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='ZNF225-SRR5197085.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='ZNF225-SRR5197085/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 ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.1248049736 s Creating peak regions... Creating peak regions took 78.0654089451 s Estimating background... Estimating background took 75.6777069569 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.9990670681 s Creating peak regions... Creating peak regions took 41.815885067 s Estimating background... Estimating background took 28.3770530224 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.69848608971 s Creating peak regions... Creating peak regions took 37.2818181515 s Estimating background... Estimating background took 26.6135511398 s Processing ZNF225-SRR5197085.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='ZNF225-SRR5197085.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='ZNF225-SRR5197085/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 ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.60956907272 s Creating peak regions... Creating peak regions took 80.1278049946 s Estimating background... Estimating background took 85.7495081425 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.40563702583 s Creating peak regions... Creating peak regions took 44.8339509964 s Estimating background... Estimating background took 34.0994839668 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.42219305038 s Creating peak regions... Creating peak regions took 43.0235879421 s Estimating background... Estimating background took 32.2376909256 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.69697904587 s Creating peak regions... Creating peak regions took 43.5216460228 s Estimating background... Estimating background took 34.818308115 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.39170002937 s Creating peak regions... Creating peak regions took 35.7121348381 s Estimating background... Estimating background took 44.926817894 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.43127298355 s Creating peak regions... Creating peak regions took 35.4449510574 s Estimating background... Estimating background took 23.1266248226 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.11054611206 s Creating peak regions... Creating peak regions took 31.8449838161 s Estimating background... Estimating background took 25.0220890045 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.25800609589 s Creating peak regions... Creating peak regions took 29.4868278503 s Estimating background... Estimating background took 21.3947060108 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.28942394257 s Creating peak regions... Creating peak regions took 28.6367161274 s Estimating background... Estimating background took 25.3757531643 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.50630307198 s Creating peak regions... Creating peak regions took 26.150851965 s Estimating background... Estimating background took 19.1550219059 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.21669483185 s Creating peak regions... Creating peak regions took 19.477025032 s Estimating background... Estimating background took 16.0328888893 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.55807495117 s Creating peak regions... Creating peak regions took 76.8808410168 s Estimating background... Estimating background took 61.4962849617 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.34245991707 s Creating peak regions... Creating peak regions took 23.5024709702 s Estimating background... Estimating background took 16.324354887 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.3278028965 s Creating peak regions... Creating peak regions took 15.7147819996 s Estimating background... Estimating background took 10.181281805 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7163438797 s Creating peak regions... Creating peak regions took 17.7829861641 s Estimating background... Estimating background took 15.6901469231 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.36482405663 s Creating peak regions... Creating peak regions took 67.72853899 s Estimating background... Estimating background took 44.3668680191 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.4642329216 s Creating peak regions... Creating peak regions took 62.5677559376 s Estimating background... Estimating background took 34.7759578228 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.51342701912 s Creating peak regions... Creating peak regions took 49.4381990433 s Estimating background... Estimating background took 40.6187858582 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.03617691994 s Creating peak regions... Creating peak regions took 55.5218532085 s Estimating background... Estimating background took 45.623942852 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.06038379669 s Creating peak regions... Creating peak regions took 46.1555697918 s Estimating background... Estimating background took 35.4616029263 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.57398104668 s Creating peak regions... Creating peak regions took 38.7295658588 s Estimating background... Estimating background took 25.7332820892 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.92046403885 s Creating peak regions... Creating peak regions took 35.9068582058 s Estimating background... Estimating background took 24.0100579262 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.275630950928 s Creating peak regions... Creating peak regions took 0.227230072021 s Estimating background... Estimating background took 0.797575950623 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.46499490738 s Creating peak regions... Creating peak regions took 42.4064588547 s Estimating background... Estimating background took 41.222463131 s Processing ZNF225-SRR5197085.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.247818946838 s Creating peak regions... Creating peak regions took 14.263078928 s Estimating background... Estimating background took 0.882375001907 s