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='ZNF610-SRR5197193.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='ZNF610-SRR5197193/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 ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.83277702332 s Creating peak regions... Creating peak regions took 74.9431328773 s Estimating background... Estimating background took 27.6259520054 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.03442716599 s Creating peak regions... Creating peak regions took 39.0678458214 s Estimating background... Estimating background took 11.8516919613 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.13017988205 s Creating peak regions... Creating peak regions took 41.5094501972 s Estimating background... Estimating background took 12.1505560875 s Processing ZNF610-SRR5197193.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='ZNF610-SRR5197193.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='ZNF610-SRR5197193/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 ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.13276600838 s Creating peak regions... Creating peak regions took 72.6942930222 s Estimating background... Estimating background took 26.9247210026 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98572802544 s Creating peak regions... Creating peak regions took 37.8449130058 s Estimating background... Estimating background took 11.8322029114 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.14582395554 s Creating peak regions... Creating peak regions took 40.31208992 s Estimating background... Estimating background took 12.0387210846 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.9744451046 s Creating peak regions... Creating peak regions took 40.164180994 s Estimating background... Estimating background took 12.4954078197 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7064511776 s Creating peak regions... Creating peak regions took 32.2836608887 s Estimating background... Estimating background took 10.4986991882 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.50530910492 s Creating peak regions... Creating peak regions took 29.6570498943 s Estimating background... Estimating background took 7.86595702171 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.38020992279 s Creating peak regions... Creating peak regions took 29.9259750843 s Estimating background... Estimating background took 8.9671690464 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.36825895309 s Creating peak regions... Creating peak regions took 26.8242049217 s Estimating background... Estimating background took 9.13482284546 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7190759182 s Creating peak regions... Creating peak regions took 25.9030890465 s Estimating background... Estimating background took 11.7848899364 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.01341581345 s Creating peak regions... Creating peak regions took 22.8860430717 s Estimating background... Estimating background took 5.88441109657 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.27529597282 s Creating peak regions... Creating peak regions took 18.0931429863 s Estimating background... Estimating background took 8.19343900681 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.32547402382 s Creating peak regions... Creating peak regions took 68.4265570641 s Estimating background... Estimating background took 18.9360239506 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.20272803307 s Creating peak regions... Creating peak regions took 20.3783459663 s Estimating background... Estimating background took 7.52489304543 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.672380924225 s Creating peak regions... Creating peak regions took 12.5791809559 s Estimating background... Estimating background took 4.15457010269 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.9426009655 s Creating peak regions... Creating peak regions took 15.3355000019 s Estimating background... Estimating background took 7.295814991 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.80261516571 s Creating peak regions... Creating peak regions took 56.3793029785 s Estimating background... Estimating background took 15.2423582077 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.16258597374 s Creating peak regions... Creating peak regions took 52.6586120129 s Estimating background... Estimating background took 11.7137210369 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.33183884621 s Creating peak regions... Creating peak regions took 51.1749968529 s Estimating background... Estimating background took 14.1335949898 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.64401602745 s Creating peak regions... Creating peak regions took 48.9202060699 s Estimating background... Estimating background took 15.910296917 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39597606659 s Creating peak regions... Creating peak regions took 45.3218111992 s Estimating background... Estimating background took 15.0035130978 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.04137086868 s Creating peak regions... Creating peak regions took 43.4370498657 s Estimating background... Estimating background took 10.5969009399 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.80719900131 s Creating peak regions... Creating peak regions took 41.1419930458 s Estimating background... Estimating background took 10.8421440125 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0758519172668 s Creating peak regions... Creating peak regions took 0.134336948395 s Estimating background... Estimating background took 0.549514055252 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.36558699608 s Creating peak regions... Creating peak regions took 47.6324250698 s Estimating background... Estimating background took 13.617898941 s Processing ZNF610-SRR5197193.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0982739925385 s Creating peak regions... Creating peak regions took 15.4163470268 s Estimating background... Estimating background took 0.549459934235 s