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='ZNF492-SRR5197158.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='ZNF492-SRR5197158/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 ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.56237792969 s Creating peak regions... Creating peak regions took 81.7241439819 s Estimating background... Estimating background took 81.9021019936 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.83738493919 s Creating peak regions... Creating peak regions took 43.3631088734 s Estimating background... Estimating background took 26.3130180836 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.73064017296 s Creating peak regions... Creating peak regions took 35.5440151691 s Estimating background... Estimating background took 27.147149086 s Processing ZNF492-SRR5197158.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='ZNF492-SRR5197158.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='ZNF492-SRR5197158/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 ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.85390210152 s Creating peak regions... Creating peak regions took 85.9312050343 s Estimating background... Estimating background took 83.486205101 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.74475908279 s Creating peak regions... Creating peak regions took 46.9132270813 s Estimating background... Estimating background took 31.298707962 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.57887792587 s Creating peak regions... Creating peak regions took 46.4030649662 s Estimating background... Estimating background took 33.2774119377 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.88590812683 s Creating peak regions... Creating peak regions took 45.6328401566 s Estimating background... Estimating background took 33.3347198963 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.24426484108 s Creating peak regions... Creating peak regions took 39.3423860073 s Estimating background... Estimating background took 39.9825611115 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.49819993973 s Creating peak regions... Creating peak regions took 34.537322998 s Estimating background... Estimating background took 21.3448770046 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.05209088326 s Creating peak regions... Creating peak regions took 34.5098779202 s Estimating background... Estimating background took 24.6175649166 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.08674192429 s Creating peak regions... Creating peak regions took 30.9746441841 s Estimating background... Estimating background took 21.5359671116 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.30299806595 s Creating peak regions... Creating peak regions took 29.0884311199 s Estimating background... Estimating background took 26.6864359379 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.67189097404 s Creating peak regions... Creating peak regions took 27.5227210522 s Estimating background... Estimating background took 17.1951210499 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06236290932 s Creating peak regions... Creating peak regions took 19.8120849133 s Estimating background... Estimating background took 15.7381188869 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.49692296982 s Creating peak regions... Creating peak regions took 86.672524929 s Estimating background... Estimating background took 56.3432409763 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32617998123 s Creating peak regions... Creating peak regions took 23.8708150387 s Estimating background... Estimating background took 18.5120329857 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.5533220768 s Creating peak regions... Creating peak regions took 16.1113681793 s Estimating background... Estimating background took 10.8877289295 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.81900215149 s Creating peak regions... Creating peak regions took 18.4653270245 s Estimating background... Estimating background took 17.3506700993 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.15625214577 s Creating peak regions... Creating peak regions took 67.1407701969 s Estimating background... Estimating background took 44.6909880638 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.23809504509 s Creating peak regions... Creating peak regions took 55.4452679157 s Estimating background... Estimating background took 26.970788002 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.01081800461 s Creating peak regions... Creating peak regions took 50.4259638786 s Estimating background... Estimating background took 34.7329101562 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.94339799881 s Creating peak regions... Creating peak regions took 46.538697958 s Estimating background... Estimating background took 39.1368379593 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.35048413277 s Creating peak regions... Creating peak regions took 44.9014701843 s Estimating background... Estimating background took 33.8866860867 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.58836293221 s Creating peak regions... Creating peak regions took 40.3774719238 s Estimating background... Estimating background took 24.8287467957 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.01866698265 s Creating peak regions... Creating peak regions took 37.3672111034 s Estimating background... Estimating background took 23.3673348427 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0991070270538 s Creating peak regions... Creating peak regions took 0.179045200348 s Estimating background... Estimating background took 0.556873083115 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.56822514534 s Creating peak regions... Creating peak regions took 44.1202170849 s Estimating background... Estimating background took 39.7539589405 s Processing ZNF492-SRR5197158.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.219409942627 s Creating peak regions... Creating peak regions took 14.6876721382 s Estimating background... Estimating background took 0.744381904602 s