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='ZNF816-SRR5197256.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='ZNF816-SRR5197256/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 ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.42054486275 s Creating peak regions... Creating peak regions took 80.3827800751 s Estimating background... Estimating background took 63.7302420139 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.62496781349 s Creating peak regions... Creating peak regions took 42.9402251244 s Estimating background... Estimating background took 25.1450059414 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.25488615036 s Creating peak regions... Creating peak regions took 38.0329060555 s Estimating background... Estimating background took 21.9668300152 s Processing ZNF816-SRR5197256.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='ZNF816-SRR5197256.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='ZNF816-SRR5197256/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 ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.57607293129 s Creating peak regions... Creating peak regions took 81.1178228855 s Estimating background... Estimating background took 67.2462451458 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.94805288315 s Creating peak regions... Creating peak regions took 46.5183529854 s Estimating background... Estimating background took 26.5279788971 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.94385695457 s Creating peak regions... Creating peak regions took 43.487555027 s Estimating background... Estimating background took 26.3935639858 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.07221078873 s Creating peak regions... Creating peak regions took 42.2094321251 s Estimating background... Estimating background took 27.4856600761 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.37140798569 s Creating peak regions... Creating peak regions took 36.7837300301 s Estimating background... Estimating background took 27.3277680874 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.90324497223 s Creating peak regions... Creating peak regions took 33.2344591618 s Estimating background... Estimating background took 17.4488661289 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.49636888504 s Creating peak regions... Creating peak regions took 33.4806470871 s Estimating background... Estimating background took 19.9648840427 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.7759809494 s Creating peak regions... Creating peak regions took 27.9717731476 s Estimating background... Estimating background took 18.5933511257 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.04870009422 s Creating peak regions... Creating peak regions took 27.0017390251 s Estimating background... Estimating background took 23.1318249702 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.07398700714 s Creating peak regions... Creating peak regions took 24.2402489185 s Estimating background... Estimating background took 13.7793381214 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.10576796532 s Creating peak regions... Creating peak regions took 18.9477050304 s Estimating background... Estimating background took 15.1886138916 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.52450489998 s Creating peak regions... Creating peak regions took 82.6578421593 s Estimating background... Estimating background took 43.3286049366 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.12585878372 s Creating peak regions... Creating peak regions took 21.7739121914 s Estimating background... Estimating background took 15.157749176 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.4083211422 s Creating peak regions... Creating peak regions took 14.6957130432 s Estimating background... Estimating background took 8.50404596329 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.6212720871 s Creating peak regions... Creating peak regions took 15.3029389381 s Estimating background... Estimating background took 14.9486470222 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.07858586311 s Creating peak regions... Creating peak regions took 62.1627590656 s Estimating background... Estimating background took 33.8353960514 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.51452302933 s Creating peak regions... Creating peak regions took 59.0395350456 s Estimating background... Estimating background took 25.1687550545 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.93585109711 s Creating peak regions... Creating peak regions took 57.0642380714 s Estimating background... Estimating background took 33.7381589413 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.27933883667 s Creating peak regions... Creating peak regions took 55.1588299274 s Estimating background... Estimating background took 37.0655429363 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.76922082901 s Creating peak regions... Creating peak regions took 51.2326178551 s Estimating background... Estimating background took 33.9703700542 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.88251018524 s Creating peak regions... Creating peak regions took 44.7651720047 s Estimating background... Estimating background took 23.2596600056 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.26219916344 s Creating peak regions... Creating peak regions took 41.6869878769 s Estimating background... Estimating background took 21.9881739616 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.112959861755 s Creating peak regions... Creating peak regions took 0.198558092117 s Estimating background... Estimating background took 0.783040046692 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.68960094452 s Creating peak regions... Creating peak regions took 46.2145209312 s Estimating background... Estimating background took 33.1288352013 s Processing ZNF816-SRR5197256.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.175231933594 s Creating peak regions... Creating peak regions took 14.2703471184 s Estimating background... Estimating background took 0.812813043594 s