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='ZNF287-SRR5197103.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='ZNF287-SRR5197103/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 ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 10.5152029991 s Creating peak regions... Creating peak regions took 83.9704189301 s Estimating background... Estimating background took 176.586470127 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.40501594543 s Creating peak regions... Creating peak regions took 45.9272110462 s Estimating background... Estimating background took 61.4764699936 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.02015280724 s Creating peak regions... Creating peak regions took 40.5947110653 s Estimating background... Estimating background took 55.3832759857 s Processing ZNF287-SRR5197103.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='ZNF287-SRR5197103.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='ZNF287-SRR5197103/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 ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 13.4408559799 s Creating peak regions... Creating peak regions took 90.0167410374 s Estimating background... Estimating background took 148.874078035 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.32199501991 s Creating peak regions... Creating peak regions took 40.793473959 s Estimating background... Estimating background took 56.1337409019 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.48056006432 s Creating peak regions... Creating peak regions took 38.2155070305 s Estimating background... Estimating background took 54.7780148983 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.94156599045 s Creating peak regions... Creating peak regions took 40.9720368385 s Estimating background... Estimating background took 61.658531189 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.3779630661 s Creating peak regions... Creating peak regions took 36.2010400295 s Estimating background... Estimating background took 66.8173439503 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.06801795959 s Creating peak regions... Creating peak regions took 31.7201700211 s Estimating background... Estimating background took 39.102191925 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.24483203888 s Creating peak regions... Creating peak regions took 29.6537029743 s Estimating background... Estimating background took 40.5488271713 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.56430315971 s Creating peak regions... Creating peak regions took 26.3888449669 s Estimating background... Estimating background took 35.660736084 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.08764600754 s Creating peak regions... Creating peak regions took 25.5449578762 s Estimating background... Estimating background took 43.7197799683 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.46184515953 s Creating peak regions... Creating peak regions took 23.7388651371 s Estimating background... Estimating background took 29.7821428776 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.94807004929 s Creating peak regions... Creating peak regions took 18.408288002 s Estimating background... Estimating background took 26.9991700649 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.36955904961 s Creating peak regions... Creating peak regions took 71.9579720497 s Estimating background... Estimating background took 97.9579589367 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.88181185722 s Creating peak regions... Creating peak regions took 21.8358590603 s Estimating background... Estimating background took 30.3294980526 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.6183590889 s Creating peak regions... Creating peak regions took 13.651679039 s Estimating background... Estimating background took 16.5809788704 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39947295189 s Creating peak regions... Creating peak regions took 14.1473050117 s Estimating background... Estimating background took 26.4118878841 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.43705391884 s Creating peak regions... Creating peak regions took 56.8794801235 s Estimating background... Estimating background took 78.0653460026 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.59206604958 s Creating peak regions... Creating peak regions took 55.1011719704 s Estimating background... Estimating background took 63.1938369274 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.47433114052 s Creating peak regions... Creating peak regions took 54.451982975 s Estimating background... Estimating background took 73.6068711281 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.8907828331 s Creating peak regions... Creating peak regions took 52.9139780998 s Estimating background... Estimating background took 83.6304068565 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.81361699104 s Creating peak regions... Creating peak regions took 48.9274940491 s Estimating background... Estimating background took 73.4401671886 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.72494292259 s Creating peak regions... Creating peak regions took 43.5046858788 s Estimating background... Estimating background took 52.1258459091 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.81651496887 s Creating peak regions... Creating peak regions took 40.1743879318 s Estimating background... Estimating background took 49.4391717911 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.233059167862 s Creating peak regions... Creating peak regions took 0.342355966568 s Estimating background... Estimating background took 0.652316093445 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.99201393127 s Creating peak regions... Creating peak regions took 47.1619608402 s Estimating background... Estimating background took 81.9968800545 s Processing ZNF287-SRR5197103.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.496891021729 s Creating peak regions... Creating peak regions took 15.2691409588 s Estimating background... Estimating background took 1.24887013435 s