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='ZNF181-SRR5197069.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='ZNF181-SRR5197069/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 ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.78003191948 s Creating peak regions... Creating peak regions took 76.6108670235 s Estimating background... Estimating background took 43.2108440399 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.01401305199 s Creating peak regions... Creating peak regions took 40.3527781963 s Estimating background... Estimating background took 17.2864949703 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.53109407425 s Creating peak regions... Creating peak regions took 40.195579052 s Estimating background... Estimating background took 17.3964049816 s Processing ZNF181-SRR5197069.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='ZNF181-SRR5197069.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='ZNF181-SRR5197069/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 ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.30565595627 s Creating peak regions... Creating peak regions took 72.8580691814 s Estimating background... Estimating background took 40.9874808788 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.53189396858 s Creating peak regions... Creating peak regions took 38.4644610882 s Estimating background... Estimating background took 16.364675045 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.07771110535 s Creating peak regions... Creating peak regions took 38.8389539719 s Estimating background... Estimating background took 16.5729219913 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.22056388855 s Creating peak regions... Creating peak regions took 38.378524065 s Estimating background... Estimating background took 17.9799201488 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.90656900406 s Creating peak regions... Creating peak regions took 31.5977408886 s Estimating background... Estimating background took 18.9815878868 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.92608189583 s Creating peak regions... Creating peak regions took 29.6752340794 s Estimating background... Estimating background took 11.3471112251 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39032006264 s Creating peak regions... Creating peak regions took 28.0002100468 s Estimating background... Estimating background took 12.6137800217 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.66470909119 s Creating peak regions... Creating peak regions took 25.5397348404 s Estimating background... Estimating background took 11.7482089996 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.56308913231 s Creating peak regions... Creating peak regions took 24.5854380131 s Estimating background... Estimating background took 14.7362987995 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.84302401543 s Creating peak regions... Creating peak regions took 24.5370190144 s Estimating background... Estimating background took 9.12306404114 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.65522217751 s Creating peak regions... Creating peak regions took 18.3695120811 s Estimating background... Estimating background took 9.46305298805 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.18274998665 s Creating peak regions... Creating peak regions took 73.0621948242 s Estimating background... Estimating background took 28.0611429214 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.25508904457 s Creating peak regions... Creating peak regions took 19.487680912 s Estimating background... Estimating background took 9.89184379578 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06446290016 s Creating peak regions... Creating peak regions took 14.3775579929 s Estimating background... Estimating background took 5.76255893707 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.11867499352 s Creating peak regions... Creating peak regions took 15.3174819946 s Estimating background... Estimating background took 8.75387310982 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.5667591095 s Creating peak regions... Creating peak regions took 60.5883979797 s Estimating background... Estimating background took 21.5768258572 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.78077292442 s Creating peak regions... Creating peak regions took 51.5605869293 s Estimating background... Estimating background took 17.4553310871 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.30641388893 s Creating peak regions... Creating peak regions took 52.0544378757 s Estimating background... Estimating background took 21.8282170296 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.59687995911 s Creating peak regions... Creating peak regions took 49.979072094 s Estimating background... Estimating background took 24.3354549408 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.96920084953 s Creating peak regions... Creating peak regions took 46.2518517971 s Estimating background... Estimating background took 22.2631151676 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.6845729351 s Creating peak regions... Creating peak regions took 41.9371871948 s Estimating background... Estimating background took 15.5891458988 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.44701600075 s Creating peak regions... Creating peak regions took 42.3070089817 s Estimating background... Estimating background took 15.7550828457 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0924251079559 s Creating peak regions... Creating peak regions took 0.164556026459 s Estimating background... Estimating background took 0.657338857651 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.99698901176 s Creating peak regions... Creating peak regions took 47.0051958561 s Estimating background... Estimating background took 24.0567131042 s Processing ZNF181-SRR5197069.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.188068151474 s Creating peak regions... Creating peak regions took 15.840143919 s Estimating background... Estimating background took 0.698856115341 s