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='ZNF682-SRR5197215.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='ZNF682-SRR5197215/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 ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.20191001892 s Creating peak regions... Creating peak regions took 60.2284641266 s Estimating background... Estimating background took 17.0607481003 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.52822399139 s Creating peak regions... Creating peak regions took 31.8022279739 s Estimating background... Estimating background took 8.56489896774 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.54404711723 s Creating peak regions... Creating peak regions took 34.6435728073 s Estimating background... Estimating background took 7.76103591919 s Processing ZNF682-SRR5197215.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='ZNF682-SRR5197215.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='ZNF682-SRR5197215/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 ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.98836302757 s Creating peak regions... Creating peak regions took 69.6838679314 s Estimating background... Estimating background took 19.4408180714 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.88401603699 s Creating peak regions... Creating peak regions took 37.9868621826 s Estimating background... Estimating background took 8.9845058918 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.56636786461 s Creating peak regions... Creating peak regions took 39.4903869629 s Estimating background... Estimating background took 8.04739093781 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.88598108292 s Creating peak regions... Creating peak regions took 36.2121069431 s Estimating background... Estimating background took 8.60602688789 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.47698783875 s Creating peak regions... Creating peak regions took 30.9502658844 s Estimating background... Estimating background took 8.10903501511 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.04126191139 s Creating peak regions... Creating peak regions took 31.9560248852 s Estimating background... Estimating background took 5.88948512077 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.02621102333 s Creating peak regions... Creating peak regions took 29.4646720886 s Estimating background... Estimating background took 5.7495059967 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.12859916687 s Creating peak regions... Creating peak regions took 26.8795130253 s Estimating background... Estimating background took 6.11862897873 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.54954695702 s Creating peak regions... Creating peak regions took 25.485380888 s Estimating background... Estimating background took 7.52782607079 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.950906038284 s Creating peak regions... Creating peak regions took 24.193333149 s Estimating background... Estimating background took 4.70875906944 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.10350513458 s Creating peak regions... Creating peak regions took 19.3909218311 s Estimating background... Estimating background took 5.73345398903 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.96763205528 s Creating peak regions... Creating peak regions took 76.240350008 s Estimating background... Estimating background took 13.4516720772 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.1829559803 s Creating peak regions... Creating peak regions took 20.9436659813 s Estimating background... Estimating background took 5.43534612656 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.01919794083 s Creating peak regions... Creating peak regions took 14.2022490501 s Estimating background... Estimating background took 3.00310015678 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.804047107697 s Creating peak regions... Creating peak regions took 14.3870429993 s Estimating background... Estimating background took 4.81108188629 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.1464779377 s Creating peak regions... Creating peak regions took 60.3258550167 s Estimating background... Estimating background took 11.2823688984 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.18666005135 s Creating peak regions... Creating peak regions took 62.0014250278 s Estimating background... Estimating background took 10.0591230392 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.05270385742 s Creating peak regions... Creating peak regions took 52.5934510231 s Estimating background... Estimating background took 10.0203897953 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37818598747 s Creating peak regions... Creating peak regions took 52.4422860146 s Estimating background... Estimating background took 12.3234050274 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.19335794449 s Creating peak regions... Creating peak regions took 50.8166921139 s Estimating background... Estimating background took 11.0645470619 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.74016499519 s Creating peak regions... Creating peak regions took 44.5523660183 s Estimating background... Estimating background took 8.18088912964 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.50975108147 s Creating peak regions... Creating peak regions took 41.3144071102 s Estimating background... Estimating background took 7.90524101257 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0728578567505 s Creating peak regions... Creating peak regions took 0.130172014236 s Estimating background... Estimating background took 0.598968029022 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28992795944 s Creating peak regions... Creating peak regions took 48.6952390671 s Estimating background... Estimating background took 9.11545181274 s Processing ZNF682-SRR5197215.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0877850055695 s Creating peak regions... Creating peak regions took 14.9546518326 s Estimating background... Estimating background took 0.51676607132 s