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='ZNF84-SRR5197260.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='ZNF84-SRR5197260/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 ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.39449119568 s Creating peak regions... Creating peak regions took 77.0551009178 s Estimating background... Estimating background took 34.590321064 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.76645898819 s Creating peak regions... Creating peak regions took 39.7485091686 s Estimating background... Estimating background took 13.8703560829 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.5509750843 s Creating peak regions... Creating peak regions took 38.6230318546 s Estimating background... Estimating background took 13.6827628613 s Processing ZNF84-SRR5197260.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='ZNF84-SRR5197260.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='ZNF84-SRR5197260/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 ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.11041688919 s Creating peak regions... Creating peak regions took 77.6393470764 s Estimating background... Estimating background took 35.2677640915 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.68472194672 s Creating peak regions... Creating peak regions took 39.894536972 s Estimating background... Estimating background took 14.2145330906 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.46907114983 s Creating peak regions... Creating peak regions took 40.1536941528 s Estimating background... Estimating background took 14.3796670437 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53884601593 s Creating peak regions... Creating peak regions took 39.8142290115 s Estimating background... Estimating background took 15.1696610451 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.36244893074 s Creating peak regions... Creating peak regions took 34.1250030994 s Estimating background... Estimating background took 17.0280299187 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.79834008217 s Creating peak regions... Creating peak regions took 31.4105172157 s Estimating background... Estimating background took 10.0763301849 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.6216981411 s Creating peak regions... Creating peak regions took 29.5965881348 s Estimating background... Estimating background took 10.2764661312 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.706346035 s Creating peak regions... Creating peak regions took 27.8635640144 s Estimating background... Estimating background took 9.25091910362 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.76346206665 s Creating peak regions... Creating peak regions took 24.884542942 s Estimating background... Estimating background took 11.1714940071 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.55563306808 s Creating peak regions... Creating peak regions took 25.1858980656 s Estimating background... Estimating background took 8.47799801826 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.37444400787 s Creating peak regions... Creating peak regions took 17.5064330101 s Estimating background... Estimating background took 7.21823000908 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.11882686615 s Creating peak regions... Creating peak regions took 71.6447179317 s Estimating background... Estimating background took 22.8071980476 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.33172893524 s Creating peak regions... Creating peak regions took 20.0406010151 s Estimating background... Estimating background took 8.01906085014 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.793646812439 s Creating peak regions... Creating peak regions took 14.6639719009 s Estimating background... Estimating background took 4.58864116669 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.04694604874 s Creating peak regions... Creating peak regions took 15.8240430355 s Estimating background... Estimating background took 6.47947001457 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.59652519226 s Creating peak regions... Creating peak regions took 59.1579191685 s Estimating background... Estimating background took 19.581236124 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.89968109131 s Creating peak regions... Creating peak regions took 59.3242070675 s Estimating background... Estimating background took 15.1472759247 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.48493695259 s Creating peak regions... Creating peak regions took 53.9405481815 s Estimating background... Estimating background took 19.4618349075 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.68671107292 s Creating peak regions... Creating peak regions took 52.1077029705 s Estimating background... Estimating background took 22.4186649323 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.34009099007 s Creating peak regions... Creating peak regions took 48.2684640884 s Estimating background... Estimating background took 18.8160510063 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53664302826 s Creating peak regions... Creating peak regions took 43.458122015 s Estimating background... Estimating background took 13.0879070759 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.26323699951 s Creating peak regions... Creating peak regions took 40.7273919582 s Estimating background... Estimating background took 12.7460849285 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.081827878952 s Creating peak regions... Creating peak regions took 0.170222043991 s Estimating background... Estimating background took 0.66871714592 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.28243803978 s Creating peak regions... Creating peak regions took 49.1338100433 s Estimating background... Estimating background took 18.8467228413 s Processing ZNF84-SRR5197260.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.105885028839 s Creating peak regions... Creating peak regions took 16.0969188213 s Estimating background... Estimating background took 0.58825302124 s