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='ZNF273-SRR5197096.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='ZNF273-SRR5197096/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 ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.06542396545 s Creating peak regions... Creating peak regions took 76.5251851082 s Estimating background... Estimating background took 32.6214489937 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45993280411 s Creating peak regions... Creating peak regions took 39.5667898655 s Estimating background... Estimating background took 12.4368460178 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.44956111908 s Creating peak regions... Creating peak regions took 39.16467309 s Estimating background... Estimating background took 11.8551330566 s Processing ZNF273-SRR5197096.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='ZNF273-SRR5197096.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='ZNF273-SRR5197096/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 ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.77839779854 s Creating peak regions... Creating peak regions took 72.9797120094 s Estimating background... Estimating background took 33.1190969944 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.44857788086 s Creating peak regions... Creating peak regions took 40.5453338623 s Estimating background... Estimating background took 12.9423458576 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37555503845 s Creating peak regions... Creating peak regions took 32.7402758598 s Estimating background... Estimating background took 10.8278720379 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.04821109772 s Creating peak regions... Creating peak regions took 31.2726378441 s Estimating background... Estimating background took 11.0709929466 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.78445696831 s Creating peak regions... Creating peak regions took 27.5561528206 s Estimating background... Estimating background took 10.7296140194 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.49867892265 s Creating peak regions... Creating peak regions took 26.8861420155 s Estimating background... Estimating background took 7.47884297371 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.25410699844 s Creating peak regions... Creating peak regions took 23.6910660267 s Estimating background... Estimating background took 7.95475912094 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.34987783432 s Creating peak regions... Creating peak regions took 21.5048959255 s Estimating background... Estimating background took 7.47386598587 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.65587091446 s Creating peak regions... Creating peak regions took 19.5156970024 s Estimating background... Estimating background took 10.7082569599 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.07262301445 s Creating peak regions... Creating peak regions took 19.1294968128 s Estimating background... Estimating background took 5.26420283318 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.24282312393 s Creating peak regions... Creating peak regions took 15.3213839531 s Estimating background... Estimating background took 6.69480586052 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.43495082855 s Creating peak regions... Creating peak regions took 58.4581320286 s Estimating background... Estimating background took 17.4551911354 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.04551386833 s Creating peak regions... Creating peak regions took 16.3725020885 s Estimating background... Estimating background took 5.99872708321 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.690428972244 s Creating peak regions... Creating peak regions took 11.8923530579 s Estimating background... Estimating background took 3.40615200996 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.08112311363 s Creating peak regions... Creating peak regions took 13.1691319942 s Estimating background... Estimating background took 6.10280895233 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.65518403053 s Creating peak regions... Creating peak regions took 47.3715980053 s Estimating background... Estimating background took 13.4606690407 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.29639005661 s Creating peak regions... Creating peak regions took 43.0847790241 s Estimating background... Estimating background took 11.3679778576 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.44795703888 s Creating peak regions... Creating peak regions took 43.9739830494 s Estimating background... Estimating background took 13.0848579407 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.73337602615 s Creating peak regions... Creating peak regions took 41.6656959057 s Estimating background... Estimating background took 15.0299599171 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.52017402649 s Creating peak regions... Creating peak regions took 39.7484688759 s Estimating background... Estimating background took 13.8534989357 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.03366088867 s Creating peak regions... Creating peak regions took 37.3495419025 s Estimating background... Estimating background took 9.99626302719 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.91145586967 s Creating peak regions... Creating peak regions took 35.386785984 s Estimating background... Estimating background took 9.74232387543 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0814759731293 s Creating peak regions... Creating peak regions took 0.132557868958 s Estimating background... Estimating background took 0.544365167618 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.44496893883 s Creating peak regions... Creating peak regions took 40.3807311058 s Estimating background... Estimating background took 11.4655320644 s Processing ZNF273-SRR5197096.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0975971221924 s Creating peak regions... Creating peak regions took 12.2960991859 s Estimating background... Estimating background took 0.460902929306 s