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='ZNF211-SRR5197078.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='ZNF211-SRR5197078/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 ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.61519384384 s Creating peak regions... Creating peak regions took 62.0944910049 s Estimating background... Estimating background took 26.2692501545 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.75767111778 s Creating peak regions... Creating peak regions took 32.5069589615 s Estimating background... Estimating background took 10.9862041473 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.77211594582 s Creating peak regions... Creating peak regions took 33.3242340088 s Estimating background... Estimating background took 11.0072979927 s Processing ZNF211-SRR5197078.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='ZNF211-SRR5197078.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='ZNF211-SRR5197078/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 ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.50188183784 s Creating peak regions... Creating peak regions took 69.3074650764 s Estimating background... Estimating background took 31.9486160278 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.26796603203 s Creating peak regions... Creating peak regions took 39.6200120449 s Estimating background... Estimating background took 13.5254089832 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53151011467 s Creating peak regions... Creating peak regions took 39.9905030727 s Estimating background... Estimating background took 12.8570408821 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.56405687332 s Creating peak regions... Creating peak regions took 41.9441771507 s Estimating background... Estimating background took 13.9448399544 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.10240483284 s Creating peak regions... Creating peak regions took 34.1155881882 s Estimating background... Estimating background took 14.875975132 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.61965703964 s Creating peak regions... Creating peak regions took 30.8025169373 s Estimating background... Estimating background took 9.13190102577 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.53198385239 s Creating peak regions... Creating peak regions took 28.3265860081 s Estimating background... Estimating background took 10.4451379776 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.46265697479 s Creating peak regions... Creating peak regions took 26.3465518951 s Estimating background... Estimating background took 8.99530410767 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.83566999435 s Creating peak regions... Creating peak regions took 25.3443989754 s Estimating background... Estimating background took 11.5188500881 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.203343153 s Creating peak regions... Creating peak regions took 25.0556879044 s Estimating background... Estimating background took 6.87180495262 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.15427708626 s Creating peak regions... Creating peak regions took 18.4728751183 s Estimating background... Estimating background took 7.40590190887 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.93275403976 s Creating peak regions... Creating peak regions took 71.9753599167 s Estimating background... Estimating background took 22.3977460861 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.23363900185 s Creating peak regions... Creating peak regions took 20.2072679996 s Estimating background... Estimating background took 7.60498094559 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.682567834854 s Creating peak regions... Creating peak regions took 14.5080878735 s Estimating background... Estimating background took 4.61895489693 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.936393022537 s Creating peak regions... Creating peak regions took 15.7481191158 s Estimating background... Estimating background took 7.15484786034 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.13271093369 s Creating peak regions... Creating peak regions took 60.2298021317 s Estimating background... Estimating background took 17.9525370598 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.16816592216 s Creating peak regions... Creating peak regions took 58.8106539249 s Estimating background... Estimating background took 14.4224920273 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.96674203873 s Creating peak regions... Creating peak regions took 53.2470262051 s Estimating background... Estimating background took 17.2222521305 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.67309594154 s Creating peak regions... Creating peak regions took 51.4991481304 s Estimating background... Estimating background took 19.5575110912 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.79425597191 s Creating peak regions... Creating peak regions took 47.4121611118 s Estimating background... Estimating background took 17.0745780468 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.42691397667 s Creating peak regions... Creating peak regions took 42.6511089802 s Estimating background... Estimating background took 12.197314024 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95983099937 s Creating peak regions... Creating peak regions took 41.2302210331 s Estimating background... Estimating background took 12.1753330231 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0834240913391 s Creating peak regions... Creating peak regions took 0.14769411087 s Estimating background... Estimating background took 0.688062906265 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.98307609558 s Creating peak regions... Creating peak regions took 49.8422820568 s Estimating background... Estimating background took 17.7952959538 s Processing ZNF211-SRR5197078.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.113544940948 s Creating peak regions... Creating peak regions took 15.0946650505 s Estimating background... Estimating background took 0.652682065964 s