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='ZNF184-SRR5197071.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='ZNF184-SRR5197071/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 ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.37477588654 s Creating peak regions... Creating peak regions took 73.6686110497 s Estimating background... Estimating background took 30.210517168 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.19096398354 s Creating peak regions... Creating peak regions took 38.8843998909 s Estimating background... Estimating background took 12.2337529659 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.22426009178 s Creating peak regions... Creating peak regions took 38.8839268684 s Estimating background... Estimating background took 12.3945889473 s Processing ZNF184-SRR5197071.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='ZNF184-SRR5197071.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='ZNF184-SRR5197071/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 ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.59687805176 s Creating peak regions... Creating peak regions took 71.1342320442 s Estimating background... Estimating background took 29.7186739445 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.13243889809 s Creating peak regions... Creating peak regions took 37.2756710052 s Estimating background... Estimating background took 12.3379809856 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.19437599182 s Creating peak regions... Creating peak regions took 37.2998940945 s Estimating background... Estimating background took 12.162940979 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.42072606087 s Creating peak regions... Creating peak regions took 39.6052849293 s Estimating background... Estimating background took 12.8640921116 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.83496212959 s Creating peak regions... Creating peak regions took 31.8678228855 s Estimating background... Estimating background took 12.113353014 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.52595496178 s Creating peak regions... Creating peak regions took 29.5904920101 s Estimating background... Estimating background took 8.34929394722 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.6623442173 s Creating peak regions... Creating peak regions took 27.6681098938 s Estimating background... Estimating background took 10.2895860672 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.52789521217 s Creating peak regions... Creating peak regions took 25.8732049465 s Estimating background... Estimating background took 9.06250882149 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.72922086716 s Creating peak regions... Creating peak regions took 24.6877379417 s Estimating background... Estimating background took 10.7419731617 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.11748600006 s Creating peak regions... Creating peak regions took 22.5554010868 s Estimating background... Estimating background took 6.51743602753 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.13898015022 s Creating peak regions... Creating peak regions took 17.6659321785 s Estimating background... Estimating background took 7.55733799934 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.8098487854 s Creating peak regions... Creating peak regions took 68.3115949631 s Estimating background... Estimating background took 20.3416309357 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.14278101921 s Creating peak regions... Creating peak regions took 18.533921957 s Estimating background... Estimating background took 6.81288099289 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.657767772675 s Creating peak regions... Creating peak regions took 12.2102210522 s Estimating background... Estimating background took 4.16079497337 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.04728603363 s Creating peak regions... Creating peak regions took 15.0354428291 s Estimating background... Estimating background took 6.63392901421 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.74858498573 s Creating peak regions... Creating peak regions took 54.1588199139 s Estimating background... Estimating background took 15.8689370155 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.47952985764 s Creating peak regions... Creating peak regions took 51.7129018307 s Estimating background... Estimating background took 12.0897321701 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.83317518234 s Creating peak regions... Creating peak regions took 48.9704239368 s Estimating background... Estimating background took 15.4384250641 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.99295711517 s Creating peak regions... Creating peak regions took 47.3902668953 s Estimating background... Estimating background took 16.6017279625 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.61666417122 s Creating peak regions... Creating peak regions took 44.8818318844 s Estimating background... Estimating background took 15.3863019943 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.19428300858 s Creating peak regions... Creating peak regions took 42.876003027 s Estimating background... Estimating background took 10.7167849541 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.91078996658 s Creating peak regions... Creating peak regions took 40.4606428146 s Estimating background... Estimating background took 11.3147881031 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.086856842041 s Creating peak regions... Creating peak regions took 0.173955917358 s Estimating background... Estimating background took 0.674762964249 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.84521603584 s Creating peak regions... Creating peak regions took 46.4517719746 s Estimating background... Estimating background took 16.1185019016 s Processing ZNF184-SRR5197071.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.106189966202 s Creating peak regions... Creating peak regions took 15.2736868858 s Estimating background... Estimating background took 0.57040309906 s