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='ZNF714-SRR5197224.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='ZNF714-SRR5197224/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 ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.29799604416 s Creating peak regions... Creating peak regions took 78.5411279202 s Estimating background... Estimating background took 44.6537790298 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.24522304535 s Creating peak regions... Creating peak regions took 42.3098449707 s Estimating background... Estimating background took 17.7384951115 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.24302506447 s Creating peak regions... Creating peak regions took 40.0599219799 s Estimating background... Estimating background took 16.6197659969 s Processing ZNF714-SRR5197224.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='ZNF714-SRR5197224.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='ZNF714-SRR5197224/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 ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.28752994537 s Creating peak regions... Creating peak regions took 78.0118429661 s Estimating background... Estimating background took 44.6088721752 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.37567996979 s Creating peak regions... Creating peak regions took 42.2486538887 s Estimating background... Estimating background took 17.8678598404 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.25462508202 s Creating peak regions... Creating peak regions took 40.9754951 s Estimating background... Estimating background took 18.0892269611 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.23135900497 s Creating peak regions... Creating peak regions took 40.1395149231 s Estimating background... Estimating background took 19.1208679676 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.90031909943 s Creating peak regions... Creating peak regions took 34.6992371082 s Estimating background... Estimating background took 18.9650349617 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.26906704903 s Creating peak regions... Creating peak regions took 30.401045084 s Estimating background... Estimating background took 12.1066958904 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32970309258 s Creating peak regions... Creating peak regions took 30.1913998127 s Estimating background... Estimating background took 13.6594390869 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.11146402359 s Creating peak regions... Creating peak regions took 27.5137989521 s Estimating background... Estimating background took 12.9858350754 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.67481303215 s Creating peak regions... Creating peak regions took 25.9412519932 s Estimating background... Estimating background took 17.2606809139 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.71147990227 s Creating peak regions... Creating peak regions took 25.6118519306 s Estimating background... Estimating background took 9.07200193405 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.77964186668 s Creating peak regions... Creating peak regions took 18.1810760498 s Estimating background... Estimating background took 11.1816811562 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.25165295601 s Creating peak regions... Creating peak regions took 74.3318171501 s Estimating background... Estimating background took 29.8267431259 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.82153296471 s Creating peak regions... Creating peak regions took 20.7491490841 s Estimating background... Estimating background took 10.6411731243 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.876673936844 s Creating peak regions... Creating peak regions took 13.8027648926 s Estimating background... Estimating background took 5.89656090736 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.36144304276 s Creating peak regions... Creating peak regions took 16.421656847 s Estimating background... Estimating background took 10.9620330334 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.2159948349 s Creating peak regions... Creating peak regions took 59.8671491146 s Estimating background... Estimating background took 22.5554020405 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.47395086288 s Creating peak regions... Creating peak regions took 56.4229340553 s Estimating background... Estimating background took 18.0493991375 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.01754379272 s Creating peak regions... Creating peak regions took 54.4196958542 s Estimating background... Estimating background took 22.5249319077 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.20561480522 s Creating peak regions... Creating peak regions took 52.1302220821 s Estimating background... Estimating background took 25.732448101 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.03834819794 s Creating peak regions... Creating peak regions took 48.4071469307 s Estimating background... Estimating background took 23.1439740658 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.35645318031 s Creating peak regions... Creating peak regions took 46.0075671673 s Estimating background... Estimating background took 15.8376410007 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.71980690956 s Creating peak regions... Creating peak regions took 40.7920818329 s Estimating background... Estimating background took 16.3384048939 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0925660133362 s Creating peak regions... Creating peak regions took 0.181477069855 s Estimating background... Estimating background took 0.6938560009 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.77737593651 s Creating peak regions... Creating peak regions took 49.6792821884 s Estimating background... Estimating background took 23.0485200882 s Processing ZNF714-SRR5197224.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.160586833954 s Creating peak regions... Creating peak regions took 15.1760120392 s Estimating background... Estimating background took 0.704399824142 s