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='ZNF124-SRR5197056.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='ZNF124-SRR5197056/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 ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.16346096992 s Creating peak regions... Creating peak regions took 81.4841351509 s Estimating background... Estimating background took 89.7293958664 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.23914504051 s Creating peak regions... Creating peak regions took 42.6119809151 s Estimating background... Estimating background took 30.7260041237 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.6305000782 s Creating peak regions... Creating peak regions took 37.9947090149 s Estimating background... Estimating background took 31.2656798363 s Processing ZNF124-SRR5197056.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='ZNF124-SRR5197056.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='ZNF124-SRR5197056/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 ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.38250112534 s Creating peak regions... Creating peak regions took 68.218806982 s Estimating background... Estimating background took 72.6906411648 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.37580609322 s Creating peak regions... Creating peak regions took 36.938601017 s Estimating background... Estimating background took 29.2465689182 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.36630916595 s Creating peak regions... Creating peak regions took 37.1990959644 s Estimating background... Estimating background took 30.3397288322 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.68289589882 s Creating peak regions... Creating peak regions took 36.8632609844 s Estimating background... Estimating background took 32.3852410316 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.1312148571 s Creating peak regions... Creating peak regions took 30.113407135 s Estimating background... Estimating background took 30.384553194 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.40030884743 s Creating peak regions... Creating peak regions took 28.7166979313 s Estimating background... Estimating background took 19.8645699024 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.27272486687 s Creating peak regions... Creating peak regions took 27.2855730057 s Estimating background... Estimating background took 22.024148941 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.36878180504 s Creating peak regions... Creating peak regions took 24.8132929802 s Estimating background... Estimating background took 22.143119812 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.82057499886 s Creating peak regions... Creating peak regions took 23.9770870209 s Estimating background... Estimating background took 29.016053915 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.87316393852 s Creating peak regions... Creating peak regions took 21.5082919598 s Estimating background... Estimating background took 14.3913581371 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.07618689537 s Creating peak regions... Creating peak regions took 16.8847591877 s Estimating background... Estimating background took 19.9031729698 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.72440600395 s Creating peak regions... Creating peak regions took 65.6797058582 s Estimating background... Estimating background took 50.715512991 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.03004193306 s Creating peak regions... Creating peak regions took 19.7215769291 s Estimating background... Estimating background took 19.3069651127 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.27767109871 s Creating peak regions... Creating peak regions took 12.8919849396 s Estimating background... Estimating background took 8.89720416069 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.60364794731 s Creating peak regions... Creating peak regions took 14.1994891167 s Estimating background... Estimating background took 18.8836550713 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.38936495781 s Creating peak regions... Creating peak regions took 53.3972790241 s Estimating background... Estimating background took 39.2458329201 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.06719279289 s Creating peak regions... Creating peak regions took 50.9668061733 s Estimating background... Estimating background took 30.7700641155 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.30152988434 s Creating peak regions... Creating peak regions took 49.8241131306 s Estimating background... Estimating background took 37.8925259113 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.90977501869 s Creating peak regions... Creating peak regions took 48.2516140938 s Estimating background... Estimating background took 41.8534810543 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.38081097603 s Creating peak regions... Creating peak regions took 43.6839311123 s Estimating background... Estimating background took 39.14032197 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.72334885597 s Creating peak regions... Creating peak regions took 41.95875597 s Estimating background... Estimating background took 28.3506100178 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.12212300301 s Creating peak regions... Creating peak regions took 38.8721468449 s Estimating background... Estimating background took 27.899668932 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.154637813568 s Creating peak regions... Creating peak regions took 0.230593204498 s Estimating background... Estimating background took 0.57063794136 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.28100204468 s Creating peak regions... Creating peak regions took 43.8808040619 s Estimating background... Estimating background took 38.1622781754 s Processing ZNF124-SRR5197056.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.541697978973 s Creating peak regions... Creating peak regions took 14.7867629528 s Estimating background... Estimating background took 0.768234014511 s