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='ZNF547-SRR5197170.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='ZNF547-SRR5197170/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 ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.46118712425 s Creating peak regions... Creating peak regions took 79.5107471943 s Estimating background... Estimating background took 55.8988969326 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.30305099487 s Creating peak regions... Creating peak regions took 42.2168087959 s Estimating background... Estimating background took 21.9685430527 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.2600338459 s Creating peak regions... Creating peak regions took 40.5682170391 s Estimating background... Estimating background took 21.3501908779 s Processing ZNF547-SRR5197170.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='ZNF547-SRR5197170.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='ZNF547-SRR5197170/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 ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.09123897552 s Creating peak regions... Creating peak regions took 79.1806092262 s Estimating background... Estimating background took 57.9385969639 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.30338597298 s Creating peak regions... Creating peak regions took 41.9337649345 s Estimating background... Estimating background took 23.5989890099 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.56555700302 s Creating peak regions... Creating peak regions took 42.7575311661 s Estimating background... Estimating background took 21.3408541679 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.65261411667 s Creating peak regions... Creating peak regions took 39.3920640945 s Estimating background... Estimating background took 24.421145916 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.10751819611 s Creating peak regions... Creating peak regions took 36.0221419334 s Estimating background... Estimating background took 25.4034771919 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.35847306252 s Creating peak regions... Creating peak regions took 31.8217821121 s Estimating background... Estimating background took 15.6285028458 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.46353793144 s Creating peak regions... Creating peak regions took 31.6637020111 s Estimating background... Estimating background took 19.9875378609 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28150105476 s Creating peak regions... Creating peak regions took 28.0543768406 s Estimating background... Estimating background took 15.2633440495 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51509094238 s Creating peak regions... Creating peak regions took 26.2042298317 s Estimating background... Estimating background took 21.8059370518 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.18239307404 s Creating peak regions... Creating peak regions took 23.8843719959 s Estimating background... Estimating background took 12.163918972 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.99602794647 s Creating peak regions... Creating peak regions took 20.3223910332 s Estimating background... Estimating background took 15.2689011097 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.81859087944 s Creating peak regions... Creating peak regions took 78.6201541424 s Estimating background... Estimating background took 38.2143931389 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.87150096893 s Creating peak regions... Creating peak regions took 20.6219239235 s Estimating background... Estimating background took 11.8516881466 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.01479291916 s Creating peak regions... Creating peak regions took 14.1076920033 s Estimating background... Estimating background took 6.80114412308 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.35994410515 s Creating peak regions... Creating peak regions took 15.8958210945 s Estimating background... Estimating background took 13.3367829323 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.44740891457 s Creating peak regions... Creating peak regions took 62.8674571514 s Estimating background... Estimating background took 28.0376360416 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.82348418236 s Creating peak regions... Creating peak regions took 58.69313097 s Estimating background... Estimating background took 24.6462161541 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.35189294815 s Creating peak regions... Creating peak regions took 55.5047821999 s Estimating background... Estimating background took 28.0573449135 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.13710093498 s Creating peak regions... Creating peak regions took 53.3644039631 s Estimating background... Estimating background took 31.5163280964 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.53205490112 s Creating peak regions... Creating peak regions took 40.6706259251 s Estimating background... Estimating background took 23.935967207 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.58659505844 s Creating peak regions... Creating peak regions took 36.2111082077 s Estimating background... Estimating background took 17.0786130428 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.16579294205 s Creating peak regions... Creating peak regions took 36.5827240944 s Estimating background... Estimating background took 17.0807070732 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0913488864899 s Creating peak regions... Creating peak regions took 0.177171945572 s Estimating background... Estimating background took 0.797103881836 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.23820304871 s Creating peak regions... Creating peak regions took 39.6678659916 s Estimating background... Estimating background took 25.6556768417 s Processing ZNF547-SRR5197170.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.127703905106 s Creating peak regions... Creating peak regions took 13.4205009937 s Estimating background... Estimating background took 0.639997959137 s