802498 s Creating peak regions... Creating peak regions took 33.7963080406 s Estimating background... Estimating background took 45.8560180664 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.99671506882 s Creating peak regions... Creating peak regions took 30.1158938408 s Estimating background... Estimating background took 24.6625618935 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.93548607826 s Creating peak regions... Creating peak regions took 28.238574028 s Estimating background... Estimating background took 25.7160451412 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.95856189728 s Creating peak regions... Creating peak regions took 25.4331710339 s Estimating background... Estimating background took 25.3872411251 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.20800900459 s Creating peak regions... Creating peak regions took 23.2499341965 s Estimating background... Estimating background took 30.0254158974 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.43724989891 s Creating peak regions... Creating peak regions took 21.77643013 s Estimating background... Estimating background took 19.8632099628 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.25077605247 s Creating peak regions... Creating peak regions took 17.2587180138 s Estimating background... Estimating background took 21.2166950703 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.37783908844 s Creating peak regions... Creating peak regions took 67.966176033 s Estimating background... Estimating background took 63.4503889084 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45228815079 s Creating peak regions... Creating peak regions took 20.53510499 s Estimating background... Estimating background took 22.0924158096 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.41653299332 s Creating peak regions... Creating peak regions took 12.5038440228 s Estimating background... Estimating background took 12.0307769775 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.79641103745 s Creating peak regions... Creating peak regions took 14.6135101318 s Estimating background... Estimating background took 20.2334568501 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.87873601913 s Creating peak regions... Creating peak regions took 55.1702721119 s Estimating background... Estimating background took 49.3539919853 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.30556821823 s Creating peak regions... Creating peak regions took 54.5620729923 s Estimating background... Estimating background took 40.2978460789 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.88054895401 s Creating peak regions... Creating peak regions took 49.1340169907 s Estimating background... Estimating background took 49.7969150543 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.63709592819 s Creating peak regions... Creating peak regions took 52.5222949982 s Estimating background... Estimating background took 57.404540062 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.99581885338 s Creating peak regions... Creating peak regions took 48.2596518993 s Estimating background... Estimating background took 51.5676298141 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.97658109665 s Creating peak regions... Creating peak regions took 42.4640460014 s Estimating background... Estimating background took 38.2917509079 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.73886013031 s Creating peak regions... Creating peak regions took 38.443557024 s Estimating background... Estimating background took 33.1259961128 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.154726982117 s Creating peak regions... Creating peak regions took 0.25380897522 s Estimating background... Estimating background took 0.77659702301 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.33397984505 s Creating peak regions... Creating peak regions took 43.9376130104 s Estimating background... Estimating background took 53.0335459709 s Processing ZNF114-SRR5197055.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.339663982391 s Creating peak regions... Creating peak regions took 14.4178059101 s Estimating background... Estimating background took 0.840864896774 s