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='ZNF486-SRR5197156.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='ZNF486-SRR5197156/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 ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.06898593903 s Creating peak regions... Creating peak regions took 76.8010189533 s Estimating background... Estimating background took 35.158752203 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.73870515823 s Creating peak regions... Creating peak regions took 41.7333800793 s Estimating background... Estimating background took 13.9608418941 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.63751506805 s Creating peak regions... Creating peak regions took 40.3910970688 s Estimating background... Estimating background took 12.598195076 s Processing ZNF486-SRR5197156.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='ZNF486-SRR5197156.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='ZNF486-SRR5197156/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 ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.14364004135 s Creating peak regions... Creating peak regions took 76.2546069622 s Estimating background... Estimating background took 36.1377339363 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.6616101265 s Creating peak regions... Creating peak regions took 39.9311790466 s Estimating background... Estimating background took 13.3197939396 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51753211021 s Creating peak regions... Creating peak regions took 41.4980449677 s Estimating background... Estimating background took 14.1681051254 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.68957901001 s Creating peak regions... Creating peak regions took 42.4660100937 s Estimating background... Estimating background took 14.2566230297 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45975089073 s Creating peak regions... Creating peak regions took 34.4635658264 s Estimating background... Estimating background took 17.1418459415 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.67290091515 s Creating peak regions... Creating peak regions took 33.5466940403 s Estimating background... Estimating background took 9.78564190865 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.62102198601 s Creating peak regions... Creating peak regions took 28.0393300056 s Estimating background... Estimating background took 8.74934792519 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.76749396324 s Creating peak regions... Creating peak regions took 25.5817251205 s Estimating background... Estimating background took 8.73820996284 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.9092040062 s Creating peak regions... Creating peak regions took 25.4210460186 s Estimating background... Estimating background took 11.5602297783 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.43222403526 s Creating peak regions... Creating peak regions took 24.9946401119 s Estimating background... Estimating background took 8.35434007645 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.27484989166 s Creating peak regions... Creating peak regions took 18.0831229687 s Estimating background... Estimating background took 6.96820497513 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.51730298996 s Creating peak regions... Creating peak regions took 76.5128610134 s Estimating background... Estimating background took 24.4474110603 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.33100199699 s Creating peak regions... Creating peak regions took 21.0000710487 s Estimating background... Estimating background took 7.46253299713 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.707136869431 s Creating peak regions... Creating peak regions took 13.4483311176 s Estimating background... Estimating background took 4.75952291489 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.01160407066 s Creating peak regions... Creating peak regions took 15.7211070061 s Estimating background... Estimating background took 6.79585695267 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.34097909927 s Creating peak regions... Creating peak regions took 59.4417541027 s Estimating background... Estimating background took 18.6476039886 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.89789891243 s Creating peak regions... Creating peak regions took 54.8873121738 s Estimating background... Estimating background took 15.9216430187 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.57969284058 s Creating peak regions... Creating peak regions took 55.8832559586 s Estimating background... Estimating background took 19.7314059734 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.78571915627 s Creating peak regions... Creating peak regions took 52.1224610806 s Estimating background... Estimating background took 21.7022058964 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.38438391685 s Creating peak regions... Creating peak regions took 49.8430941105 s Estimating background... Estimating background took 17.9942648411 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.92298197746 s Creating peak regions... Creating peak regions took 43.4565360546 s Estimating background... Estimating background took 12.777463913 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39995408058 s Creating peak regions... Creating peak regions took 43.3454101086 s Estimating background... Estimating background took 12.1783959866 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0861001014709 s Creating peak regions... Creating peak regions took 0.167097091675 s Estimating background... Estimating background took 0.641983985901 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.38874697685 s Creating peak regions... Creating peak regions took 40.6476099491 s Estimating background... Estimating background took 16.7876858711 s Processing ZNF486-SRR5197156.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.116016149521 s Creating peak regions... Creating peak regions took 13.9513938427 s Estimating background... Estimating background took 0.772974014282 s