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='ZNF141-SRR5197062.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='ZNF141-SRR5197062/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 ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.7801220417 s Creating peak regions... Creating peak regions took 83.1204829216 s Estimating background... Estimating background took 76.1039540768 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.18423604965 s Creating peak regions... Creating peak regions took 45.3515188694 s Estimating background... Estimating background took 28.9523971081 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.31807899475 s Creating peak regions... Creating peak regions took 38.6811439991 s Estimating background... Estimating background took 27.5671579838 s Processing ZNF141-SRR5197062.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='ZNF141-SRR5197062.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='ZNF141-SRR5197062/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 ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.62770581245 s Creating peak regions... Creating peak regions took 72.3608739376 s Estimating background... Estimating background took 66.4313309193 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.46590590477 s Creating peak regions... Creating peak regions took 37.6663210392 s Estimating background... Estimating background took 31.3744399548 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.97186803818 s Creating peak regions... Creating peak regions took 42.5285148621 s Estimating background... Estimating background took 31.5442390442 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.26784086227 s Creating peak regions... Creating peak regions took 42.6013538837 s Estimating background... Estimating background took 33.4987969398 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.66608500481 s Creating peak regions... Creating peak regions took 36.8427350521 s Estimating background... Estimating background took 33.2985949516 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.69728302956 s Creating peak regions... Creating peak regions took 33.5072350502 s Estimating background... Estimating background took 20.8165421486 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.57629609108 s Creating peak regions... Creating peak regions took 31.099132061 s Estimating background... Estimating background took 22.5738019943 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.80350208282 s Creating peak regions... Creating peak regions took 28.4534800053 s Estimating background... Estimating background took 21.2689971924 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.99189186096 s Creating peak regions... Creating peak regions took 28.5629630089 s Estimating background... Estimating background took 29.5372970104 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.11562299728 s Creating peak regions... Creating peak regions took 25.6826639175 s Estimating background... Estimating background took 15.9858498573 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.27591300011 s Creating peak regions... Creating peak regions took 19.273542881 s Estimating background... Estimating background took 19.9707150459 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.36542797089 s Creating peak regions... Creating peak regions took 77.8203730583 s Estimating background... Estimating background took 53.5776929855 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.426445961 s Creating peak regions... Creating peak regions took 23.0880889893 s Estimating background... Estimating background took 19.1178719997 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.20260620117 s Creating peak regions... Creating peak regions took 14.922907114 s Estimating background... Estimating background took 9.97754788399 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.68565201759 s Creating peak regions... Creating peak regions took 15.5358178616 s Estimating background... Estimating background took 17.995620966 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.15571403503 s Creating peak regions... Creating peak regions took 62.5897769928 s Estimating background... Estimating background took 44.2473120689 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.7283270359 s Creating peak regions... Creating peak regions took 60.7952740192 s Estimating background... Estimating background took 33.0755450726 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.98861312866 s Creating peak regions... Creating peak regions took 55.56356287 s Estimating background... Estimating background took 39.9991128445 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.35339808464 s Creating peak regions... Creating peak regions took 55.9889280796 s Estimating background... Estimating background took 44.8013489246 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.80540919304 s Creating peak regions... Creating peak regions took 53.0634908676 s Estimating background... Estimating background took 40.8460719585 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.03827309608 s Creating peak regions... Creating peak regions took 46.2918140888 s Estimating background... Estimating background took 28.3589651585 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.28466701508 s Creating peak regions... Creating peak regions took 42.4171350002 s Estimating background... Estimating background took 27.872120142 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.150876998901 s Creating peak regions... Creating peak regions took 0.246374130249 s Estimating background... Estimating background took 0.70331788063 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.54238700867 s Creating peak regions... Creating peak regions took 46.6497180462 s Estimating background... Estimating background took 37.6748588085 s Processing ZNF141-SRR5197062.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.249051094055 s Creating peak regions... Creating peak regions took 16.6493589878 s Estimating background... Estimating background took 0.782611131668 s