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='ZNF540-SRR5197168.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='ZNF540-SRR5197168/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 ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.66450405121 s Creating peak regions... Creating peak regions took 75.700371027 s Estimating background... Estimating background took 22.5747640133 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.89776492119 s Creating peak regions... Creating peak regions took 38.4663488865 s Estimating background... Estimating background took 10.1283512115 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98604106903 s Creating peak regions... Creating peak regions took 38.6193571091 s Estimating background... Estimating background took 9.38123893738 s Processing ZNF540-SRR5197168.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='ZNF540-SRR5197168.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='ZNF540-SRR5197168/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 ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.81453680992 s Creating peak regions... Creating peak regions took 74.4770851135 s Estimating background... Estimating background took 23.7508051395 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.07999682426 s Creating peak regions... Creating peak regions took 38.4876410961 s Estimating background... Estimating background took 10.0579349995 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.85654401779 s Creating peak regions... Creating peak regions took 39.2638020515 s Estimating background... Estimating background took 9.98206377029 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.03418493271 s Creating peak regions... Creating peak regions took 41.7495141029 s Estimating background... Estimating background took 10.331622839 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.8337199688 s Creating peak regions... Creating peak regions took 32.5807030201 s Estimating background... Estimating background took 10.6793408394 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.42221498489 s Creating peak regions... Creating peak regions took 31.9566469193 s Estimating background... Estimating background took 6.81521916389 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.30231499672 s Creating peak regions... Creating peak regions took 30.802795887 s Estimating background... Estimating background took 7.70995903015 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.25069522858 s Creating peak regions... Creating peak regions took 25.2522130013 s Estimating background... Estimating background took 6.66550397873 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.45751094818 s Creating peak regions... Creating peak regions took 24.9570660591 s Estimating background... Estimating background took 8.10401082039 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.940888166428 s Creating peak regions... Creating peak regions took 22.9233601093 s Estimating background... Estimating background took 5.71352386475 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.08814787865 s Creating peak regions... Creating peak regions took 18.5947840214 s Estimating background... Estimating background took 5.79554796219 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.37038683891 s Creating peak regions... Creating peak regions took 72.2778968811 s Estimating background... Estimating background took 16.3909261227 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.02127194405 s Creating peak regions... Creating peak regions took 19.7363340855 s Estimating background... Estimating background took 5.58556485176 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.701385974884 s Creating peak regions... Creating peak regions took 14.624614954 s Estimating background... Estimating background took 2.40575504303 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.03374004364 s Creating peak regions... Creating peak regions took 16.2603590488 s Estimating background... Estimating background took 5.34844493866 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.72166395187 s Creating peak regions... Creating peak regions took 60.5605299473 s Estimating background... Estimating background took 12.4446139336 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39349389076 s Creating peak regions... Creating peak regions took 57.5661790371 s Estimating background... Estimating background took 9.82645797729 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.43459486961 s Creating peak regions... Creating peak regions took 50.8245708942 s Estimating background... Estimating background took 12.4447460175 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.82568311691 s Creating peak regions... Creating peak regions took 48.6960818768 s Estimating background... Estimating background took 14.1825959682 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.6279630661 s Creating peak regions... Creating peak regions took 48.8327460289 s Estimating background... Estimating background took 11.9196488857 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.989538908 s Creating peak regions... Creating peak regions took 45.7821369171 s Estimating background... Estimating background took 9.65531301498 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.08734107018 s Creating peak regions... Creating peak regions took 40.282733202 s Estimating background... Estimating background took 8.15829396248 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0760729312897 s Creating peak regions... Creating peak regions took 0.148813009262 s Estimating background... Estimating background took 0.534775972366 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51723790169 s Creating peak regions... Creating peak regions took 48.2420709133 s Estimating background... Estimating background took 13.2048201561 s Processing ZNF540-SRR5197168.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.127863883972 s Creating peak regions... Creating peak regions took 15.0804209709 s Estimating background... Estimating background took 2.3433508873 s