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='ZNF480-SRR5197152.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='ZNF480-SRR5197152/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 ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.23127698898 s Creating peak regions... Creating peak regions took 76.2342851162 s Estimating background... Estimating background took 30.0201058388 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24944901466 s Creating peak regions... Creating peak regions took 40.0948960781 s Estimating background... Estimating background took 12.6619360447 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24723219872 s Creating peak regions... Creating peak regions took 39.5014541149 s Estimating background... Estimating background took 12.3899130821 s Processing ZNF480-SRR5197152.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='ZNF480-SRR5197152.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='ZNF480-SRR5197152/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 ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.56856608391 s Creating peak regions... Creating peak regions took 73.9887478352 s Estimating background... Estimating background took 31.5002048016 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.33988809586 s Creating peak regions... Creating peak regions took 39.1753110886 s Estimating background... Estimating background took 12.8496100903 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.2261800766 s Creating peak regions... Creating peak regions took 40.4799220562 s Estimating background... Estimating background took 13.3838670254 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.35181689262 s Creating peak regions... Creating peak regions took 40.2259027958 s Estimating background... Estimating background took 14.2378599644 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.00566601753 s Creating peak regions... Creating peak regions took 33.1890730858 s Estimating background... Estimating background took 14.5202579498 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.50353503227 s Creating peak regions... Creating peak regions took 31.0194199085 s Estimating background... Estimating background took 8.74572205544 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.56686306 s Creating peak regions... Creating peak regions took 31.3768889904 s Estimating background... Estimating background took 10.9119520187 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.5141210556 s Creating peak regions... Creating peak regions took 26.9119360447 s Estimating background... Estimating background took 8.96491289139 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7883310318 s Creating peak regions... Creating peak regions took 26.4070501328 s Estimating background... Estimating background took 12.2671179771 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.2788631916 s Creating peak regions... Creating peak regions took 24.317440033 s Estimating background... Estimating background took 7.20584797859 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.17734289169 s Creating peak regions... Creating peak regions took 19.227905035 s Estimating background... Estimating background took 7.73750185966 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.9762160778 s Creating peak regions... Creating peak regions took 71.9422020912 s Estimating background... Estimating background took 22.767747879 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.24450612068 s Creating peak regions... Creating peak regions took 20.1771101952 s Estimating background... Estimating background took 7.78070688248 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.684265851974 s Creating peak regions... Creating peak regions took 14.8627169132 s Estimating background... Estimating background took 4.51449990273 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.52942585945 s Creating peak regions... Creating peak regions took 15.4393420219 s Estimating background... Estimating background took 7.34986710548 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.07104301453 s Creating peak regions... Creating peak regions took 58.9748930931 s Estimating background... Estimating background took 16.7566399574 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.79452204704 s Creating peak regions... Creating peak regions took 54.9070770741 s Estimating background... Estimating background took 13.2473781109 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.04709792137 s Creating peak regions... Creating peak regions took 57.2113759518 s Estimating background... Estimating background took 18.2966902256 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.20587587357 s Creating peak regions... Creating peak regions took 51.6675248146 s Estimating background... Estimating background took 17.5775709152 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.01880788803 s Creating peak regions... Creating peak regions took 51.5118439198 s Estimating background... Estimating background took 16.7653019428 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51007914543 s Creating peak regions... Creating peak regions took 42.7685351372 s Estimating background... Estimating background took 12.3903131485 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.07433390617 s Creating peak regions... Creating peak regions took 42.913269043 s Estimating background... Estimating background took 11.8918640614 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0789940357208 s Creating peak regions... Creating peak regions took 0.167078971863 s Estimating background... Estimating background took 0.555825948715 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.96509695053 s Creating peak regions... Creating peak regions took 48.7617828846 s Estimating background... Estimating background took 15.8192708492 s Processing ZNF480-SRR5197152.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.104218006134 s Creating peak regions... Creating peak regions took 13.6186330318 s Estimating background... Estimating background took 0.659663915634 s