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='ZNF429-SRR5197135.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='ZNF429-SRR5197135/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 ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.20632410049 s Creating peak regions... Creating peak regions took 81.1388540268 s Estimating background... Estimating background took 50.1475129128 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.42948317528 s Creating peak regions... Creating peak regions took 42.4685559273 s Estimating background... Estimating background took 20.7909510136 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.07010388374 s Creating peak regions... Creating peak regions took 41.2161278725 s Estimating background... Estimating background took 18.0382699966 s Processing ZNF429-SRR5197135.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='ZNF429-SRR5197135.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='ZNF429-SRR5197135/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 ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.35177087784 s Creating peak regions... Creating peak regions took 77.9159181118 s Estimating background... Estimating background took 51.8511750698 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.2795650959 s Creating peak regions... Creating peak regions took 41.5323941708 s Estimating background... Estimating background took 21.4207010269 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.13783383369 s Creating peak regions... Creating peak regions took 42.3180861473 s Estimating background... Estimating background took 19.6536049843 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.57419204712 s Creating peak regions... Creating peak regions took 40.6565818787 s Estimating background... Estimating background took 21.4482359886 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.18511295319 s Creating peak regions... Creating peak regions took 36.1976468563 s Estimating background... Estimating background took 26.3387410641 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.10969901085 s Creating peak regions... Creating peak regions took 30.8079419136 s Estimating background... Estimating background took 12.749076128 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.13174200058 s Creating peak regions... Creating peak regions took 30.7880520821 s Estimating background... Estimating background took 15.9250249863 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.04673504829 s Creating peak regions... Creating peak regions took 28.0276999474 s Estimating background... Estimating background took 13.8064930439 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.58642411232 s Creating peak regions... Creating peak regions took 25.0929620266 s Estimating background... Estimating background took 15.4104599953 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.72268295288 s Creating peak regions... Creating peak regions took 24.243293047 s Estimating background... Estimating background took 11.2768309116 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.48062705994 s Creating peak regions... Creating peak regions took 19.5553719997 s Estimating background... Estimating background took 10.4574391842 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.38982701302 s Creating peak regions... Creating peak regions took 78.4582509995 s Estimating background... Estimating background took 33.4582428932 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7359919548 s Creating peak regions... Creating peak regions took 21.1751439571 s Estimating background... Estimating background took 10.3305230141 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.910145998001 s Creating peak regions... Creating peak regions took 13.7304458618 s Estimating background... Estimating background took 5.90744709969 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.16523599625 s Creating peak regions... Creating peak regions took 15.1261651516 s Estimating background... Estimating background took 8.391040802 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.35771894455 s Creating peak regions... Creating peak regions took 60.927959919 s Estimating background... Estimating background took 28.1015241146 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.01983499527 s Creating peak regions... Creating peak regions took 53.7372410297 s Estimating background... Estimating background took 23.2358071804 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.27488613129 s Creating peak regions... Creating peak regions took 57.4209508896 s Estimating background... Estimating background took 25.0500218868 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.91647791862 s Creating peak regions... Creating peak regions took 53.4146649837 s Estimating background... Estimating background took 29.6181750298 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.11317420006 s Creating peak regions... Creating peak regions took 48.5527939796 s Estimating background... Estimating background took 21.759401083 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.73393106461 s Creating peak regions... Creating peak regions took 37.2275979519 s Estimating background... Estimating background took 19.4208030701 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.16299319267 s Creating peak regions... Creating peak regions took 34.5438790321 s Estimating background... Estimating background took 14.5112099648 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0995600223541 s Creating peak regions... Creating peak regions took 0.185677051544 s Estimating background... Estimating background took 0.764558076859 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.28705787659 s Creating peak regions... Creating peak regions took 40.1601879597 s Estimating background... Estimating background took 25.0418591499 s Processing ZNF429-SRR5197135.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.117555856705 s Creating peak regions... Creating peak regions took 13.6574440002 s Estimating background... Estimating background took 0.659693956375 s