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='ZNF419-rep2-SRR5197133.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='ZNF419-rep2-SRR5197133/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 ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.07228589058 s Creating peak regions... Creating peak regions took 82.3788490295 s Estimating background... Estimating background took 72.9987719059 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.0884540081 s Creating peak regions... Creating peak regions took 43.4721059799 s Estimating background... Estimating background took 27.5930261612 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.50203800201 s Creating peak regions... Creating peak regions took 41.1428630352 s Estimating background... Estimating background took 26.6235120296 s Processing ZNF419-rep2-SRR5197133.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='ZNF419-rep2-SRR5197133.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='ZNF419-rep2-SRR5197133/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 ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.81758713722 s Creating peak regions... Creating peak regions took 81.1702370644 s Estimating background... Estimating background took 74.5496571064 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.96436190605 s Creating peak regions... Creating peak regions took 43.8767240047 s Estimating background... Estimating background took 29.4309139252 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.62567782402 s Creating peak regions... Creating peak regions took 43.3556220531 s Estimating background... Estimating background took 28.9378979206 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.42817497253 s Creating peak regions... Creating peak regions took 42.9335289001 s Estimating background... Estimating background took 30.9935150146 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.07931995392 s Creating peak regions... Creating peak regions took 36.2310230732 s Estimating background... Estimating background took 37.5533630848 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.24788308144 s Creating peak regions... Creating peak regions took 34.7385690212 s Estimating background... Estimating background took 20.4635379314 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.77954602242 s Creating peak regions... Creating peak regions took 29.8541340828 s Estimating background... Estimating background took 20.577849865 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.65648698807 s Creating peak regions... Creating peak regions took 29.0342259407 s Estimating background... Estimating background took 19.2216219902 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.33455395699 s Creating peak regions... Creating peak regions took 29.6472160816 s Estimating background... Estimating background took 24.5925629139 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.01509404182 s Creating peak regions... Creating peak regions took 25.5326628685 s Estimating background... Estimating background took 15.6518969536 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.332020998 s Creating peak regions... Creating peak regions took 19.1189248562 s Estimating background... Estimating background took 13.9584109783 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.04649496078 s Creating peak regions... Creating peak regions took 75.8565969467 s Estimating background... Estimating background took 51.8316819668 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.31608510017 s Creating peak regions... Creating peak regions took 22.9903850555 s Estimating background... Estimating background took 16.8607809544 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.37745094299 s Creating peak regions... Creating peak regions took 16.2672269344 s Estimating background... Estimating background took 8.62600302696 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.53538703918 s Creating peak regions... Creating peak regions took 16.8801701069 s Estimating background... Estimating background took 13.5270190239 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.95128321648 s Creating peak regions... Creating peak regions took 64.764081955 s Estimating background... Estimating background took 40.8213119507 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.39408779144 s Creating peak regions... Creating peak regions took 61.7141721249 s Estimating background... Estimating background took 31.9184410572 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.33569598198 s Creating peak regions... Creating peak regions took 51.4307508469 s Estimating background... Estimating background took 35.6010210514 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.86384987831 s Creating peak regions... Creating peak regions took 55.1077330112 s Estimating background... Estimating background took 42.1427929401 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.78173899651 s Creating peak regions... Creating peak regions took 46.6083078384 s Estimating background... Estimating background took 30.9683220387 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.62196087837 s Creating peak regions... Creating peak regions took 38.9729640484 s Estimating background... Estimating background took 22.345156908 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.82263803482 s Creating peak regions... Creating peak regions took 36.1361320019 s Estimating background... Estimating background took 21.8129370213 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.147471904755 s Creating peak regions... Creating peak regions took 0.213819980621 s Estimating background... Estimating background took 0.767233133316 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.38959693909 s Creating peak regions... Creating peak regions took 43.0078971386 s Estimating background... Estimating background took 35.8973500729 s Processing ZNF419-rep2-SRR5197133.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.246450185776 s Creating peak regions... Creating peak regions took 14.5147109032 s Estimating background... Estimating background took 0.764971017838 s