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='ZNF525-SRR5197162.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='ZNF525-SRR5197162/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 ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.35298705101 s Creating peak regions... Creating peak regions took 77.0877189636 s Estimating background... Estimating background took 26.7175610065 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.03193902969 s Creating peak regions... Creating peak regions took 40.0556411743 s Estimating background... Estimating background took 10.4247570038 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06130194664 s Creating peak regions... Creating peak regions took 40.4688501358 s Estimating background... Estimating background took 10.5891299248 s Processing ZNF525-SRR5197162.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='ZNF525-SRR5197162.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='ZNF525-SRR5197162/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 ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.36970090866 s Creating peak regions... Creating peak regions took 74.9787609577 s Estimating background... Estimating background took 27.7380127907 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.11454200745 s Creating peak regions... Creating peak regions took 38.6202471256 s Estimating background... Estimating background took 10.1577410698 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.17141413689 s Creating peak regions... Creating peak regions took 40.1217041016 s Estimating background... Estimating background took 11.0503590107 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.25117492676 s Creating peak regions... Creating peak regions took 39.6066420078 s Estimating background... Estimating background took 10.2836670876 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.02671909332 s Creating peak regions... Creating peak regions took 35.8327171803 s Estimating background... Estimating background took 12.7274041176 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.48137593269 s Creating peak regions... Creating peak regions took 30.6510281563 s Estimating background... Estimating background took 7.49841809273 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.37929701805 s Creating peak regions... Creating peak regions took 30.3197119236 s Estimating background... Estimating background took 8.25761389732 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.30004692078 s Creating peak regions... Creating peak regions took 25.2109270096 s Estimating background... Estimating background took 7.31871891022 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.50742411613 s Creating peak regions... Creating peak regions took 26.2117049694 s Estimating background... Estimating background took 8.92338895798 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.15984797478 s Creating peak regions... Creating peak regions took 23.6730101109 s Estimating background... Estimating background took 6.24115085602 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.16793298721 s Creating peak regions... Creating peak regions took 18.8517289162 s Estimating background... Estimating background took 6.24566888809 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.67622613907 s Creating peak regions... Creating peak regions took 76.9104540348 s Estimating background... Estimating background took 18.5828139782 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.2051050663 s Creating peak regions... Creating peak regions took 21.5172848701 s Estimating background... Estimating background took 6.26785802841 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.678796052933 s Creating peak regions... Creating peak regions took 14.7193520069 s Estimating background... Estimating background took 3.73039984703 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.75152182579 s Creating peak regions... Creating peak regions took 14.58056283 s Estimating background... Estimating background took 5.48784589767 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.78280210495 s Creating peak regions... Creating peak regions took 61.415913105 s Estimating background... Estimating background took 14.257953167 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45853900909 s Creating peak regions... Creating peak regions took 54.0576899052 s Estimating background... Estimating background took 11.4185140133 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.74205899239 s Creating peak regions... Creating peak regions took 52.899394989 s Estimating background... Estimating background took 14.4446690083 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.90917611122 s Creating peak regions... Creating peak regions took 54.4210848808 s Estimating background... Estimating background took 14.8625071049 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.67244911194 s Creating peak regions... Creating peak regions took 47.4459850788 s Estimating background... Estimating background took 14.4904978275 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24018216133 s Creating peak regions... Creating peak regions took 46.3266170025 s Estimating background... Estimating background took 9.63938188553 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.87914514542 s Creating peak regions... Creating peak regions took 42.1838247776 s Estimating background... Estimating background took 10.0492069721 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0962870121002 s Creating peak regions... Creating peak regions took 0.200990200043 s Estimating background... Estimating background took 0.644273996353 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.86717700958 s Creating peak regions... Creating peak regions took 46.2221181393 s Estimating background... Estimating background took 15.3841099739 s Processing ZNF525-SRR5197162.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.103636026382 s Creating peak regions... Creating peak regions took 15.8176789284 s Estimating background... Estimating background took 0.590855121613 s