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='ZNF705G-SRR5197221.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='ZNF705G-SRR5197221/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 ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.73677611351 s Creating peak regions... Creating peak regions took 76.1295130253 s Estimating background... Estimating background took 28.0401668549 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.21433401108 s Creating peak regions... Creating peak regions took 39.6344189644 s Estimating background... Estimating background took 11.161648035 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.14098191261 s Creating peak regions... Creating peak regions took 41.9804110527 s Estimating background... Estimating background took 11.2054429054 s Processing ZNF705G-SRR5197221.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='ZNF705G-SRR5197221.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='ZNF705G-SRR5197221/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 ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.93535089493 s Creating peak regions... Creating peak regions took 67.0886580944 s Estimating background... Estimating background took 24.2376029491 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.0593829155 s Creating peak regions... Creating peak regions took 41.7298829556 s Estimating background... Estimating background took 11.0034320354 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.20586895943 s Creating peak regions... Creating peak regions took 40.4373669624 s Estimating background... Estimating background took 9.34065103531 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.93388414383 s Creating peak regions... Creating peak regions took 48.2929418087 s Estimating background... Estimating background took 11.4653120041 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06909704208 s Creating peak regions... Creating peak regions took 33.8068239689 s Estimating background... Estimating background took 12.9867019653 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.44163799286 s Creating peak regions... Creating peak regions took 31.6922249794 s Estimating background... Estimating background took 7.26969695091 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.39852714539 s Creating peak regions... Creating peak regions took 27.5623509884 s Estimating background... Estimating background took 8.08712697029 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.55586385727 s Creating peak regions... Creating peak regions took 27.8579280376 s Estimating background... Estimating background took 6.78170204163 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.55629897118 s Creating peak regions... Creating peak regions took 23.8227379322 s Estimating background... Estimating background took 8.75917887688 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.1486749649 s Creating peak regions... Creating peak regions took 22.1778419018 s Estimating background... Estimating background took 6.4674551487 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.06536912918 s Creating peak regions... Creating peak regions took 18.0278351307 s Estimating background... Estimating background took 5.52589392662 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.77336382866 s Creating peak regions... Creating peak regions took 76.9719889164 s Estimating background... Estimating background took 17.7975730896 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.21886897087 s Creating peak regions... Creating peak regions took 21.7418589592 s Estimating background... Estimating background took 6.6276268959 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.665814876556 s Creating peak regions... Creating peak regions took 13.6155028343 s Estimating background... Estimating background took 4.12569594383 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.854557037354 s Creating peak regions... Creating peak regions took 15.5540010929 s Estimating background... Estimating background took 5.32169508934 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.23266816139 s Creating peak regions... Creating peak regions took 63.9561340809 s Estimating background... Estimating background took 14.8377361298 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.29570484161 s Creating peak regions... Creating peak regions took 49.793076992 s Estimating background... Estimating background took 12.9322299957 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.92721390724 s Creating peak regions... Creating peak regions took 56.2943360806 s Estimating background... Estimating background took 13.9166400433 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85761499405 s Creating peak regions... Creating peak regions took 62.8788118362 s Estimating background... Estimating background took 17.1012039185 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.97087097168 s Creating peak regions... Creating peak regions took 49.455769062 s Estimating background... Estimating background took 14.0364530087 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.4555990696 s Creating peak regions... Creating peak regions took 47.291986227 s Estimating background... Estimating background took 10.3908991814 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.04427599907 s Creating peak regions... Creating peak regions took 39.6518881321 s Estimating background... Estimating background took 9.84163379669 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.110012054443 s Creating peak regions... Creating peak regions took 0.214836835861 s Estimating background... Estimating background took 0.817108869553 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.95128798485 s Creating peak regions... Creating peak regions took 47.8704829216 s Estimating background... Estimating background took 15.0498378277 s Processing ZNF705G-SRR5197221.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.51796913147 s Creating peak regions... Creating peak regions took 18.0566120148 s Estimating background... Estimating background took 0.588309049606 s