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='ZNF69-SRR5197219.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='ZNF69-SRR5197219/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 ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.98252606392 s Creating peak regions... Creating peak regions took 75.1441509724 s Estimating background... Estimating background took 23.2580571175 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06903505325 s Creating peak regions... Creating peak regions took 41.1914520264 s Estimating background... Estimating background took 10.4035520554 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98020005226 s Creating peak regions... Creating peak regions took 41.5565891266 s Estimating background... Estimating background took 10.1311810017 s Processing ZNF69-SRR5197219.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='ZNF69-SRR5197219.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='ZNF69-SRR5197219/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 ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.79228687286 s Creating peak regions... Creating peak regions took 70.6604659557 s Estimating background... Estimating background took 22.2267200947 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.83486700058 s Creating peak regions... Creating peak regions took 42.5691530704 s Estimating background... Estimating background took 10.1692199707 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.00304794312 s Creating peak regions... Creating peak regions took 47.7438249588 s Estimating background... Estimating background took 9.6190469265 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.14791989326 s Creating peak regions... Creating peak regions took 39.8257761002 s Estimating background... Estimating background took 9.86992406845 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.59395503998 s Creating peak regions... Creating peak regions took 36.1484189034 s Estimating background... Estimating background took 10.0764579773 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.5027410984 s Creating peak regions... Creating peak regions took 34.3293538094 s Estimating background... Estimating background took 7.03436899185 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.22794985771 s Creating peak regions... Creating peak regions took 29.8838429451 s Estimating background... Estimating background took 7.49530100822 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.34118199348 s Creating peak regions... Creating peak regions took 27.7869331837 s Estimating background... Estimating background took 6.81933498383 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.55707883835 s Creating peak regions... Creating peak regions took 26.1235711575 s Estimating background... Estimating background took 8.17447304726 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.05622291565 s Creating peak regions... Creating peak regions took 23.2145841122 s Estimating background... Estimating background took 5.50290298462 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.16985607147 s Creating peak regions... Creating peak regions took 18.338613987 s Estimating background... Estimating background took 5.3804628849 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.24800610542 s Creating peak regions... Creating peak regions took 76.8879389763 s Estimating background... Estimating background took 16.5330018997 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.08886003494 s Creating peak regions... Creating peak regions took 20.6072130203 s Estimating background... Estimating background took 5.98349690437 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.693773984909 s Creating peak regions... Creating peak regions took 14.6364779472 s Estimating background... Estimating background took 3.67379808426 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.829934835434 s Creating peak regions... Creating peak regions took 15.6130349636 s Estimating background... Estimating background took 5.53481507301 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.99286603928 s Creating peak regions... Creating peak regions took 65.3594172001 s Estimating background... Estimating background took 12.1520998478 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.40479516983 s Creating peak regions... Creating peak regions took 62.3582129478 s Estimating background... Estimating background took 10.2626609802 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.95177793503 s Creating peak regions... Creating peak regions took 57.1742601395 s Estimating background... Estimating background took 12.101282835 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.59374499321 s Creating peak regions... Creating peak regions took 55.9961049557 s Estimating background... Estimating background took 13.714908123 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.59771299362 s Creating peak regions... Creating peak regions took 49.8944070339 s Estimating background... Estimating background took 12.877491951 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98700094223 s Creating peak regions... Creating peak regions took 41.7670869827 s Estimating background... Estimating background took 9.45304179192 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.76880097389 s Creating peak regions... Creating peak regions took 41.0236909389 s Estimating background... Estimating background took 8.60135698318 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0897479057312 s Creating peak regions... Creating peak regions took 0.145419120789 s Estimating background... Estimating background took 1.21561598778 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.25800800323 s Creating peak regions... Creating peak regions took 46.0387439728 s Estimating background... Estimating background took 11.9508600235 s Processing ZNF69-SRR5197219.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.120880842209 s Creating peak regions... Creating peak regions took 16.308786869 s Estimating background... Estimating background took 0.610720157623 s