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='ZNF669-SRR5197208.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='ZNF669-SRR5197208/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 ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.30418515205 s Creating peak regions... Creating peak regions took 75.7888889313 s Estimating background... Estimating background took 23.1400170326 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.82091188431 s Creating peak regions... Creating peak regions took 40.6266441345 s Estimating background... Estimating background took 9.67995500565 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.83856797218 s Creating peak regions... Creating peak regions took 38.8035998344 s Estimating background... Estimating background took 9.86857700348 s Processing ZNF669-SRR5197208.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='ZNF669-SRR5197208.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='ZNF669-SRR5197208/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 ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.66164803505 s Creating peak regions... Creating peak regions took 76.3497319221 s Estimating background... Estimating background took 22.2034831047 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.63392019272 s Creating peak regions... Creating peak regions took 41.4822778702 s Estimating background... Estimating background took 9.48310518265 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.8006670475 s Creating peak regions... Creating peak regions took 39.3463120461 s Estimating background... Estimating background took 9.30484890938 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92381596565 s Creating peak regions... Creating peak regions took 39.374917984 s Estimating background... Estimating background took 9.90981602669 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.57313394547 s Creating peak regions... Creating peak regions took 35.4960038662 s Estimating background... Estimating background took 9.69841814041 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.22585105896 s Creating peak regions... Creating peak regions took 32.815320015 s Estimating background... Estimating background took 6.61796021461 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.18148612976 s Creating peak regions... Creating peak regions took 30.888327837 s Estimating background... Estimating background took 7.22130608559 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.34821295738 s Creating peak regions... Creating peak regions took 26.5367379189 s Estimating background... Estimating background took 7.5608279705 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.46958208084 s Creating peak regions... Creating peak regions took 26.0148208141 s Estimating background... Estimating background took 8.65902495384 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.908318042755 s Creating peak regions... Creating peak regions took 24.7629630566 s Estimating background... Estimating background took 5.20883011818 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.03994512558 s Creating peak regions... Creating peak regions took 17.7000861168 s Estimating background... Estimating background took 6.15724110603 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.90440106392 s Creating peak regions... Creating peak regions took 76.6201190948 s Estimating background... Estimating background took 15.5657849312 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.03770089149 s Creating peak regions... Creating peak regions took 19.8447749615 s Estimating background... Estimating background took 6.30121588707 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.55699801445 s Creating peak regions... Creating peak regions took 13.8108780384 s Estimating background... Estimating background took 3.4228990078 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.919991970062 s Creating peak regions... Creating peak regions took 16.3626101017 s Estimating background... Estimating background took 5.78990507126 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28455495834 s Creating peak regions... Creating peak regions took 61.6690688133 s Estimating background... Estimating background took 12.0382211208 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.15976309776 s Creating peak regions... Creating peak regions took 58.5428040028 s Estimating background... Estimating background took 10.2592759132 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.20386695862 s Creating peak regions... Creating peak regions took 52.6489510536 s Estimating background... Estimating background took 11.9824337959 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.41592407227 s Creating peak regions... Creating peak regions took 53.5301139355 s Estimating background... Estimating background took 12.3359670639 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.31551790237 s Creating peak regions... Creating peak regions took 50.3150720596 s Estimating background... Estimating background took 12.3180088997 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7784781456 s Creating peak regions... Creating peak regions took 45.2277112007 s Estimating background... Estimating background took 8.95170402527 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.64787197113 s Creating peak regions... Creating peak regions took 40.0846560001 s Estimating background... Estimating background took 9.21474695206 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0735929012299 s Creating peak regions... Creating peak regions took 0.157235860825 s Estimating background... Estimating background took 0.552892208099 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.17814397812 s Creating peak regions... Creating peak regions took 44.3403477669 s Estimating background... Estimating background took 11.5219202042 s Processing ZNF669-SRR5197208.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0918309688568 s Creating peak regions... Creating peak regions took 16.0821428299 s Estimating background... Estimating background took 0.588658809662 s