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='ZNF432-SRR5197138.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='ZNF432-SRR5197138/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 ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.67955899239 s Creating peak regions... Creating peak regions took 82.3365910053 s Estimating background... Estimating background took 76.1639311314 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.06839704514 s Creating peak regions... Creating peak regions took 45.6444149017 s Estimating background... Estimating background took 29.905479908 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.98329401016 s Creating peak regions... Creating peak regions took 40.529998064 s Estimating background... Estimating background took 27.9685981274 s Processing ZNF432-SRR5197138.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='ZNF432-SRR5197138.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='ZNF432-SRR5197138/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 ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.76873111725 s Creating peak regions... Creating peak regions took 80.2890100479 s Estimating background... Estimating background took 75.8564109802 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.84084105492 s Creating peak regions... Creating peak regions took 42.1778690815 s Estimating background... Estimating background took 31.5507819653 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.21216392517 s Creating peak regions... Creating peak regions took 42.962059021 s Estimating background... Estimating background took 30.559114933 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.24959397316 s Creating peak regions... Creating peak regions took 43.0537731647 s Estimating background... Estimating background took 33.0706350803 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.66773414612 s Creating peak regions... Creating peak regions took 36.9554669857 s Estimating background... Estimating background took 33.6584029198 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.92954611778 s Creating peak regions... Creating peak regions took 34.630822897 s Estimating background... Estimating background took 21.070622921 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.82934498787 s Creating peak regions... Creating peak regions took 33.1031839848 s Estimating background... Estimating background took 23.730440855 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.62562179565 s Creating peak regions... Creating peak regions took 28.7979829311 s Estimating background... Estimating background took 22.8570001125 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.21489906311 s Creating peak regions... Creating peak regions took 28.288064003 s Estimating background... Estimating background took 29.3402340412 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.33994603157 s Creating peak regions... Creating peak regions took 25.489730835 s Estimating background... Estimating background took 15.8991398811 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.2624900341 s Creating peak regions... Creating peak regions took 19.7155370712 s Estimating background... Estimating background took 19.3700239658 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.64968204498 s Creating peak regions... Creating peak regions took 75.7901070118 s Estimating background... Estimating background took 52.6059820652 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39193105698 s Creating peak regions... Creating peak regions took 23.066838026 s Estimating background... Estimating background took 18.7273619175 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.33656382561 s Creating peak regions... Creating peak regions took 15.4549520016 s Estimating background... Estimating background took 8.60793018341 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.72380495071 s Creating peak regions... Creating peak regions took 16.1606230736 s Estimating background... Estimating background took 17.8311889172 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.57995295525 s Creating peak regions... Creating peak regions took 64.5677220821 s Estimating background... Estimating background took 40.0254790783 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.73057889938 s Creating peak regions... Creating peak regions took 57.1279678345 s Estimating background... Estimating background took 29.7768449783 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.12781977654 s Creating peak regions... Creating peak regions took 53.3575870991 s Estimating background... Estimating background took 31.4043290615 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.84269404411 s Creating peak regions... Creating peak regions took 43.8633499146 s Estimating background... Estimating background took 36.0523748398 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.99965596199 s Creating peak regions... Creating peak regions took 43.7529830933 s Estimating background... Estimating background took 32.5618240833 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.07180118561 s Creating peak regions... Creating peak regions took 38.2023458481 s Estimating background... Estimating background took 22.0836920738 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.64930605888 s Creating peak regions... Creating peak regions took 35.5863380432 s Estimating background... Estimating background took 21.7938120365 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.121161937714 s Creating peak regions... Creating peak regions took 0.209901809692 s Estimating background... Estimating background took 0.681080102921 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.97089099884 s Creating peak regions... Creating peak regions took 41.5715839863 s Estimating background... Estimating background took 34.189136982 s Processing ZNF432-SRR5197138.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.256114006042 s Creating peak regions... Creating peak regions took 14.2815010548 s Estimating background... Estimating background took 0.908952951431 s