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='ZNF135-SRR5197060.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='ZNF135-SRR5197060/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 ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.1370408535 s Creating peak regions... Creating peak regions took 76.4292039871 s Estimating background... Estimating background took 32.9726469517 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.52171993256 s Creating peak regions... Creating peak regions took 42.259939909 s Estimating background... Estimating background took 12.9469630718 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.42912101746 s Creating peak regions... Creating peak regions took 40.2543530464 s Estimating background... Estimating background took 12.1958491802 s Processing ZNF135-SRR5197060.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='ZNF135-SRR5197060.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='ZNF135-SRR5197060/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 ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.23273181915 s Creating peak regions... Creating peak regions took 67.2395460606 s Estimating background... Estimating background took 29.2726690769 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.02397203445 s Creating peak regions... Creating peak regions took 35.9185209274 s Estimating background... Estimating background took 11.5613698959 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.99393200874 s Creating peak regions... Creating peak regions took 35.516392231 s Estimating background... Estimating background took 11.7840361595 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.15599322319 s Creating peak regions... Creating peak regions took 35.3731491566 s Estimating background... Estimating background took 12.783246994 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.87010502815 s Creating peak regions... Creating peak regions took 30.5925190449 s Estimating background... Estimating background took 12.7084882259 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.33865308762 s Creating peak regions... Creating peak regions took 27.3749129772 s Estimating background... Estimating background took 8.37202215195 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.3916759491 s Creating peak regions... Creating peak regions took 25.9126019478 s Estimating background... Estimating background took 9.37091016769 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40267181396 s Creating peak regions... Creating peak regions took 24.6696329117 s Estimating background... Estimating background took 8.31176280975 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.55565595627 s Creating peak regions... Creating peak regions took 23.6828157902 s Estimating background... Estimating background took 10.8779811859 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.22718715668 s Creating peak regions... Creating peak regions took 20.7122530937 s Estimating background... Estimating background took 6.2012090683 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.13731908798 s Creating peak regions... Creating peak regions took 15.8924250603 s Estimating background... Estimating background took 7.17694497108 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.52507090569 s Creating peak regions... Creating peak regions took 66.6925878525 s Estimating background... Estimating background took 19.3963990211 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.971097946167 s Creating peak regions... Creating peak regions took 16.7433068752 s Estimating background... Estimating background took 6.53491592407 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.601199865341 s Creating peak regions... Creating peak regions took 12.8540189266 s Estimating background... Estimating background took 3.8200571537 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.914628982544 s Creating peak regions... Creating peak regions took 14.2660491467 s Estimating background... Estimating background took 6.17544984818 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.56439614296 s Creating peak regions... Creating peak regions took 51.5445790291 s Estimating background... Estimating background took 15.4984688759 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.1659989357 s Creating peak regions... Creating peak regions took 46.4043850899 s Estimating background... Estimating background took 12.0507991314 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.58269309998 s Creating peak regions... Creating peak regions took 50.4364790916 s Estimating background... Estimating background took 14.5928680897 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.9033100605 s Creating peak regions... Creating peak regions took 44.1916899681 s Estimating background... Estimating background took 16.9078550339 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.41995787621 s Creating peak regions... Creating peak regions took 41.8631739616 s Estimating background... Estimating background took 15.156498909 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.04613900185 s Creating peak regions... Creating peak regions took 37.6839659214 s Estimating background... Estimating background took 10.7999420166 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7602519989 s Creating peak regions... Creating peak regions took 35.7987999916 s Estimating background... Estimating background took 11.0088131428 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0819449424744 s Creating peak regions... Creating peak regions took 0.159983873367 s Estimating background... Estimating background took 0.69286608696 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51573991776 s Creating peak regions... Creating peak regions took 43.8605849743 s Estimating background... Estimating background took 14.45977211 s Processing ZNF135-SRR5197060.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0976440906525 s Creating peak regions... Creating peak regions took 13.3737239838 s Estimating background... Estimating background took 0.577646017075 s