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='ZNF337-SRR5197118.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='ZNF337-SRR5197118/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 ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.47092103958 s Creating peak regions... Creating peak regions took 78.5352749825 s Estimating background... Estimating background took 46.9592020512 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.82212615013 s Creating peak regions... Creating peak regions took 44.0534949303 s Estimating background... Estimating background took 18.5617070198 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.03315210342 s Creating peak regions... Creating peak regions took 37.275801897 s Estimating background... Estimating background took 15.3301858902 s Processing ZNF337-SRR5197118.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='ZNF337-SRR5197118.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='ZNF337-SRR5197118/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 ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.77279400826 s Creating peak regions... Creating peak regions took 79.6365778446 s Estimating background... Estimating background took 46.9851229191 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85335421562 s Creating peak regions... Creating peak regions took 43.228402853 s Estimating background... Estimating background took 19.0624449253 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85396313667 s Creating peak regions... Creating peak regions took 42.6641619205 s Estimating background... Estimating background took 18.4502398968 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.13179802895 s Creating peak regions... Creating peak regions took 45.976952076 s Estimating background... Estimating background took 20.4207148552 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.64506816864 s Creating peak regions... Creating peak regions took 35.9583101273 s Estimating background... Estimating background took 18.0541810989 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.02145504951 s Creating peak regions... Creating peak regions took 34.7966208458 s Estimating background... Estimating background took 12.14585495 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.91564083099 s Creating peak regions... Creating peak regions took 31.5750467777 s Estimating background... Estimating background took 14.0227508545 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.60813784599 s Creating peak regions... Creating peak regions took 27.6691567898 s Estimating background... Estimating background took 13.171831131 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.41428804398 s Creating peak regions... Creating peak regions took 27.4258849621 s Estimating background... Estimating background took 17.8353009224 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.45826411247 s Creating peak regions... Creating peak regions took 25.4338150024 s Estimating background... Estimating background took 9.510668993 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.72302103043 s Creating peak regions... Creating peak regions took 17.9778161049 s Estimating background... Estimating background took 11.0917360783 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.53714680672 s Creating peak regions... Creating peak regions took 81.9776830673 s Estimating background... Estimating background took 31.6559810638 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.26698803902 s Creating peak regions... Creating peak regions took 21.5993540287 s Estimating background... Estimating background took 10.8215680122 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.896146059036 s Creating peak regions... Creating peak regions took 15.6420450211 s Estimating background... Estimating background took 5.88113307953 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.38722896576 s Creating peak regions... Creating peak regions took 17.0093178749 s Estimating background... Estimating background took 11.3881690502 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.03022313118 s Creating peak regions... Creating peak regions took 62.6063621044 s Estimating background... Estimating background took 22.8659551144 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.01991796494 s Creating peak regions... Creating peak regions took 59.7865469456 s Estimating background... Estimating background took 18.327944994 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.62482404709 s Creating peak regions... Creating peak regions took 56.0436460972 s Estimating background... Estimating background took 23.2986228466 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.72336006165 s Creating peak regions... Creating peak regions took 56.1389129162 s Estimating background... Estimating background took 26.6996920109 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.69685411453 s Creating peak regions... Creating peak regions took 50.4421408176 s Estimating background... Estimating background took 23.7921030521 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.68511891365 s Creating peak regions... Creating peak regions took 44.915956974 s Estimating background... Estimating background took 15.732872963 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.61205506325 s Creating peak regions... Creating peak regions took 35.4794390202 s Estimating background... Estimating background took 13.937939167 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0821599960327 s Creating peak regions... Creating peak regions took 0.175745010376 s Estimating background... Estimating background took 0.593559980392 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53562283516 s Creating peak regions... Creating peak regions took 42.5799260139 s Estimating background... Estimating background took 18.2401120663 s Processing ZNF337-SRR5197118.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.110054016113 s Creating peak regions... Creating peak regions took 14.1587328911 s Estimating background... Estimating background took 0.528568029404 s