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='ZNF180-SRR5197068.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='ZNF180-SRR5197068/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 ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.27834606171 s Creating peak regions... Creating peak regions took 77.2145819664 s Estimating background... Estimating background took 58.1530981064 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.30497503281 s Creating peak regions... Creating peak regions took 40.811152935 s Estimating background... Estimating background took 21.7402999401 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.4112970829 s Creating peak regions... Creating peak regions took 40.5469841957 s Estimating background... Estimating background took 22.9484198093 s Processing ZNF180-SRR5197068.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='ZNF180-SRR5197068.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='ZNF180-SRR5197068/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 ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.69701004028 s Creating peak regions... Creating peak regions took 71.120098114 s Estimating background... Estimating background took 54.3300938606 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.9580078125 s Creating peak regions... Creating peak regions took 37.8065350056 s Estimating background... Estimating background took 20.6771068573 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.03788614273 s Creating peak regions... Creating peak regions took 38.2368528843 s Estimating background... Estimating background took 22.0418200493 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.20994091034 s Creating peak regions... Creating peak regions took 36.6536040306 s Estimating background... Estimating background took 22.9924829006 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.43102788925 s Creating peak regions... Creating peak regions took 30.0271699429 s Estimating background... Estimating background took 20.0702660084 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37405586243 s Creating peak regions... Creating peak regions took 28.876251936 s Estimating background... Estimating background took 14.5577340126 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.65855312347 s Creating peak regions... Creating peak regions took 29.0371179581 s Estimating background... Estimating background took 15.3380219936 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.13883900642 s Creating peak regions... Creating peak regions took 24.8811769485 s Estimating background... Estimating background took 16.5862429142 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53387498856 s Creating peak regions... Creating peak regions took 23.8403229713 s Estimating background... Estimating background took 20.369519949 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.25966095924 s Creating peak regions... Creating peak regions took 21.9693489075 s Estimating background... Estimating background took 9.9523229599 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.02033782005 s Creating peak regions... Creating peak regions took 18.1877219677 s Estimating background... Estimating background took 13.9411549568 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.68094992638 s Creating peak regions... Creating peak regions took 70.5849490166 s Estimating background... Estimating background took 34.7487819195 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.87415122986 s Creating peak regions... Creating peak regions took 19.3971660137 s Estimating background... Estimating background took 13.2361249924 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.942745923996 s Creating peak regions... Creating peak regions took 12.867672205 s Estimating background... Estimating background took 6.94856905937 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.41431212425 s Creating peak regions... Creating peak regions took 15.4239521027 s Estimating background... Estimating background took 13.5149021149 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.05218195915 s Creating peak regions... Creating peak regions took 57.9955770969 s Estimating background... Estimating background took 27.4997909069 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.31184697151 s Creating peak regions... Creating peak regions took 51.0053451061 s Estimating background... Estimating background took 20.2823429108 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.79299902916 s Creating peak regions... Creating peak regions took 49.3912959099 s Estimating background... Estimating background took 26.9886419773 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.08766198158 s Creating peak regions... Creating peak regions took 47.9848918915 s Estimating background... Estimating background took 29.6371080875 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.80264687538 s Creating peak regions... Creating peak regions took 42.6531429291 s Estimating background... Estimating background took 27.4653990269 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.00821590424 s Creating peak regions... Creating peak regions took 40.3529448509 s Estimating background... Estimating background took 18.5459640026 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.73180508614 s Creating peak regions... Creating peak regions took 37.4359529018 s Estimating background... Estimating background took 19.161605835 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.105004787445 s Creating peak regions... Creating peak regions took 0.196571111679 s Estimating background... Estimating background took 0.534918069839 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.84585881233 s Creating peak regions... Creating peak regions took 43.1712040901 s Estimating background... Estimating background took 27.8415939808 s Processing ZNF180-SRR5197068.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.198714971542 s Creating peak regions... Creating peak regions took 15.0539929867 s Estimating background... Estimating background took 0.66788983345 s