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='ZNF324-SRR5197114.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='ZNF324-SRR5197114/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 ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.74752902985 s Creating peak regions... Creating peak regions took 76.0356080532 s Estimating background... Estimating background took 27.4833950996 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32862305641 s Creating peak regions... Creating peak regions took 38.9831690788 s Estimating background... Estimating background took 11.2757148743 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.16942596436 s Creating peak regions... Creating peak regions took 41.7855501175 s Estimating background... Estimating background took 11.2994019985 s Processing ZNF324-SRR5197114.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='ZNF324-SRR5197114.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='ZNF324-SRR5197114/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 ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.84358000755 s Creating peak regions... Creating peak regions took 72.3267018795 s Estimating background... Estimating background took 28.3639338017 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.13665914536 s Creating peak regions... Creating peak regions took 40.3262050152 s Estimating background... Estimating background took 11.6313991547 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.09526515007 s Creating peak regions... Creating peak regions took 41.7001149654 s Estimating background... Estimating background took 11.1787950993 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28943800926 s Creating peak regions... Creating peak regions took 42.695775032 s Estimating background... Estimating background took 12.2233331203 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.07419490814 s Creating peak regions... Creating peak regions took 36.0059049129 s Estimating background... Estimating background took 10.4279260635 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.47926902771 s Creating peak regions... Creating peak regions took 32.472276926 s Estimating background... Estimating background took 7.96643781662 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.47668504715 s Creating peak regions... Creating peak regions took 28.5840680599 s Estimating background... Estimating background took 8.49425315857 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.53285288811 s Creating peak regions... Creating peak regions took 26.133535862 s Estimating background... Estimating background took 8.11483597755 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.57652997971 s Creating peak regions... Creating peak regions took 24.3640480042 s Estimating background... Estimating background took 8.78329205513 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.25220990181 s Creating peak regions... Creating peak regions took 22.5274281502 s Estimating background... Estimating background took 5.5054769516 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.19547700882 s Creating peak regions... Creating peak regions took 18.6263170242 s Estimating background... Estimating background took 7.09823012352 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.65743303299 s Creating peak regions... Creating peak regions took 69.04073596 s Estimating background... Estimating background took 18.0866761208 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.17075490952 s Creating peak regions... Creating peak regions took 19.503606081 s Estimating background... Estimating background took 7.03045201302 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.650905132294 s Creating peak regions... Creating peak regions took 14.7966039181 s Estimating background... Estimating background took 3.93753886223 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.01169300079 s Creating peak regions... Creating peak regions took 16.2233099937 s Estimating background... Estimating background took 7.23982000351 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.78865909576 s Creating peak regions... Creating peak regions took 58.1746408939 s Estimating background... Estimating background took 14.1574120522 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.40404510498 s Creating peak regions... Creating peak regions took 58.6383340359 s Estimating background... Estimating background took 12.0605251789 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.52776694298 s Creating peak regions... Creating peak regions took 54.3245549202 s Estimating background... Estimating background took 14.2200620174 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.63751888275 s Creating peak regions... Creating peak regions took 51.7072319984 s Estimating background... Estimating background took 16.2451820374 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85411000252 s Creating peak regions... Creating peak regions took 46.9668390751 s Estimating background... Estimating background took 14.9873900414 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.20077800751 s Creating peak regions... Creating peak regions took 45.7441310883 s Estimating background... Estimating background took 11.1205267906 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.053358078 s Creating peak regions... Creating peak regions took 41.111905098 s Estimating background... Estimating background took 9.4679441452 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.085165977478 s Creating peak regions... Creating peak regions took 0.183697938919 s Estimating background... Estimating background took 0.637698888779 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.69864988327 s Creating peak regions... Creating peak regions took 49.260573864 s Estimating background... Estimating background took 14.825245142 s Processing ZNF324-SRR5197114.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.104011058807 s Creating peak regions... Creating peak regions took 15.4445490837 s Estimating background... Estimating background took 0.577769041061 s