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='ZNF320-SRR5197112.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='ZNF320-SRR5197112/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 ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.27196216583 s Creating peak regions... Creating peak regions took 84.3565030098 s Estimating background... Estimating background took 104.96061182 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.07079386711 s Creating peak regions... Creating peak regions took 44.0350029469 s Estimating background... Estimating background took 36.5224020481 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.39589691162 s Creating peak regions... Creating peak regions took 39.1601750851 s Estimating background... Estimating background took 36.3977618217 s Processing ZNF320-SRR5197112.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='ZNF320-SRR5197112.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='ZNF320-SRR5197112/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 ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.9764611721 s Creating peak regions... Creating peak regions took 82.7931540012 s Estimating background... Estimating background took 106.05664587 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.81870698929 s Creating peak regions... Creating peak regions took 46.3602919579 s Estimating background... Estimating background took 42.2101719379 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.11906886101 s Creating peak regions... Creating peak regions took 44.3217179775 s Estimating background... Estimating background took 42.6445000172 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.29631900787 s Creating peak regions... Creating peak regions took 45.1425909996 s Estimating background... Estimating background took 42.8270020485 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.31431698799 s Creating peak regions... Creating peak regions took 37.1414542198 s Estimating background... Estimating background took 42.3855412006 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.68984007835 s Creating peak regions... Creating peak regions took 34.8232469559 s Estimating background... Estimating background took 27.3072371483 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.45163106918 s Creating peak regions... Creating peak regions took 34.0627379417 s Estimating background... Estimating background took 31.2279310226 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.7148308754 s Creating peak regions... Creating peak regions took 30.4139580727 s Estimating background... Estimating background took 30.0343370438 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.01136207581 s Creating peak regions... Creating peak regions took 29.0592489243 s Estimating background... Estimating background took 38.4928228855 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.6841070652 s Creating peak regions... Creating peak regions took 25.9221692085 s Estimating background... Estimating background took 19.2512450218 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.70055103302 s Creating peak regions... Creating peak regions took 20.2013008595 s Estimating background... Estimating background took 26.2581989765 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.44403886795 s Creating peak regions... Creating peak regions took 81.1737949848 s Estimating background... Estimating background took 71.7450020313 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.0782752037 s Creating peak regions... Creating peak regions took 24.7372851372 s Estimating background... Estimating background took 26.0851280689 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.64944505692 s Creating peak regions... Creating peak regions took 15.0497629642 s Estimating background... Estimating background took 12.8451662064 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.19273781776 s Creating peak regions... Creating peak regions took 17.0584640503 s Estimating background... Estimating background took 24.1343820095 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.90630102158 s Creating peak regions... Creating peak regions took 64.1527459621 s Estimating background... Estimating background took 48.2628390789 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.4622220993 s Creating peak regions... Creating peak regions took 48.6245839596 s Estimating background... Estimating background took 31.8133618832 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.43116593361 s Creating peak regions... Creating peak regions took 59.2028100491 s Estimating background... Estimating background took 50.3486728668 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.23950600624 s Creating peak regions... Creating peak regions took 51.505753994 s Estimating background... Estimating background took 50.7220900059 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.19165611267 s Creating peak regions... Creating peak regions took 45.6439368725 s Estimating background... Estimating background took 44.2812299728 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.24716901779 s Creating peak regions... Creating peak regions took 39.6004610062 s Estimating background... Estimating background took 29.4130551815 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.46698117256 s Creating peak regions... Creating peak regions took 37.1095519066 s Estimating background... Estimating background took 29.6707220078 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.175196170807 s Creating peak regions... Creating peak regions took 0.262833118439 s Estimating background... Estimating background took 0.540569067001 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.82882595062 s Creating peak regions... Creating peak regions took 43.1061849594 s Estimating background... Estimating background took 43.900840044 s Processing ZNF320-SRR5197112.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.290259122849 s Creating peak regions... Creating peak regions took 14.4825720787 s Estimating background... Estimating background took 0.998884916306 s