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='RBAK-SRR5197036.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='RBAK-SRR5197036/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 RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.42370390892 s Creating peak regions... Creating peak regions took 65.7689871788 s Estimating background... Estimating background took 30.5260128975 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95970010757 s Creating peak regions... Creating peak regions took 34.6749751568 s Estimating background... Estimating background took 12.6453640461 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.10248279572 s Creating peak regions... Creating peak regions took 36.3697528839 s Estimating background... Estimating background took 12.1473908424 s Processing RBAK-SRR5197036.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='RBAK-SRR5197036.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='RBAK-SRR5197036/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 RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.21143507957 s Creating peak regions... Creating peak regions took 66.1674649715 s Estimating background... Estimating background took 30.5586178303 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.02290391922 s Creating peak regions... Creating peak regions took 34.6624958515 s Estimating background... Estimating background took 12.5047569275 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.03731179237 s Creating peak regions... Creating peak regions took 36.5811080933 s Estimating background... Estimating background took 12.5271458626 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.10309004784 s Creating peak regions... Creating peak regions took 33.977905035 s Estimating background... Estimating background took 13.5786428452 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.84918212891 s Creating peak regions... Creating peak regions took 28.8596661091 s Estimating background... Estimating background took 11.779088974 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.45050811768 s Creating peak regions... Creating peak regions took 26.7461848259 s Estimating background... Estimating background took 9.04104804993 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.4864089489 s Creating peak regions... Creating peak regions took 25.1196060181 s Estimating background... Estimating background took 10.0861918926 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.64176893234 s Creating peak regions... Creating peak regions took 24.2911398411 s Estimating background... Estimating background took 9.52623105049 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.71583485603 s Creating peak regions... Creating peak regions took 23.47853899 s Estimating background... Estimating background took 12.421350956 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.15908908844 s Creating peak regions... Creating peak regions took 21.9392111301 s Estimating background... Estimating background took 6.45432209969 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.27704000473 s Creating peak regions... Creating peak regions took 15.5533320904 s Estimating background... Estimating background took 8.57033491135 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.38205194473 s Creating peak regions... Creating peak regions took 61.1312088966 s Estimating background... Estimating background took 20.7320358753 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.32837200165 s Creating peak regions... Creating peak regions took 18.6877260208 s Estimating background... Estimating background took 8.07905602455 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.608327150345 s Creating peak regions... Creating peak regions took 11.7452590466 s Estimating background... Estimating background took 4.15752100945 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.10661482811 s Creating peak regions... Creating peak regions took 14.0673680305 s Estimating background... Estimating background took 7.6845510006 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.7368850708 s Creating peak regions... Creating peak regions took 53.4430091381 s Estimating background... Estimating background took 16.0562899113 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24702501297 s Creating peak regions... Creating peak regions took 50.3524980545 s Estimating background... Estimating background took 12.7216410637 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.60031509399 s Creating peak regions... Creating peak regions took 46.1519889832 s Estimating background... Estimating background took 15.4897499084 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.73962402344 s Creating peak regions... Creating peak regions took 44.2433350086 s Estimating background... Estimating background took 17.3679249287 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.67751193047 s Creating peak regions... Creating peak regions took 39.757570982 s Estimating background... Estimating background took 16.3003661633 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.09195113182 s Creating peak regions... Creating peak regions took 37.0661189556 s Estimating background... Estimating background took 11.5392599106 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.78753805161 s Creating peak regions... Creating peak regions took 35.4079949856 s Estimating background... Estimating background took 11.8298199177 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0813519954681 s Creating peak regions... Creating peak regions took 0.154972076416 s Estimating background... Estimating background took 0.560378074646 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.55859184265 s Creating peak regions... Creating peak regions took 39.9375388622 s Estimating background... Estimating background took 15.3667559624 s Processing RBAK-SRR5197036.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.113376140594 s Creating peak regions... Creating peak regions took 13.0977809429 s Estimating background... Estimating background took 0.603955984116 s