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='ZNF614-SRR5197196.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='ZNF614-SRR5197196/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 ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.27955889702 s Creating peak regions... Creating peak regions took 65.5830950737 s Estimating background... Estimating background took 55.0622110367 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.29100608826 s Creating peak regions... Creating peak regions took 36.2491471767 s Estimating background... Estimating background took 21.8698999882 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.17692112923 s Creating peak regions... Creating peak regions took 35.5255479813 s Estimating background... Estimating background took 21.5831458569 s Processing ZNF614-SRR5197196.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='ZNF614-SRR5197196.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='ZNF614-SRR5197196/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 ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.44525694847 s Creating peak regions... Creating peak regions took 65.2242090702 s Estimating background... Estimating background took 46.6909370422 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.09531402588 s Creating peak regions... Creating peak regions took 34.8255958557 s Estimating background... Estimating background took 18.6021020412 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.97388792038 s Creating peak regions... Creating peak regions took 34.3015639782 s Estimating background... Estimating background took 18.3437829018 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.21126484871 s Creating peak regions... Creating peak regions took 34.3258559704 s Estimating background... Estimating background took 19.340086937 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.90178084373 s Creating peak regions... Creating peak regions took 28.3661370277 s Estimating background... Estimating background took 21.7043819427 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.34985208511 s Creating peak regions... Creating peak regions took 27.1640119553 s Estimating background... Estimating background took 11.8769991398 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.47961997986 s Creating peak regions... Creating peak regions took 29.863462925 s Estimating background... Estimating background took 15.3610320091 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.49761104584 s Creating peak regions... Creating peak regions took 28.2726311684 s Estimating background... Estimating background took 14.1845629215 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.91841197014 s Creating peak regions... Creating peak regions took 27.3518929482 s Estimating background... Estimating background took 17.1246340275 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.13622617722 s Creating peak regions... Creating peak regions took 25.9317750931 s Estimating background... Estimating background took 11.9519610405 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.86290693283 s Creating peak regions... Creating peak regions took 19.03606987 s Estimating background... Estimating background took 10.7471110821 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.72310900688 s Creating peak regions... Creating peak regions took 83.7804880142 s Estimating background... Estimating background took 37.28469491 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.90224599838 s Creating peak regions... Creating peak regions took 21.3864378929 s Estimating background... Estimating background took 11.3660612106 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.57235312462 s Creating peak regions... Creating peak regions took 15.9299819469 s Estimating background... Estimating background took 6.8884677887 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.85579109192 s Creating peak regions... Creating peak regions took 16.0508570671 s Estimating background... Estimating background took 10.5298252106 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.33293700218 s Creating peak regions... Creating peak regions took 63.5027170181 s Estimating background... Estimating background took 30.0230548382 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.77657294273 s Creating peak regions... Creating peak regions took 60.4379599094 s Estimating background... Estimating background took 22.3008019924 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.30534291267 s Creating peak regions... Creating peak regions took 59.3445899487 s Estimating background... Estimating background took 29.9076180458 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.46893215179 s Creating peak regions... Creating peak regions took 57.0276248455 s Estimating background... Estimating background took 33.2434740067 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.04715514183 s Creating peak regions... Creating peak regions took 51.2404010296 s Estimating background... Estimating background took 29.0108549595 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.09372711182 s Creating peak regions... Creating peak regions took 48.1174941063 s Estimating background... Estimating background took 20.5826160908 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.4799849987 s Creating peak regions... Creating peak regions took 44.8098671436 s Estimating background... Estimating background took 19.7868440151 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.157467842102 s Creating peak regions... Creating peak regions took 0.313133955002 s Estimating background... Estimating background took 0.671638011932 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.0655169487 s Creating peak regions... Creating peak regions took 51.4616749287 s Estimating background... Estimating background took 31.5091891289 s Processing ZNF614-SRR5197196.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.319602012634 s Creating peak regions... Creating peak regions took 17.6294519901 s Estimating background... Estimating background took 0.656912088394 s