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='ZNF785-SRR5197243.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='ZNF785-SRR5197243/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 ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.25459718704 s Creating peak regions... Creating peak regions took 75.918227911 s Estimating background... Estimating background took 27.2372200489 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.14517211914 s Creating peak regions... Creating peak regions took 40.0443520546 s Estimating background... Estimating background took 11.3938479424 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.0984890461 s Creating peak regions... Creating peak regions took 42.1438930035 s Estimating background... Estimating background took 11.6679580212 s Processing ZNF785-SRR5197243.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='ZNF785-SRR5197243.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='ZNF785-SRR5197243/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 ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.53217601776 s Creating peak regions... Creating peak regions took 72.9921298027 s Estimating background... Estimating background took 25.8671839237 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06968998909 s Creating peak regions... Creating peak regions took 37.8154740334 s Estimating background... Estimating background took 11.0865380764 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.09965991974 s Creating peak regions... Creating peak regions took 38.1698770523 s Estimating background... Estimating background took 11.2062160969 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28590512276 s Creating peak regions... Creating peak regions took 40.0720639229 s Estimating background... Estimating background took 11.3915588856 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.78333592415 s Creating peak regions... Creating peak regions took 34.2130839825 s Estimating background... Estimating background took 10.3998889923 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.50869393349 s Creating peak regions... Creating peak regions took 31.4548192024 s Estimating background... Estimating background took 7.76738810539 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.2749311924 s Creating peak regions... Creating peak regions took 28.0843770504 s Estimating background... Estimating background took 8.28611302376 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.52360510826 s Creating peak regions... Creating peak regions took 24.6504790783 s Estimating background... Estimating background took 8.45221710205 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.64400410652 s Creating peak regions... Creating peak regions took 23.9141328335 s Estimating background... Estimating background took 10.5078039169 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.06981801987 s Creating peak regions... Creating peak regions took 23.4127488136 s Estimating background... Estimating background took 5.40386295319 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.4481511116 s Creating peak regions... Creating peak regions took 18.0482039452 s Estimating background... Estimating background took 7.48324203491 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.40207982063 s Creating peak regions... Creating peak regions took 68.3966801167 s Estimating background... Estimating background took 17.8264188766 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.21628880501 s Creating peak regions... Creating peak regions took 20.3147161007 s Estimating background... Estimating background took 7.19646501541 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.676933050156 s Creating peak regions... Creating peak regions took 12.9502680302 s Estimating background... Estimating background took 3.69751191139 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.96324801445 s Creating peak regions... Creating peak regions took 14.5576658249 s Estimating background... Estimating background took 6.88847303391 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.97820711136 s Creating peak regions... Creating peak regions took 55.6022701263 s Estimating background... Estimating background took 14.1674859524 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.40099096298 s Creating peak regions... Creating peak regions took 52.7136991024 s Estimating background... Estimating background took 11.0988631248 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.62367916107 s Creating peak regions... Creating peak regions took 54.1059629917 s Estimating background... Estimating background took 13.8769478798 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.73060107231 s Creating peak regions... Creating peak regions took 48.4475269318 s Estimating background... Estimating background took 14.2752699852 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.72004699707 s Creating peak regions... Creating peak regions took 48.5082881451 s Estimating background... Estimating background took 13.8725860119 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.14607191086 s Creating peak regions... Creating peak regions took 40.9259529114 s Estimating background... Estimating background took 10.4243700504 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06817698479 s Creating peak regions... Creating peak regions took 38.855905056 s Estimating background... Estimating background took 10.1917150021 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0817289352417 s Creating peak regions... Creating peak regions took 0.159910202026 s Estimating background... Estimating background took 0.552602052689 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.75386786461 s Creating peak regions... Creating peak regions took 44.4519598484 s Estimating background... Estimating background took 14.1822421551 s Processing ZNF785-SRR5197243.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.104650020599 s Creating peak regions... Creating peak regions took 14.471765995 s Estimating background... Estimating background took 0.595313072205 s