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='ZNF749-SRR5197229.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='ZNF749-SRR5197229/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 ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.36711406708 s Creating peak regions... Creating peak regions took 77.1858160496 s Estimating background... Estimating background took 39.3897049427 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.96245789528 s Creating peak regions... Creating peak regions took 42.6981170177 s Estimating background... Estimating background took 17.4030170441 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.97358202934 s Creating peak regions... Creating peak regions took 41.0027630329 s Estimating background... Estimating background took 16.9474279881 s Processing ZNF749-SRR5197229.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='ZNF749-SRR5197229.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='ZNF749-SRR5197229/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 ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.31212592125 s Creating peak regions... Creating peak regions took 77.3441138268 s Estimating background... Estimating background took 38.6345591545 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.00155377388 s Creating peak regions... Creating peak regions took 40.6604549885 s Estimating background... Estimating background took 17.1553890705 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.99599599838 s Creating peak regions... Creating peak regions took 40.5354130268 s Estimating background... Estimating background took 17.5261991024 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.28223204613 s Creating peak regions... Creating peak regions took 40.2061731815 s Estimating background... Estimating background took 18.1575911045 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.59893798828 s Creating peak regions... Creating peak regions took 34.6116812229 s Estimating background... Estimating background took 17.0580670834 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.07411599159 s Creating peak regions... Creating peak regions took 30.0565838814 s Estimating background... Estimating background took 11.9928700924 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.958548069 s Creating peak regions... Creating peak regions took 29.7219059467 s Estimating background... Estimating background took 11.2783250809 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.03118014336 s Creating peak regions... Creating peak regions took 28.7500917912 s Estimating background... Estimating background took 12.4533650875 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39167404175 s Creating peak regions... Creating peak regions took 25.6856219769 s Estimating background... Estimating background took 15.5789129734 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.5120549202 s Creating peak regions... Creating peak regions took 23.9676659107 s Estimating background... Estimating background took 8.38535714149 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.62155294418 s Creating peak regions... Creating peak regions took 17.933013916 s Estimating background... Estimating background took 10.3375740051 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.97242093086 s Creating peak regions... Creating peak regions took 79.0447280407 s Estimating background... Estimating background took 28.9368431568 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.78013801575 s Creating peak regions... Creating peak regions took 21.2003018856 s Estimating background... Estimating background took 11.5380909443 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.945145130157 s Creating peak regions... Creating peak regions took 15.0034279823 s Estimating background... Estimating background took 5.4230029583 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.32943892479 s Creating peak regions... Creating peak regions took 16.3421499729 s Estimating background... Estimating background took 9.94338107109 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.06773996353 s Creating peak regions... Creating peak regions took 62.7129359245 s Estimating background... Estimating background took 23.9804828167 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.48965501785 s Creating peak regions... Creating peak regions took 56.6950728893 s Estimating background... Estimating background took 18.2327420712 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.98056912422 s Creating peak regions... Creating peak regions took 54.9019889832 s Estimating background... Estimating background took 23.6656141281 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.13352894783 s Creating peak regions... Creating peak regions took 52.384553194 s Estimating background... Estimating background took 24.4207069874 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.37715697289 s Creating peak regions... Creating peak regions took 47.9819309711 s Estimating background... Estimating background took 19.1237790585 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.0786819458 s Creating peak regions... Creating peak regions took 43.6187019348 s Estimating background... Estimating background took 15.7148427963 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.5625140667 s Creating peak regions... Creating peak regions took 43.4958770275 s Estimating background... Estimating background took 15.595405817 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0965669155121 s Creating peak regions... Creating peak regions took 0.191134929657 s Estimating background... Estimating background took 0.788990974426 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.45875597 s Creating peak regions... Creating peak regions took 46.8683590889 s Estimating background... Estimating background took 20.9250910282 s Processing ZNF749-SRR5197229.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.118334054947 s Creating peak regions... Creating peak regions took 16.3619787693 s Estimating background... Estimating background took 0.667526960373 s