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='ZNF202-SRR5197076.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='ZNF202-SRR5197076/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 ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.64758396149 s Creating peak regions... Creating peak regions took 66.4422791004 s Estimating background... Estimating background took 42.3650791645 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.59673595428 s Creating peak regions... Creating peak regions took 40.3708939552 s Estimating background... Estimating background took 17.513671875 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.74405002594 s Creating peak regions... Creating peak regions took 45.4124128819 s Estimating background... Estimating background took 18.6262528896 s Processing ZNF202-SRR5197076.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='ZNF202-SRR5197076.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='ZNF202-SRR5197076/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 ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.27203989029 s Creating peak regions... Creating peak regions took 75.868103981 s Estimating background... Estimating background took 41.3331918716 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.5694630146 s Creating peak regions... Creating peak regions took 40.6631808281 s Estimating background... Estimating background took 18.3705029488 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.71953105927 s Creating peak regions... Creating peak regions took 43.2045879364 s Estimating background... Estimating background took 18.1465418339 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.83120179176 s Creating peak regions... Creating peak regions took 40.0704951286 s Estimating background... Estimating background took 20.1978390217 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.4630548954 s Creating peak regions... Creating peak regions took 37.3540608883 s Estimating background... Estimating background took 15.3062078953 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98719191551 s Creating peak regions... Creating peak regions took 33.0061190128 s Estimating background... Estimating background took 12.2343320847 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.82969117165 s Creating peak regions... Creating peak regions took 30.0436570644 s Estimating background... Estimating background took 14.7503240108 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.05838108063 s Creating peak regions... Creating peak regions took 26.3765449524 s Estimating background... Estimating background took 13.4075820446 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.27663207054 s Creating peak regions... Creating peak regions took 25.921890974 s Estimating background... Estimating background took 20.3636479378 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.48208189011 s Creating peak regions... Creating peak regions took 24.2776629925 s Estimating background... Estimating background took 8.99598193169 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.63512015343 s Creating peak regions... Creating peak regions took 19.958507061 s Estimating background... Estimating background took 14.9982609749 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.7243449688 s Creating peak regions... Creating peak regions took 77.5779440403 s Estimating background... Estimating background took 29.9899420738 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.5537750721 s Creating peak regions... Creating peak regions took 21.1854310036 s Estimating background... Estimating background took 10.6718220711 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.97029209137 s Creating peak regions... Creating peak regions took 13.5224018097 s Estimating background... Estimating background took 5.18475604057 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.29434013367 s Creating peak regions... Creating peak regions took 16.052614212 s Estimating background... Estimating background took 11.0241580009 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.82538986206 s Creating peak regions... Creating peak regions took 62.9481577873 s Estimating background... Estimating background took 21.3864901066 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.20808696747 s Creating peak regions... Creating peak regions took 54.1812570095 s Estimating background... Estimating background took 17.7247219086 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.51232981682 s Creating peak regions... Creating peak regions took 55.7115120888 s Estimating background... Estimating background took 21.8121500015 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.96130800247 s Creating peak regions... Creating peak regions took 51.6098740101 s Estimating background... Estimating background took 25.1870748997 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.49478793144 s Creating peak regions... Creating peak regions took 50.6936290264 s Estimating background... Estimating background took 21.6914799213 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.88988995552 s Creating peak regions... Creating peak regions took 43.2890760899 s Estimating background... Estimating background took 15.6271870136 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.38818883896 s Creating peak regions... Creating peak regions took 40.4075469971 s Estimating background... Estimating background took 16.1267180443 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.101624965668 s Creating peak regions... Creating peak regions took 0.172653198242 s Estimating background... Estimating background took 0.744583845139 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.51305913925 s Creating peak regions... Creating peak regions took 38.6067259312 s Estimating background... Estimating background took 16.7128460407 s Processing ZNF202-SRR5197076.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.10135602951 s Creating peak regions... Creating peak regions took 12.6292250156 s Estimating background... Estimating background took 0.586752176285 s