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='ZNF791-SRR5197247.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='ZNF791-SRR5197247/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 ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.48132801056 s Creating peak regions... Creating peak regions took 81.7988920212 s Estimating background... Estimating background took 83.3376531601 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.46944117546 s Creating peak regions... Creating peak regions took 43.3282649517 s Estimating background... Estimating background took 26.4427030087 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.45446014404 s Creating peak regions... Creating peak regions took 35.4672350883 s Estimating background... Estimating background took 23.6290900707 s Processing ZNF791-SRR5197247.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='ZNF791-SRR5197247.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='ZNF791-SRR5197247/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 ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.56907486916 s Creating peak regions... Creating peak regions took 76.7527899742 s Estimating background... Estimating background took 75.8078579903 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.24178314209 s Creating peak regions... Creating peak regions took 40.591958046 s Estimating background... Estimating background took 26.8284111023 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.73133182526 s Creating peak regions... Creating peak regions took 39.2086930275 s Estimating background... Estimating background took 26.0199809074 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.78267288208 s Creating peak regions... Creating peak regions took 40.1765179634 s Estimating background... Estimating background took 27.6311759949 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.47249794006 s Creating peak regions... Creating peak regions took 34.0259912014 s Estimating background... Estimating background took 27.8867709637 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.71518206596 s Creating peak regions... Creating peak regions took 30.6892900467 s Estimating background... Estimating background took 18.108738184 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.79533481598 s Creating peak regions... Creating peak regions took 29.8098549843 s Estimating background... Estimating background took 23.8836708069 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.68368792534 s Creating peak regions... Creating peak regions took 25.5330119133 s Estimating background... Estimating background took 19.2526769638 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.04731488228 s Creating peak regions... Creating peak regions took 24.9298810959 s Estimating background... Estimating background took 27.2054200172 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.13750100136 s Creating peak regions... Creating peak regions took 23.4243221283 s Estimating background... Estimating background took 13.6816110611 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.93907499313 s Creating peak regions... Creating peak regions took 18.5444300175 s Estimating background... Estimating background took 13.981153965 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.14009904861 s Creating peak regions... Creating peak regions took 75.2194299698 s Estimating background... Estimating background took 45.1577868462 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95205307007 s Creating peak regions... Creating peak regions took 20.3977649212 s Estimating background... Estimating background took 13.7569820881 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.13488698006 s Creating peak regions... Creating peak regions took 12.9021191597 s Estimating background... Estimating background took 7.94185805321 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.75538992882 s Creating peak regions... Creating peak regions took 15.6763520241 s Estimating background... Estimating background took 16.2214698792 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.15603804588 s Creating peak regions... Creating peak regions took 57.2547011375 s Estimating background... Estimating background took 36.9782159328 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.26645112038 s Creating peak regions... Creating peak regions took 53.5511651039 s Estimating background... Estimating background took 25.9547429085 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.76545095444 s Creating peak regions... Creating peak regions took 53.0104730129 s Estimating background... Estimating background took 32.1154301167 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.03238606453 s Creating peak regions... Creating peak regions took 48.0263888836 s Estimating background... Estimating background took 38.2077169418 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.67584609985 s Creating peak regions... Creating peak regions took 46.3539948463 s Estimating background... Estimating background took 32.5816221237 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.50078487396 s Creating peak regions... Creating peak regions took 41.2563829422 s Estimating background... Estimating background took 21.0069191456 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.19821691513 s Creating peak regions... Creating peak regions took 38.2581400871 s Estimating background... Estimating background took 23.5897011757 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.151268005371 s Creating peak regions... Creating peak regions took 0.218740940094 s Estimating background... Estimating background took 0.799144983292 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.45191884041 s Creating peak regions... Creating peak regions took 43.3281869888 s Estimating background... Estimating background took 35.2011539936 s Processing ZNF791-SRR5197247.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.321603059769 s Creating peak regions... Creating peak regions took 14.2923820019 s Estimating background... Estimating background took 0.669276952744 s