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='ZNF627-SRR5197203.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='ZNF627-SRR5197203/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 ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.88865709305 s Creating peak regions... Creating peak regions took 75.4468390942 s Estimating background... Estimating background took 30.833137989 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.26374006271 s Creating peak regions... Creating peak regions took 39.8135988712 s Estimating background... Estimating background took 12.9291279316 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.54200601578 s Creating peak regions... Creating peak regions took 39.052462101 s Estimating background... Estimating background took 12.310459137 s Processing ZNF627-SRR5197203.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='ZNF627-SRR5197203.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='ZNF627-SRR5197203/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 ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.50484919548 s Creating peak regions... Creating peak regions took 73.6928517818 s Estimating background... Estimating background took 30.3371188641 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37989997864 s Creating peak regions... Creating peak regions took 38.6256120205 s Estimating background... Estimating background took 12.5998802185 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28835892677 s Creating peak regions... Creating peak regions took 38.9817519188 s Estimating background... Estimating background took 12.2530851364 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.40944004059 s Creating peak regions... Creating peak regions took 40.6611089706 s Estimating background... Estimating background took 13.067414999 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06259417534 s Creating peak regions... Creating peak regions took 32.9225099087 s Estimating background... Estimating background took 14.4078409672 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.57519578934 s Creating peak regions... Creating peak regions took 29.9554629326 s Estimating background... Estimating background took 8.98731613159 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.54611206055 s Creating peak regions... Creating peak regions took 30.3677728176 s Estimating background... Estimating background took 9.39362597466 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.90671014786 s Creating peak regions... Creating peak regions took 25.5738070011 s Estimating background... Estimating background took 8.84871292114 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.56572794914 s Creating peak regions... Creating peak regions took 25.6691958904 s Estimating background... Estimating background took 10.872396946 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.31653594971 s Creating peak regions... Creating peak regions took 24.0335731506 s Estimating background... Estimating background took 7.05240893364 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.17524385452 s Creating peak regions... Creating peak regions took 17.3466529846 s Estimating background... Estimating background took 7.22816610336 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.88136792183 s Creating peak regions... Creating peak regions took 70.9705650806 s Estimating background... Estimating background took 21.334195137 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.20107698441 s Creating peak regions... Creating peak regions took 18.3445022106 s Estimating background... Estimating background took 7.47676992416 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.661512136459 s Creating peak regions... Creating peak regions took 12.7155468464 s Estimating background... Estimating background took 4.25350308418 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.29203796387 s Creating peak regions... Creating peak regions took 15.5688471794 s Estimating background... Estimating background took 7.34839606285 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.97499990463 s Creating peak regions... Creating peak regions took 55.8869788647 s Estimating background... Estimating background took 16.2172560692 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.64342498779 s Creating peak regions... Creating peak regions took 53.3061270714 s Estimating background... Estimating background took 13.4261779785 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.77770900726 s Creating peak regions... Creating peak regions took 54.919850111 s Estimating background... Estimating background took 15.8673110008 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.09982085228 s Creating peak regions... Creating peak regions took 49.1748161316 s Estimating background... Estimating background took 17.9409248829 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.89011383057 s Creating peak regions... Creating peak regions took 48.7246689796 s Estimating background... Estimating background took 16.4682400227 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32114291191 s Creating peak regions... Creating peak regions took 43.8908348083 s Estimating background... Estimating background took 11.678994894 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.02139401436 s Creating peak regions... Creating peak regions took 41.4394137859 s Estimating background... Estimating background took 11.526291132 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0763380527496 s Creating peak regions... Creating peak regions took 0.151788949966 s Estimating background... Estimating background took 0.566660881042 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.81762313843 s Creating peak regions... Creating peak regions took 47.6663501263 s Estimating background... Estimating background took 16.5101158619 s Processing ZNF627-SRR5197203.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.10674905777 s Creating peak regions... Creating peak regions took 15.5844581127 s Estimating background... Estimating background took 0.696630001068 s