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='ZNF615-SRR5197197.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='ZNF615-SRR5197197/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 ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.56363010406 s Creating peak regions... Creating peak regions took 66.3925848007 s Estimating background... Estimating background took 53.6361470222 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.95699000359 s Creating peak regions... Creating peak regions took 34.9917199612 s Estimating background... Estimating background took 22.3667058945 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85412192345 s Creating peak regions... Creating peak regions took 35.7915799618 s Estimating background... Estimating background took 22.2563049793 s Processing ZNF615-SRR5197197.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='ZNF615-SRR5197197.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='ZNF615-SRR5197197/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 ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.35526895523 s Creating peak regions... Creating peak regions took 82.014467001 s Estimating background... Estimating background took 65.5075359344 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.41608595848 s Creating peak regions... Creating peak regions took 50.1081130505 s Estimating background... Estimating background took 27.7103528976 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.48931884766 s Creating peak regions... Creating peak regions took 44.9981870651 s Estimating background... Estimating background took 28.5438699722 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.02499008179 s Creating peak regions... Creating peak regions took 47.8156099319 s Estimating background... Estimating background took 27.775083065 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.62897491455 s Creating peak regions... Creating peak regions took 37.8852450848 s Estimating background... Estimating background took 31.3175752163 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.99022698402 s Creating peak regions... Creating peak regions took 34.1454339027 s Estimating background... Estimating background took 16.2385721207 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.83117604256 s Creating peak regions... Creating peak regions took 33.3975040913 s Estimating background... Estimating background took 18.4731080532 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.61408090591 s Creating peak regions... Creating peak regions took 30.7007989883 s Estimating background... Estimating background took 15.7170009613 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.12067198753 s Creating peak regions... Creating peak regions took 26.4029791355 s Estimating background... Estimating background took 18.865885973 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.49644303322 s Creating peak regions... Creating peak regions took 28.29164505 s Estimating background... Estimating background took 12.4295680523 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.84781813622 s Creating peak regions... Creating peak regions took 19.9763710499 s Estimating background... Estimating background took 10.9140160084 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.95451498032 s Creating peak regions... Creating peak regions took 72.6784598827 s Estimating background... Estimating background took 39.6187810898 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.27559304237 s Creating peak regions... Creating peak regions took 22.8963580132 s Estimating background... Estimating background took 13.8188929558 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.28350806236 s Creating peak regions... Creating peak regions took 14.7045888901 s Estimating background... Estimating background took 7.94869208336 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.72697687149 s Creating peak regions... Creating peak regions took 17.6893358231 s Estimating background... Estimating background took 11.9761910439 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.30760812759 s Creating peak regions... Creating peak regions took 58.6145119667 s Estimating background... Estimating background took 33.2667400837 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.76813983917 s Creating peak regions... Creating peak regions took 57.683401823 s Estimating background... Estimating background took 25.6825251579 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.25871300697 s Creating peak regions... Creating peak regions took 57.8388988972 s Estimating background... Estimating background took 33.6601808071 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.97108006477 s Creating peak regions... Creating peak regions took 56.6632111073 s Estimating background... Estimating background took 37.1422688961 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.03095722198 s Creating peak regions... Creating peak regions took 50.3937928677 s Estimating background... Estimating background took 30.7926080227 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.18908786774 s Creating peak regions... Creating peak regions took 44.3136200905 s Estimating background... Estimating background took 23.2412660122 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.4652299881 s Creating peak regions... Creating peak regions took 41.9941198826 s Estimating background... Estimating background took 22.6050560474 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.186480998993 s Creating peak regions... Creating peak regions took 0.247346162796 s Estimating background... Estimating background took 0.912380933762 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.80324292183 s Creating peak regions... Creating peak regions took 46.822701931 s Estimating background... Estimating background took 34.3094189167 s Processing ZNF615-SRR5197197.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.316576004028 s Creating peak regions... Creating peak regions took 14.2613990307 s Estimating background... Estimating background took 0.79611492157 s