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='ZNF274-SRR5197097.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='ZNF274-SRR5197097/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 ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.54764008522 s Creating peak regions... Creating peak regions took 66.4239010811 s Estimating background... Estimating background took 65.3107459545 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.46309900284 s Creating peak regions... Creating peak regions took 36.3808431625 s Estimating background... Estimating background took 26.4588420391 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.63249206543 s Creating peak regions... Creating peak regions took 35.3188037872 s Estimating background... Estimating background took 25.8628008366 s Processing ZNF274-SRR5197097.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='ZNF274-SRR5197097.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='ZNF274-SRR5197097/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 ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.2666990757 s Creating peak regions... Creating peak regions took 79.9801769257 s Estimating background... Estimating background took 74.8211529255 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.33976888657 s Creating peak regions... Creating peak regions took 41.5050258636 s Estimating background... Estimating background took 28.955714941 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.01773715019 s Creating peak regions... Creating peak regions took 41.5030109882 s Estimating background... Estimating background took 30.5689060688 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.5988740921 s Creating peak regions... Creating peak regions took 46.1384501457 s Estimating background... Estimating background took 31.415979147 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.12107181549 s Creating peak regions... Creating peak regions took 37.5825209618 s Estimating background... Estimating background took 37.3955469131 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.97240805626 s Creating peak regions... Creating peak regions took 33.9981679916 s Estimating background... Estimating background took 19.417703867 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.83700704575 s Creating peak regions... Creating peak regions took 31.6003479958 s Estimating background... Estimating background took 20.5502882004 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.72045612335 s Creating peak regions... Creating peak regions took 28.9114408493 s Estimating background... Estimating background took 18.9196820259 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.9483320713 s Creating peak regions... Creating peak regions took 27.2305600643 s Estimating background... Estimating background took 23.3058409691 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.26516795158 s Creating peak regions... Creating peak regions took 24.4312129021 s Estimating background... Estimating background took 15.9338788986 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.90146112442 s Creating peak regions... Creating peak regions took 19.1622741222 s Estimating background... Estimating background took 14.5275781155 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.14388012886 s Creating peak regions... Creating peak regions took 78.8716051579 s Estimating background... Estimating background took 50.7924921513 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.1318230629 s Creating peak regions... Creating peak regions took 22.5014898777 s Estimating background... Estimating background took 15.5644521713 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.2230091095 s Creating peak regions... Creating peak regions took 14.7736070156 s Estimating background... Estimating background took 9.30357813835 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.56109786034 s Creating peak regions... Creating peak regions took 16.2484018803 s Estimating background... Estimating background took 13.8504087925 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.65313100815 s Creating peak regions... Creating peak regions took 62.9881279469 s Estimating background... Estimating background took 42.5251610279 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.96707105637 s Creating peak regions... Creating peak regions took 61.0625331402 s Estimating background... Estimating background took 31.1777307987 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.3906929493 s Creating peak regions... Creating peak regions took 57.8789660931 s Estimating background... Estimating background took 39.8541259766 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.02123379707 s Creating peak regions... Creating peak regions took 57.4776740074 s Estimating background... Estimating background took 44.5599999428 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.15332102776 s Creating peak regions... Creating peak regions took 52.7121520042 s Estimating background... Estimating background took 38.9556610584 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.34868717194 s Creating peak regions... Creating peak regions took 47.2493579388 s Estimating background... Estimating background took 28.4271337986 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.59651684761 s Creating peak regions... Creating peak regions took 43.5443198681 s Estimating background... Estimating background took 26.0065591335 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.113876104355 s Creating peak regions... Creating peak regions took 0.210711956024 s Estimating background... Estimating background took 0.791549921036 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.52019190788 s Creating peak regions... Creating peak regions took 51.2503528595 s Estimating background... Estimating background took 45.3331370354 s Processing ZNF274-SRR5197097.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.299669981003 s Creating peak regions... Creating peak regions took 16.7004070282 s Estimating background... Estimating background took 0.890377044678 s