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='ZNF182-SRR5197070.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='ZNF182-SRR5197070/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 ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.15679693222 s Creating peak regions... Creating peak regions took 78.1112780571 s Estimating background... Estimating background took 76.2218761444 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.20286512375 s Creating peak regions... Creating peak regions took 42.0453948975 s Estimating background... Estimating background took 30.9486861229 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.23241996765 s Creating peak regions... Creating peak regions took 41.2078549862 s Estimating background... Estimating background took 30.0020699501 s Processing ZNF182-SRR5197070.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='ZNF182-SRR5197070.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='ZNF182-SRR5197070/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 ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.21051287651 s Creating peak regions... Creating peak regions took 74.7996850014 s Estimating background... Estimating background took 71.0691490173 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.93159389496 s Creating peak regions... Creating peak regions took 40.4000549316 s Estimating background... Estimating background took 28.9868569374 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.9129691124 s Creating peak regions... Creating peak regions took 40.1218550205 s Estimating background... Estimating background took 29.2413330078 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.05603218079 s Creating peak regions... Creating peak regions took 38.3596789837 s Estimating background... Estimating background took 31.9297349453 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.51743602753 s Creating peak regions... Creating peak regions took 33.3876821995 s Estimating background... Estimating background took 29.6323971748 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.59025192261 s Creating peak regions... Creating peak regions took 31.2740869522 s Estimating background... Estimating background took 19.8258788586 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.56856703758 s Creating peak regions... Creating peak regions took 29.6964130402 s Estimating background... Estimating background took 21.8370630741 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.8140630722 s Creating peak regions... Creating peak regions took 27.0484290123 s Estimating background... Estimating background took 21.5064330101 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.24973511696 s Creating peak regions... Creating peak regions took 24.7260241508 s Estimating background... Estimating background took 28.2591159344 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.12704586983 s Creating peak regions... Creating peak regions took 23.3079879284 s Estimating background... Estimating background took 14.4823980331 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.22400712967 s Creating peak regions... Creating peak regions took 19.0938119888 s Estimating background... Estimating background took 19.6370401382 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.60570907593 s Creating peak regions... Creating peak regions took 72.2547130585 s Estimating background... Estimating background took 47.9250919819 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32061290741 s Creating peak regions... Creating peak regions took 21.5096261501 s Estimating background... Estimating background took 18.8272931576 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.31291699409 s Creating peak regions... Creating peak regions took 13.6625270844 s Estimating background... Estimating background took 8.85212182999 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.73066115379 s Creating peak regions... Creating peak regions took 15.0947310925 s Estimating background... Estimating background took 17.7610831261 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.15937995911 s Creating peak regions... Creating peak regions took 58.7840349674 s Estimating background... Estimating background took 39.679569006 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.56139993668 s Creating peak regions... Creating peak regions took 55.728782177 s Estimating background... Estimating background took 29.6603369713 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.00398588181 s Creating peak regions... Creating peak regions took 52.2974119186 s Estimating background... Estimating background took 37.6299438477 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.80499696732 s Creating peak regions... Creating peak regions took 53.4429898262 s Estimating background... Estimating background took 43.0356891155 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.25375199318 s Creating peak regions... Creating peak regions took 49.7834830284 s Estimating background... Estimating background took 39.5436937809 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.97709512711 s Creating peak regions... Creating peak regions took 43.7948279381 s Estimating background... Estimating background took 25.5205321312 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.36847305298 s Creating peak regions... Creating peak regions took 38.8973450661 s Estimating background... Estimating background took 26.1108710766 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.140691995621 s Creating peak regions... Creating peak regions took 0.1830098629 s Estimating background... Estimating background took 0.737071990967 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.52792811394 s Creating peak regions... Creating peak regions took 45.798030138 s Estimating background... Estimating background took 32.5145840645 s Processing ZNF182-SRR5197070.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.191066026688 s Creating peak regions... Creating peak regions took 15.1150791645 s Estimating background... Estimating background took 0.700534105301 s