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='ZNF879-SRR5197263.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='ZNF879-SRR5197263/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 ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.35361289978 s Creating peak regions... Creating peak regions took 74.4690141678 s Estimating background... Estimating background took 62.9394128323 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.65977787971 s Creating peak regions... Creating peak regions took 39.8340940475 s Estimating background... Estimating background took 24.4469609261 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.49022197723 s Creating peak regions... Creating peak regions took 36.3706901073 s Estimating background... Estimating background took 22.6990609169 s Processing ZNF879-SRR5197263.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='ZNF879-SRR5197263.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='ZNF879-SRR5197263/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 ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.37726306915 s Creating peak regions... Creating peak regions took 80.9888510704 s Estimating background... Estimating background took 65.2630271912 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.78432297707 s Creating peak regions... Creating peak regions took 45.1383481026 s Estimating background... Estimating background took 26.105246067 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.66566300392 s Creating peak regions... Creating peak regions took 42.7758061886 s Estimating background... Estimating background took 25.6266691685 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.2199010849 s Creating peak regions... Creating peak regions took 40.1917908192 s Estimating background... Estimating background took 27.4627490044 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.47386407852 s Creating peak regions... Creating peak regions took 36.3782169819 s Estimating background... Estimating background took 28.9920499325 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.63124608994 s Creating peak regions... Creating peak regions took 32.726708889 s Estimating background... Estimating background took 17.379155159 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.48938798904 s Creating peak regions... Creating peak regions took 31.4143099785 s Estimating background... Estimating background took 20.000868082 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.55258893967 s Creating peak regions... Creating peak regions took 27.8182389736 s Estimating background... Estimating background took 17.2577748299 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.92555499077 s Creating peak regions... Creating peak regions took 26.7052078247 s Estimating background... Estimating background took 22.7153759003 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.26365494728 s Creating peak regions... Creating peak regions took 24.6856489182 s Estimating background... Estimating background took 13.5398919582 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.18912196159 s Creating peak regions... Creating peak regions took 18.6674380302 s Estimating background... Estimating background took 14.6643781662 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.31364583969 s Creating peak regions... Creating peak regions took 80.4853870869 s Estimating background... Estimating background took 42.9349091053 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.18722295761 s Creating peak regions... Creating peak regions took 20.7218668461 s Estimating background... Estimating background took 15.0677058697 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.21537613869 s Creating peak regions... Creating peak regions took 14.535462141 s Estimating background... Estimating background took 8.00286507607 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.56910896301 s Creating peak regions... Creating peak regions took 16.0178499222 s Estimating background... Estimating background took 13.719769001 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.87834906578 s Creating peak regions... Creating peak regions took 61.8653771877 s Estimating background... Estimating background took 33.5532479286 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.53081202507 s Creating peak regions... Creating peak regions took 59.3303239346 s Estimating background... Estimating background took 26.7912149429 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.84102797508 s Creating peak regions... Creating peak regions took 57.2672920227 s Estimating background... Estimating background took 32.543982029 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.07462215424 s Creating peak regions... Creating peak regions took 54.0471930504 s Estimating background... Estimating background took 37.160681963 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.51627397537 s Creating peak regions... Creating peak regions took 50.2360439301 s Estimating background... Estimating background took 33.259292841 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.65251302719 s Creating peak regions... Creating peak regions took 45.2777709961 s Estimating background... Estimating background took 23.4797048569 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.26466417313 s Creating peak regions... Creating peak regions took 42.2361369133 s Estimating background... Estimating background took 22.1474599838 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.120792150497 s Creating peak regions... Creating peak regions took 0.220892190933 s Estimating background... Estimating background took 0.899910926819 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.39227294922 s Creating peak regions... Creating peak regions took 46.0285928249 s Estimating background... Estimating background took 32.0540060997 s Processing ZNF879-SRR5197263.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.238383054733 s Creating peak regions... Creating peak regions took 15.1874818802 s Estimating background... Estimating background took 0.761099815369 s