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='ZNF331-SRR5197115.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='ZNF331-SRR5197115/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 ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.77983999252 s Creating peak regions... Creating peak regions took 62.1795959473 s Estimating background... Estimating background took 31.8316829205 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28800988197 s Creating peak regions... Creating peak regions took 33.4999940395 s Estimating background... Estimating background took 12.8636300564 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32265305519 s Creating peak regions... Creating peak regions took 33.4910409451 s Estimating background... Estimating background took 13.6090040207 s Processing ZNF331-SRR5197115.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='ZNF331-SRR5197115.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='ZNF331-SRR5197115/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 ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.75298690796 s Creating peak regions... Creating peak regions took 74.015075922 s Estimating background... Estimating background took 38.5481979847 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.92110204697 s Creating peak regions... Creating peak regions took 41.0825521946 s Estimating background... Estimating background took 14.6101241112 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.56828093529 s Creating peak regions... Creating peak regions took 40.9656689167 s Estimating background... Estimating background took 15.7412719727 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.83933281898 s Creating peak regions... Creating peak regions took 41.3014030457 s Estimating background... Estimating background took 16.5710060596 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.44050502777 s Creating peak regions... Creating peak regions took 33.6927769184 s Estimating background... Estimating background took 15.7531700134 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.9155459404 s Creating peak regions... Creating peak regions took 31.3954811096 s Estimating background... Estimating background took 10.4429409504 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.66514706612 s Creating peak regions... Creating peak regions took 29.0204632282 s Estimating background... Estimating background took 10.7810890675 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.86723709106 s Creating peak regions... Creating peak regions took 27.3171260357 s Estimating background... Estimating background took 10.6965348721 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24589419365 s Creating peak regions... Creating peak regions took 26.5295500755 s Estimating background... Estimating background took 14.1996209621 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.52480721474 s Creating peak regions... Creating peak regions took 24.3681008816 s Estimating background... Estimating background took 8.11238002777 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.54248785973 s Creating peak regions... Creating peak regions took 18.3971600533 s Estimating background... Estimating background took 9.96392703056 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.55952000618 s Creating peak regions... Creating peak regions took 76.8513309956 s Estimating background... Estimating background took 25.9222249985 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.65559601784 s Creating peak regions... Creating peak regions took 21.2721810341 s Estimating background... Estimating background took 9.86263394356 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.907436847687 s Creating peak regions... Creating peak regions took 14.0541949272 s Estimating background... Estimating background took 5.03983306885 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.16415095329 s Creating peak regions... Creating peak regions took 15.709428072 s Estimating background... Estimating background took 8.94481492043 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.6526889801 s Creating peak regions... Creating peak regions took 63.1159899235 s Estimating background... Estimating background took 19.1201248169 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.92502689362 s Creating peak regions... Creating peak regions took 54.3683869839 s Estimating background... Estimating background took 15.6956942081 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.54513812065 s Creating peak regions... Creating peak regions took 59.0944979191 s Estimating background... Estimating background took 20.0982241631 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.15372490883 s Creating peak regions... Creating peak regions took 52.0313718319 s Estimating background... Estimating background took 21.7996258736 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.49515295029 s Creating peak regions... Creating peak regions took 53.115044117 s Estimating background... Estimating background took 18.9300248623 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.77811694145 s Creating peak regions... Creating peak regions took 43.5725529194 s Estimating background... Estimating background took 13.7293748856 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.43827295303 s Creating peak regions... Creating peak regions took 40.9308168888 s Estimating background... Estimating background took 12.9808549881 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0920579433441 s Creating peak regions... Creating peak regions took 0.164494991302 s Estimating background... Estimating background took 0.672444105148 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.44105410576 s Creating peak regions... Creating peak regions took 42.1851329803 s Estimating background... Estimating background took 16.7340159416 s Processing ZNF331-SRR5197115.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.118301868439 s Creating peak regions... Creating peak regions took 13.2965419292 s Estimating background... Estimating background took 0.516679048538 s