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='ZNF880-SRR5197264.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='ZNF880-SRR5197264/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 ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.55745506287 s Creating peak regions... Creating peak regions took 74.0842020512 s Estimating background... Estimating background took 54.65218997 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.54113698006 s Creating peak regions... Creating peak regions took 39.4276659489 s Estimating background... Estimating background took 22.3494048119 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.33618187904 s Creating peak regions... Creating peak regions took 37.4186470509 s Estimating background... Estimating background took 20.5021588802 s Processing ZNF880-SRR5197264.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='ZNF880-SRR5197264.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='ZNF880-SRR5197264/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 ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.97475600243 s Creating peak regions... Creating peak regions took 64.7148859501 s Estimating background... Estimating background took 51.0668780804 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.32684493065 s Creating peak regions... Creating peak regions took 35.1806190014 s Estimating background... Estimating background took 21.3011851311 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.33741688728 s Creating peak regions... Creating peak regions took 34.9896860123 s Estimating background... Estimating background took 21.099490881 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.36460709572 s Creating peak regions... Creating peak regions took 34.7407531738 s Estimating background... Estimating background took 22.4767739773 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.02611398697 s Creating peak regions... Creating peak regions took 30.0013039112 s Estimating background... Estimating background took 21.1281709671 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.30344414711 s Creating peak regions... Creating peak regions took 27.0176179409 s Estimating background... Estimating background took 14.3468589783 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.13510799408 s Creating peak regions... Creating peak regions took 25.5678300858 s Estimating background... Estimating background took 15.9301791191 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.97798299789 s Creating peak regions... Creating peak regions took 22.6691730022 s Estimating background... Estimating background took 12.1284689903 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37087011337 s Creating peak regions... Creating peak regions took 23.5283470154 s Estimating background... Estimating background took 18.8011851311 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.84128904343 s Creating peak regions... Creating peak regions took 21.1824800968 s Estimating background... Estimating background took 10.3892748356 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.63392090797 s Creating peak regions... Creating peak regions took 15.2542350292 s Estimating background... Estimating background took 10.6195850372 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.50211596489 s Creating peak regions... Creating peak regions took 62.4885809422 s Estimating background... Estimating background took 35.8498630524 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.8022749424 s Creating peak regions... Creating peak regions took 17.6984100342 s Estimating background... Estimating background took 12.0572237968 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.991355895996 s Creating peak regions... Creating peak regions took 11.7098867893 s Estimating background... Estimating background took 6.20494699478 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.26402497292 s Creating peak regions... Creating peak regions took 12.6897349358 s Estimating background... Estimating background took 10.944647789 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.40048384666 s Creating peak regions... Creating peak regions took 50.3133170605 s Estimating background... Estimating background took 27.7406589985 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.67200398445 s Creating peak regions... Creating peak regions took 48.3591258526 s Estimating background... Estimating background took 20.7926290035 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.97692894936 s Creating peak regions... Creating peak regions took 47.4983389378 s Estimating background... Estimating background took 26.7159190178 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.26911687851 s Creating peak regions... Creating peak regions took 45.1885581017 s Estimating background... Estimating background took 29.0787079334 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.06769394875 s Creating peak regions... Creating peak regions took 42.0645668507 s Estimating background... Estimating background took 26.6471538544 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.33632993698 s Creating peak regions... Creating peak regions took 35.9344210625 s Estimating background... Estimating background took 20.0410239697 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.80303907394 s Creating peak regions... Creating peak regions took 35.1715180874 s Estimating background... Estimating background took 18.2304699421 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0823059082031 s Creating peak regions... Creating peak regions took 0.16593003273 s Estimating background... Estimating background took 0.654658079147 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.28325986862 s Creating peak regions... Creating peak regions took 42.5676670074 s Estimating background... Estimating background took 28.1838719845 s Processing ZNF880-SRR5197264.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.152793884277 s Creating peak regions... Creating peak regions took 12.8326001167 s Estimating background... Estimating background took 0.615375041962 s