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='ZNF527-SRR5197163.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='ZNF527-SRR5197163/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 ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.32994389534 s Creating peak regions... Creating peak regions took 75.8415949345 s Estimating background... Estimating background took 30.7736098766 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.17259097099 s Creating peak regions... Creating peak regions took 37.6143391132 s Estimating background... Estimating background took 12.1582489014 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.21290898323 s Creating peak regions... Creating peak regions took 41.6606471539 s Estimating background... Estimating background took 12.1946840286 s Processing ZNF527-SRR5197163.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='ZNF527-SRR5197163.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='ZNF527-SRR5197163/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 ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.16616892815 s Creating peak regions... Creating peak regions took 75.8428750038 s Estimating background... Estimating background took 31.3254358768 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.33268404007 s Creating peak regions... Creating peak regions took 39.4419031143 s Estimating background... Estimating background took 12.2535638809 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.2139070034 s Creating peak regions... Creating peak regions took 43.3074669838 s Estimating background... Estimating background took 12.593296051 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.35715794563 s Creating peak regions... Creating peak regions took 41.6027810574 s Estimating background... Estimating background took 12.8871569633 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98015117645 s Creating peak regions... Creating peak regions took 33.648968935 s Estimating background... Estimating background took 12.8147819042 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.64804887772 s Creating peak regions... Creating peak regions took 32.8305130005 s Estimating background... Estimating background took 8.47899580002 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.4492828846 s Creating peak regions... Creating peak regions took 29.2917749882 s Estimating background... Estimating background took 9.05388498306 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.38929104805 s Creating peak regions... Creating peak regions took 24.6626210213 s Estimating background... Estimating background took 8.6046860218 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.66075801849 s Creating peak regions... Creating peak regions took 24.9723808765 s Estimating background... Estimating background took 11.3504338264 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.30226111412 s Creating peak regions... Creating peak regions took 25.3105170727 s Estimating background... Estimating background took 6.89930701256 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.27225899696 s Creating peak regions... Creating peak regions took 18.0903959274 s Estimating background... Estimating background took 7.77485895157 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.82669186592 s Creating peak regions... Creating peak regions took 70.9647009373 s Estimating background... Estimating background took 21.2342610359 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.34396004677 s Creating peak regions... Creating peak regions took 20.8499019146 s Estimating background... Estimating background took 7.61693501472 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.666718959808 s Creating peak regions... Creating peak regions took 13.9390461445 s Estimating background... Estimating background took 4.16573095322 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.888407945633 s Creating peak regions... Creating peak regions took 14.3067688942 s Estimating background... Estimating background took 7.03824901581 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.04727602005 s Creating peak regions... Creating peak regions took 58.6350750923 s Estimating background... Estimating background took 16.2196359634 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.49088311195 s Creating peak regions... Creating peak regions took 54.5077359676 s Estimating background... Estimating background took 12.0519468784 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.65142297745 s Creating peak regions... Creating peak regions took 53.6619541645 s Estimating background... Estimating background took 16.3112840652 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.15327596664 s Creating peak regions... Creating peak regions took 50.9701290131 s Estimating background... Estimating background took 16.9138350487 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.63090610504 s Creating peak regions... Creating peak regions took 51.1706089973 s Estimating background... Estimating background took 16.1613798141 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.31054711342 s Creating peak regions... Creating peak regions took 43.2757270336 s Estimating background... Estimating background took 11.3747339249 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.91943502426 s Creating peak regions... Creating peak regions took 43.9377129078 s Estimating background... Estimating background took 11.4902210236 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0891859531403 s Creating peak regions... Creating peak regions took 0.179275989532 s Estimating background... Estimating background took 0.794538974762 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.95038700104 s Creating peak regions... Creating peak regions took 47.816054821 s Estimating background... Estimating background took 15.1087050438 s Processing ZNF527-SRR5197163.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0959429740906 s Creating peak regions... Creating peak regions took 13.1968560219 s Estimating background... Estimating background took 0.564038038254 s