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='ZNF674-SRR5197210.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='ZNF674-SRR5197210/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 ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.52359604836 s Creating peak regions... Creating peak regions took 76.8975980282 s Estimating background... Estimating background took 39.8434650898 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.77702498436 s Creating peak regions... Creating peak regions took 41.1059310436 s Estimating background... Estimating background took 15.5018789768 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.66361308098 s Creating peak regions... Creating peak regions took 41.7038581371 s Estimating background... Estimating background took 14.2215850353 s Processing ZNF674-SRR5197210.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='ZNF674-SRR5197210.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='ZNF674-SRR5197210/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 ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.92130994797 s Creating peak regions... Creating peak regions took 74.3001999855 s Estimating background... Estimating background took 37.4828920364 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.59916090965 s Creating peak regions... Creating peak regions took 38.4552960396 s Estimating background... Estimating background took 14.8219311237 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.52056002617 s Creating peak regions... Creating peak regions took 41.3401470184 s Estimating background... Estimating background took 14.9016251564 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.80204105377 s Creating peak regions... Creating peak regions took 41.0926411152 s Estimating background... Estimating background took 16.0043430328 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.27587199211 s Creating peak regions... Creating peak regions took 34.8242380619 s Estimating background... Estimating background took 14.4081790447 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.94005799294 s Creating peak regions... Creating peak regions took 30.1504399776 s Estimating background... Estimating background took 10.4380919933 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.85626602173 s Creating peak regions... Creating peak regions took 30.3122880459 s Estimating background... Estimating background took 11.8972611427 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.86941885948 s Creating peak regions... Creating peak regions took 25.640930891 s Estimating background... Estimating background took 11.3060348034 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.14288711548 s Creating peak regions... Creating peak regions took 25.8714659214 s Estimating background... Estimating background took 14.7551629543 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.44493293762 s Creating peak regions... Creating peak regions took 24.4269549847 s Estimating background... Estimating background took 7.50531482697 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.45045018196 s Creating peak regions... Creating peak regions took 17.3409070969 s Estimating background... Estimating background took 10.4900751114 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.448802948 s Creating peak regions... Creating peak regions took 71.1937718391 s Estimating background... Estimating background took 25.7774851322 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.49249696732 s Creating peak regions... Creating peak regions took 19.8531651497 s Estimating background... Estimating background took 9.06597495079 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.718855857849 s Creating peak regions... Creating peak regions took 14.094866991 s Estimating background... Estimating background took 4.7284860611 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.2624399662 s Creating peak regions... Creating peak regions took 15.8679280281 s Estimating background... Estimating background took 9.27171516418 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.46229195595 s Creating peak regions... Creating peak regions took 60.2229011059 s Estimating background... Estimating background took 18.7312860489 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.74303197861 s Creating peak regions... Creating peak regions took 53.8466458321 s Estimating background... Estimating background took 15.811371088 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.16848301888 s Creating peak regions... Creating peak regions took 55.1691749096 s Estimating background... Estimating background took 18.8482592106 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.55775809288 s Creating peak regions... Creating peak regions took 49.900121212 s Estimating background... Estimating background took 21.9073059559 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.08992099762 s Creating peak regions... Creating peak regions took 46.6697759628 s Estimating background... Estimating background took 19.4347410202 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.56785678864 s Creating peak regions... Creating peak regions took 44.4361310005 s Estimating background... Estimating background took 13.7177560329 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.30168414116 s Creating peak regions... Creating peak regions took 39.6045129299 s Estimating background... Estimating background took 13.2434749603 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0823729038239 s Creating peak regions... Creating peak regions took 0.155272960663 s Estimating background... Estimating background took 0.535382986069 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.00371479988 s Creating peak regions... Creating peak regions took 45.4935901165 s Estimating background... Estimating background took 17.2020950317 s Processing ZNF674-SRR5197210.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0979690551758 s Creating peak regions... Creating peak regions took 15.9383499622 s Estimating background... Estimating background took 0.57018995285 s