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='ZNF354B-SRR5197124.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='ZNF354B-SRR5197124/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 ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.82133507729 s Creating peak regions... Creating peak regions took 75.2631490231 s Estimating background... Estimating background took 21.1619451046 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.83552408218 s Creating peak regions... Creating peak regions took 40.7502820492 s Estimating background... Estimating background took 8.95937085152 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.93625497818 s Creating peak regions... Creating peak regions took 41.8130750656 s Estimating background... Estimating background took 8.94806313515 s Processing ZNF354B-SRR5197124.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='ZNF354B-SRR5197124.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='ZNF354B-SRR5197124/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 ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.65598106384 s Creating peak regions... Creating peak regions took 73.0162100792 s Estimating background... Estimating background took 21.9980590343 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.88856196404 s Creating peak regions... Creating peak regions took 39.6486840248 s Estimating background... Estimating background took 9.39933991432 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.97790789604 s Creating peak regions... Creating peak regions took 41.0554351807 s Estimating background... Estimating background took 8.97539305687 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.89195203781 s Creating peak regions... Creating peak regions took 39.0187020302 s Estimating background... Estimating background took 9.90762209892 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.84212398529 s Creating peak regions... Creating peak regions took 34.0995738506 s Estimating background... Estimating background took 12.2927160263 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.50926208496 s Creating peak regions... Creating peak regions took 32.2913429737 s Estimating background... Estimating background took 6.57455086708 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.33881282806 s Creating peak regions... Creating peak regions took 30.669383049 s Estimating background... Estimating background took 6.82336783409 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.16397619247 s Creating peak regions... Creating peak regions took 27.3347699642 s Estimating background... Estimating background took 5.9842479229 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.41892695427 s Creating peak regions... Creating peak regions took 24.8922438622 s Estimating background... Estimating background took 6.67493200302 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.06074500084 s Creating peak regions... Creating peak regions took 23.1627290249 s Estimating background... Estimating background took 5.19845199585 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.935683012009 s Creating peak regions... Creating peak regions took 17.8168680668 s Estimating background... Estimating background took 4.31788420677 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.16379094124 s Creating peak regions... Creating peak regions took 76.1695039272 s Estimating background... Estimating background took 16.2511560917 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.934052944183 s Creating peak regions... Creating peak regions took 18.8591189384 s Estimating background... Estimating background took 4.8985490799 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.541304826736 s Creating peak regions... Creating peak regions took 12.6294090748 s Estimating background... Estimating background took 3.35807204247 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.814437866211 s Creating peak regions... Creating peak regions took 14.7055449486 s Estimating background... Estimating background took 4.36536192894 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.77510499954 s Creating peak regions... Creating peak regions took 62.1932299137 s Estimating background... Estimating background took 12.8544139862 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.82859516144 s Creating peak regions... Creating peak regions took 57.17928195 s Estimating background... Estimating background took 11.0788428783 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.57056188583 s Creating peak regions... Creating peak regions took 52.4041199684 s Estimating background... Estimating background took 11.919164896 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.60997200012 s Creating peak regions... Creating peak regions took 51.1663589478 s Estimating background... Estimating background took 13.8145289421 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45515203476 s Creating peak regions... Creating peak regions took 50.9039590359 s Estimating background... Estimating background took 12.126101017 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.14149308205 s Creating peak regions... Creating peak regions took 44.0242409706 s Estimating background... Estimating background took 8.72833013535 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.5206720829 s Creating peak regions... Creating peak regions took 41.1016309261 s Estimating background... Estimating background took 8.96344900131 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0786871910095 s Creating peak regions... Creating peak regions took 0.187374830246 s Estimating background... Estimating background took 0.576898097992 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.5995631218 s Creating peak regions... Creating peak regions took 49.3847219944 s Estimating background... Estimating background took 13.1449730396 s Processing ZNF354B-SRR5197124.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0965669155121 s Creating peak regions... Creating peak regions took 16.0564630032 s Estimating background... Estimating background took 2.24358296394 s