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='ZNF90-SRR5197267.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='ZNF90-SRR5197267/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 ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.7144241333 s Creating peak regions... Creating peak regions took 67.488243103 s Estimating background... Estimating background took 18.0257620811 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.33555698395 s Creating peak regions... Creating peak regions took 35.2465529442 s Estimating background... Estimating background took 8.23223590851 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39700198174 s Creating peak regions... Creating peak regions took 37.9687321186 s Estimating background... Estimating background took 8.18092894554 s Processing ZNF90-SRR5197267.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='ZNF90-SRR5197267.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='ZNF90-SRR5197267/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 ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.32442784309 s Creating peak regions... Creating peak regions took 61.3845019341 s Estimating background... Estimating background took 16.3914949894 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.01836895943 s Creating peak regions... Creating peak regions took 32.0453400612 s Estimating background... Estimating background took 7.52131295204 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06210017204 s Creating peak regions... Creating peak regions took 34.805109024 s Estimating background... Estimating background took 7.72331213951 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.30675601959 s Creating peak regions... Creating peak regions took 32.0563318729 s Estimating background... Estimating background took 8.21797895432 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.76700687408 s Creating peak regions... Creating peak regions took 27.3875370026 s Estimating background... Estimating background took 6.39358091354 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.48616504669 s Creating peak regions... Creating peak regions took 26.8689198494 s Estimating background... Estimating background took 5.39758992195 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.4506919384 s Creating peak regions... Creating peak regions took 25.8400781155 s Estimating background... Estimating background took 6.04315495491 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.70855116844 s Creating peak regions... Creating peak regions took 23.4641270638 s Estimating background... Estimating background took 5.86028790474 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.91213583946 s Creating peak regions... Creating peak regions took 22.0918810368 s Estimating background... Estimating background took 7.67494297028 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.1348900795 s Creating peak regions... Creating peak regions took 19.5716440678 s Estimating background... Estimating background took 3.98535394669 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.47919893265 s Creating peak regions... Creating peak regions took 15.4043700695 s Estimating background... Estimating background took 5.20788908005 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.70082497597 s Creating peak regions... Creating peak regions took 63.7464849949 s Estimating background... Estimating background took 12.2085161209 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.34622502327 s Creating peak regions... Creating peak regions took 17.5275349617 s Estimating background... Estimating background took 5.27782201767 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.723526000977 s Creating peak regions... Creating peak regions took 12.2350170612 s Estimating background... Estimating background took 2.65367412567 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.10322999954 s Creating peak regions... Creating peak regions took 12.3775310516 s Estimating background... Estimating background took 4.93527078629 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.96145510674 s Creating peak regions... Creating peak regions took 50.5337090492 s Estimating background... Estimating background took 9.47494506836 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.47738981247 s Creating peak regions... Creating peak regions took 45.3756430149 s Estimating background... Estimating background took 8.27628803253 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.65746593475 s Creating peak regions... Creating peak regions took 42.0781490803 s Estimating background... Estimating background took 9.29541397095 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.84097909927 s Creating peak regions... Creating peak regions took 41.6988320351 s Estimating background... Estimating background took 10.2140040398 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.63398098946 s Creating peak regions... Creating peak regions took 40.8451571465 s Estimating background... Estimating background took 9.69278311729 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.18002414703 s Creating peak regions... Creating peak regions took 34.9606049061 s Estimating background... Estimating background took 7.24433493614 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95069789886 s Creating peak regions... Creating peak regions took 35.0164270401 s Estimating background... Estimating background took 7.50610995293 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0881898403168 s Creating peak regions... Creating peak regions took 0.135950088501 s Estimating background... Estimating background took 1.03105115891 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.18318009377 s Creating peak regions... Creating peak regions took 37.1230800152 s Estimating background... Estimating background took 8.02251505852 s Processing ZNF90-SRR5197267.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0789680480957 s Creating peak regions... Creating peak regions took 12.1500439644 s Estimating background... Estimating background took 0.429773807526 s