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='ZNF550-SRR5197174.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='ZNF550-SRR5197174/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 ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.60802912712 s Creating peak regions... Creating peak regions took 82.3040847778 s Estimating background... Estimating background took 81.4856829643 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.63318300247 s Creating peak regions... Creating peak regions took 46.548003912 s Estimating background... Estimating background took 28.7874779701 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.09645676613 s Creating peak regions... Creating peak regions took 36.6557109356 s Estimating background... Estimating background took 25.9643938541 s Processing ZNF550-SRR5197174.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='ZNF550-SRR5197174.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='ZNF550-SRR5197174/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 ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.38499498367 s Creating peak regions... Creating peak regions took 81.7462110519 s Estimating background... Estimating background took 83.7192280293 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.59633612633 s Creating peak regions... Creating peak regions took 47.0789999962 s Estimating background... Estimating background took 32.12864995 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.44868779182 s Creating peak regions... Creating peak regions took 44.3245928288 s Estimating background... Estimating background took 32.4142150879 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.6288921833 s Creating peak regions... Creating peak regions took 42.9491209984 s Estimating background... Estimating background took 34.320538044 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.14569616318 s Creating peak regions... Creating peak regions took 37.7915451527 s Estimating background... Estimating background took 39.8851470947 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.96627807617 s Creating peak regions... Creating peak regions took 33.8840858936 s Estimating background... Estimating background took 21.3336091042 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.81381893158 s Creating peak regions... Creating peak regions took 32.0642299652 s Estimating background... Estimating background took 21.9969830513 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.81515407562 s Creating peak regions... Creating peak regions took 28.9143249989 s Estimating background... Estimating background took 21.5818641186 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.05308103561 s Creating peak regions... Creating peak regions took 27.483673811 s Estimating background... Estimating background took 26.686016798 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51985311508 s Creating peak regions... Creating peak regions took 24.5005259514 s Estimating background... Estimating background took 17.0087599754 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.33394002914 s Creating peak regions... Creating peak regions took 19.3752081394 s Estimating background... Estimating background took 17.0251820087 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.21403384209 s Creating peak regions... Creating peak regions took 78.4301908016 s Estimating background... Estimating background took 55.5183300972 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.35332202911 s Creating peak regions... Creating peak regions took 22.8951840401 s Estimating background... Estimating background took 18.3068680763 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.48920297623 s Creating peak regions... Creating peak regions took 15.2130281925 s Estimating background... Estimating background took 10.5460410118 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.84257793427 s Creating peak regions... Creating peak regions took 16.3259830475 s Estimating background... Estimating background took 16.3007600307 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.87934613228 s Creating peak regions... Creating peak regions took 67.4599609375 s Estimating background... Estimating background took 43.630810976 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.36097884178 s Creating peak regions... Creating peak regions took 60.5504009724 s Estimating background... Estimating background took 34.4224700928 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.76717495918 s Creating peak regions... Creating peak regions took 58.7313890457 s Estimating background... Estimating background took 42.2796070576 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.73688983917 s Creating peak regions... Creating peak regions took 54.3552348614 s Estimating background... Estimating background took 47.401665926 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.26463103294 s Creating peak regions... Creating peak regions took 51.3650491238 s Estimating background... Estimating background took 41.2521750927 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.28650689125 s Creating peak regions... Creating peak regions took 41.4187648296 s Estimating background... Estimating background took 26.9606258869 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.27454519272 s Creating peak regions... Creating peak regions took 39.2940781116 s Estimating background... Estimating background took 25.1505138874 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.13676905632 s Creating peak regions... Creating peak regions took 0.230844020844 s Estimating background... Estimating background took 0.663250923157 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.7465429306 s Creating peak regions... Creating peak regions took 45.4143059254 s Estimating background... Estimating background took 39.8597509861 s Processing ZNF550-SRR5197174.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.286393880844 s Creating peak regions... Creating peak regions took 14.8640317917 s Estimating background... Estimating background took 0.928484916687 s