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='ZNF45-SRR5197148.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='ZNF45-SRR5197148/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 ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.54293012619 s Creating peak regions... Creating peak regions took 82.3727519512 s Estimating background... Estimating background took 77.1712789536 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.83477783203 s Creating peak regions... Creating peak regions took 44.5656681061 s Estimating background... Estimating background took 25.4966688156 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.07662606239 s Creating peak regions... Creating peak regions took 37.6124169827 s Estimating background... Estimating background took 26.0479388237 s Processing ZNF45-SRR5197148.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='ZNF45-SRR5197148.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='ZNF45-SRR5197148/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 ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.5113401413 s Creating peak regions... Creating peak regions took 79.633754015 s Estimating background... Estimating background took 80.6807961464 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.70615720749 s Creating peak regions... Creating peak regions took 43.4890379906 s Estimating background... Estimating background took 31.3560919762 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.87036204338 s Creating peak regions... Creating peak regions took 43.1495199203 s Estimating background... Estimating background took 30.865085125 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.0209171772 s Creating peak regions... Creating peak regions took 40.5189099312 s Estimating background... Estimating background took 32.5825340748 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.37717795372 s Creating peak regions... Creating peak regions took 36.0560910702 s Estimating background... Estimating background took 29.8690359592 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.763204813 s Creating peak regions... Creating peak regions took 33.2285649776 s Estimating background... Estimating background took 21.2034170628 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53040909767 s Creating peak regions... Creating peak regions took 32.2559628487 s Estimating background... Estimating background took 22.1794700623 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.8610830307 s Creating peak regions... Creating peak regions took 29.7004768848 s Estimating background... Estimating background took 23.7969679832 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.92820596695 s Creating peak regions... Creating peak regions took 27.9166948795 s Estimating background... Estimating background took 26.7557480335 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.57428812981 s Creating peak regions... Creating peak regions took 24.1627340317 s Estimating background... Estimating background took 15.0712080002 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.13152599335 s Creating peak regions... Creating peak regions took 20.6451721191 s Estimating background... Estimating background took 19.6587369442 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.35498595238 s Creating peak regions... Creating peak regions took 76.7415649891 s Estimating background... Estimating background took 50.5174839497 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24793815613 s Creating peak regions... Creating peak regions took 22.8770239353 s Estimating background... Estimating background took 18.8211948872 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.29370307922 s Creating peak regions... Creating peak regions took 16.1576590538 s Estimating background... Estimating background took 9.69136214256 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95225381851 s Creating peak regions... Creating peak regions took 16.5786721706 s Estimating background... Estimating background took 19.2201290131 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.20189499855 s Creating peak regions... Creating peak regions took 63.807528019 s Estimating background... Estimating background took 41.3469719887 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.47257900238 s Creating peak regions... Creating peak regions took 59.6516909599 s Estimating background... Estimating background took 30.1143510342 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.49510097504 s Creating peak regions... Creating peak regions took 55.9988689423 s Estimating background... Estimating background took 32.4849889278 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.09596800804 s Creating peak regions... Creating peak regions took 45.2209160328 s Estimating background... Estimating background took 34.5709729195 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.75082302094 s Creating peak regions... Creating peak regions took 42.3331780434 s Estimating background... Estimating background took 32.7750000954 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.93460893631 s Creating peak regions... Creating peak regions took 38.0007488728 s Estimating background... Estimating background took 22.7886669636 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.65332484245 s Creating peak regions... Creating peak regions took 35.0924320221 s Estimating background... Estimating background took 22.8044440746 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.118371009827 s Creating peak regions... Creating peak regions took 0.193717956543 s Estimating background... Estimating background took 0.657857894897 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.83531713486 s Creating peak regions... Creating peak regions took 40.8966600895 s Estimating background... Estimating background took 34.1742379665 s Processing ZNF45-SRR5197148.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.184553146362 s Creating peak regions... Creating peak regions took 12.9362490177 s Estimating background... Estimating background took 0.655845880508 s