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='ZKSCAN2-SRR5197047.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='ZKSCAN2-SRR5197047/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 ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.7048869133 s Creating peak regions... Creating peak regions took 69.1807420254 s Estimating background... Estimating background took 50.9624359608 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.34759807587 s Creating peak regions... Creating peak regions took 36.695073843 s Estimating background... Estimating background took 19.9285678864 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.35367012024 s Creating peak regions... Creating peak regions took 36.8663580418 s Estimating background... Estimating background took 19.4033789635 s Processing ZKSCAN2-SRR5197047.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='ZKSCAN2-SRR5197047.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='ZKSCAN2-SRR5197047/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 ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.34768891335 s Creating peak regions... Creating peak regions took 72.0557150841 s Estimating background... Estimating background took 52.7845489979 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.5786049366 s Creating peak regions... Creating peak regions took 37.9393179417 s Estimating background... Estimating background took 20.4926400185 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.41990089417 s Creating peak regions... Creating peak regions took 38.1640520096 s Estimating background... Estimating background took 21.0190269947 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.95561790466 s Creating peak regions... Creating peak regions took 38.8568079472 s Estimating background... Estimating background took 22.3835041523 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.12428402901 s Creating peak regions... Creating peak regions took 33.4042589664 s Estimating background... Estimating background took 22.6868910789 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.67090582848 s Creating peak regions... Creating peak regions took 30.4042711258 s Estimating background... Estimating background took 14.4892859459 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.47525596619 s Creating peak regions... Creating peak regions took 28.9378499985 s Estimating background... Estimating background took 16.1773710251 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.59111309052 s Creating peak regions... Creating peak regions took 27.6550090313 s Estimating background... Estimating background took 14.8683810234 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.93869900703 s Creating peak regions... Creating peak regions took 26.2817819118 s Estimating background... Estimating background took 19.9591441154 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98793101311 s Creating peak regions... Creating peak regions took 22.9538900852 s Estimating background... Estimating background took 10.8849830627 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92306900024 s Creating peak regions... Creating peak regions took 17.286386013 s Estimating background... Estimating background took 12.3344578743 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.01856398582 s Creating peak regions... Creating peak regions took 73.7249259949 s Estimating background... Estimating background took 35.4174859524 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.01811003685 s Creating peak regions... Creating peak regions took 19.7365069389 s Estimating background... Estimating background took 12.1674468517 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.26069402695 s Creating peak regions... Creating peak regions took 14.2627718449 s Estimating background... Estimating background took 6.92063593864 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.71288204193 s Creating peak regions... Creating peak regions took 14.9637269974 s Estimating background... Estimating background took 11.9735310078 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.08302497864 s Creating peak regions... Creating peak regions took 57.5287218094 s Estimating background... Estimating background took 27.0293109417 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.2359931469 s Creating peak regions... Creating peak regions took 54.3217251301 s Estimating background... Estimating background took 21.1657512188 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.72967004776 s Creating peak regions... Creating peak regions took 52.9520249367 s Estimating background... Estimating background took 26.3433718681 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.93500208855 s Creating peak regions... Creating peak regions took 47.7667448521 s Estimating background... Estimating background took 30.6100530624 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.48563098907 s Creating peak regions... Creating peak regions took 46.8860690594 s Estimating background... Estimating background took 27.1984329224 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.76384997368 s Creating peak regions... Creating peak regions took 41.8577179909 s Estimating background... Estimating background took 18.7968771458 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.31531095505 s Creating peak regions... Creating peak regions took 41.7152299881 s Estimating background... Estimating background took 18.8619408607 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.106470108032 s Creating peak regions... Creating peak regions took 0.202422857285 s Estimating background... Estimating background took 0.702200889587 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.91568303108 s Creating peak regions... Creating peak regions took 45.6952960491 s Estimating background... Estimating background took 30.3586528301 s Processing ZKSCAN2-SRR5197047.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.225281000137 s Creating peak regions... Creating peak regions took 16.1131770611 s Estimating background... Estimating background took 0.773494005203 s