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='ZNF235-SRR5197086.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='ZNF235-SRR5197086/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 ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.75902104378 s Creating peak regions... Creating peak regions took 70.5736849308 s Estimating background... Estimating background took 23.8809449673 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98576807976 s Creating peak regions... Creating peak regions took 36.788326025 s Estimating background... Estimating background took 9.80184006691 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.97964692116 s Creating peak regions... Creating peak regions took 39.3659219742 s Estimating background... Estimating background took 10.0820510387 s Processing ZNF235-SRR5197086.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='ZNF235-SRR5197086.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='ZNF235-SRR5197086/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 ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.43446111679 s Creating peak regions... Creating peak regions took 73.0194430351 s Estimating background... Estimating background took 26.5752360821 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.17407894135 s Creating peak regions... Creating peak regions took 40.0174717903 s Estimating background... Estimating background took 11.0352509022 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.13936090469 s Creating peak regions... Creating peak regions took 41.5265331268 s Estimating background... Estimating background took 10.5402150154 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24626922607 s Creating peak regions... Creating peak regions took 42.1254470348 s Estimating background... Estimating background took 11.6392900944 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.19370388985 s Creating peak regions... Creating peak regions took 36.3433880806 s Estimating background... Estimating background took 11.6225998402 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.44911909103 s Creating peak regions... Creating peak regions took 30.8035049438 s Estimating background... Estimating background took 7.39532208443 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.58109498024 s Creating peak regions... Creating peak regions took 30.948677063 s Estimating background... Estimating background took 7.98479413986 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40521383286 s Creating peak regions... Creating peak regions took 24.727134943 s Estimating background... Estimating background took 7.24014210701 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.73552513123 s Creating peak regions... Creating peak regions took 24.3577308655 s Estimating background... Estimating background took 8.97525596619 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.19153904915 s Creating peak regions... Creating peak regions took 24.318434 s Estimating background... Estimating background took 6.1550579071 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.15687799454 s Creating peak regions... Creating peak regions took 18.9326570034 s Estimating background... Estimating background took 6.28338313103 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.55441021919 s Creating peak regions... Creating peak regions took 75.0083920956 s Estimating background... Estimating background took 17.1002700329 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.16066598892 s Creating peak regions... Creating peak regions took 20.0408089161 s Estimating background... Estimating background took 6.31741809845 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.679500102997 s Creating peak regions... Creating peak regions took 14.7175459862 s Estimating background... Estimating background took 3.8278298378 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.980652093887 s Creating peak regions... Creating peak regions took 16.0012969971 s Estimating background... Estimating background took 6.6473069191 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.07825899124 s Creating peak regions... Creating peak regions took 61.0234830379 s Estimating background... Estimating background took 14.7695860863 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.97922897339 s Creating peak regions... Creating peak regions took 56.059237957 s Estimating background... Estimating background took 11.8306601048 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.75349211693 s Creating peak regions... Creating peak regions took 51.3105020523 s Estimating background... Estimating background took 13.8619589806 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.12592196465 s Creating peak regions... Creating peak regions took 54.7377681732 s Estimating background... Estimating background took 15.7829630375 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.71772003174 s Creating peak regions... Creating peak regions took 46.326761961 s Estimating background... Estimating background took 13.5669808388 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.29391694069 s Creating peak regions... Creating peak regions took 46.5239980221 s Estimating background... Estimating background took 10.585529089 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.87439107895 s Creating peak regions... Creating peak regions took 40.3929710388 s Estimating background... Estimating background took 9.96620106697 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0891721248627 s Creating peak regions... Creating peak regions took 0.184126138687 s Estimating background... Estimating background took 0.702125072479 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.81661105156 s Creating peak regions... Creating peak regions took 46.098995924 s Estimating background... Estimating background took 14.22915411 s Processing ZNF235-SRR5197086.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.109976053238 s Creating peak regions... Creating peak regions took 15.3584699631 s Estimating background... Estimating background took 0.562183141708 s