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='ZNF562-SRR5197180.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='ZNF562-SRR5197180/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 ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.67132401466 s Creating peak regions... Creating peak regions took 76.8372139931 s Estimating background... Estimating background took 31.5240881443 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.26255106926 s Creating peak regions... Creating peak regions took 39.9452800751 s Estimating background... Estimating background took 12.4537990093 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.38084292412 s Creating peak regions... Creating peak regions took 40.0532591343 s Estimating background... Estimating background took 12.7242610455 s Processing ZNF562-SRR5197180.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='ZNF562-SRR5197180.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='ZNF562-SRR5197180/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 ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.47370409966 s Creating peak regions... Creating peak regions took 76.3771789074 s Estimating background... Estimating background took 31.7863779068 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.25670599937 s Creating peak regions... Creating peak regions took 39.6411361694 s Estimating background... Estimating background took 12.5567588806 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.63116788864 s Creating peak regions... Creating peak regions took 40.2403600216 s Estimating background... Estimating background took 12.9097599983 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.35233187675 s Creating peak regions... Creating peak regions took 41.6883060932 s Estimating background... Estimating background took 13.5262680054 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.97943615913 s Creating peak regions... Creating peak regions took 32.2165467739 s Estimating background... Estimating background took 12.2700669765 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.52401399612 s Creating peak regions... Creating peak regions took 32.6543560028 s Estimating background... Estimating background took 8.85922598839 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.53021907806 s Creating peak regions... Creating peak regions took 29.368062973 s Estimating background... Estimating background took 9.65330910683 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.63508582115 s Creating peak regions... Creating peak regions took 27.5613119602 s Estimating background... Estimating background took 9.69160509109 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.83304095268 s Creating peak regions... Creating peak regions took 26.7285509109 s Estimating background... Estimating background took 11.5274708271 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.20321011543 s Creating peak regions... Creating peak regions took 24.5542778969 s Estimating background... Estimating background took 6.3099360466 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40786099434 s Creating peak regions... Creating peak regions took 18.8554677963 s Estimating background... Estimating background took 8.48484301567 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.62003803253 s Creating peak regions... Creating peak regions took 75.8663611412 s Estimating background... Estimating background took 20.303429842 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.46569800377 s Creating peak regions... Creating peak regions took 20.026542902 s Estimating background... Estimating background took 8.05861115456 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.658540010452 s Creating peak regions... Creating peak regions took 14.3803489208 s Estimating background... Estimating background took 4.26171588898 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.10419297218 s Creating peak regions... Creating peak regions took 15.9896500111 s Estimating background... Estimating background took 8.41423511505 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.23420882225 s Creating peak regions... Creating peak regions took 59.4912631512 s Estimating background... Estimating background took 17.5615239143 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.73065090179 s Creating peak regions... Creating peak regions took 55.8679471016 s Estimating background... Estimating background took 13.580080986 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.30054807663 s Creating peak regions... Creating peak regions took 56.6767117977 s Estimating background... Estimating background took 15.7711110115 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.99340987206 s Creating peak regions... Creating peak regions took 51.3505461216 s Estimating background... Estimating background took 17.7337119579 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.76382780075 s Creating peak regions... Creating peak regions took 47.7627329826 s Estimating background... Estimating background took 16.7253928185 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.33707118034 s Creating peak regions... Creating peak regions took 45.5306248665 s Estimating background... Estimating background took 11.7070808411 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.11040186882 s Creating peak regions... Creating peak regions took 42.0218698978 s Estimating background... Estimating background took 11.7305262089 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0889670848846 s Creating peak regions... Creating peak regions took 0.198548078537 s Estimating background... Estimating background took 0.696517944336 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.90614891052 s Creating peak regions... Creating peak regions took 48.9842088223 s Estimating background... Estimating background took 16.2175171375 s Processing ZNF562-SRR5197180.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.112950086594 s Creating peak regions... Creating peak regions took 15.3232698441 s Estimating background... Estimating background took 0.658360958099 s