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='ZNF667-SRR5197207.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='ZNF667-SRR5197207/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 ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.16535210609 s Creating peak regions... Creating peak regions took 77.3046998978 s Estimating background... Estimating background took 34.8751101494 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.84050393105 s Creating peak regions... Creating peak regions took 44.09841609 s Estimating background... Estimating background took 13.6088011265 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.72910189629 s Creating peak regions... Creating peak regions took 42.6885960102 s Estimating background... Estimating background took 12.734940052 s Processing ZNF667-SRR5197207.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='ZNF667-SRR5197207.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='ZNF667-SRR5197207/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 ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.96737909317 s Creating peak regions... Creating peak regions took 74.6281139851 s Estimating background... Estimating background took 32.7181911469 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.54613494873 s Creating peak regions... Creating peak regions took 39.0386669636 s Estimating background... Estimating background took 13.2458848953 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.44079303741 s Creating peak regions... Creating peak regions took 41.6086959839 s Estimating background... Estimating background took 13.4296557903 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.65542292595 s Creating peak regions... Creating peak regions took 38.7359359264 s Estimating background... Estimating background took 14.8045568466 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.47864103317 s Creating peak regions... Creating peak regions took 33.883275032 s Estimating background... Estimating background took 17.8729748726 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7400290966 s Creating peak regions... Creating peak regions took 32.5948958397 s Estimating background... Estimating background took 9.66115379333 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.59713602066 s Creating peak regions... Creating peak regions took 30.8261189461 s Estimating background... Estimating background took 10.2514829636 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.6225259304 s Creating peak regions... Creating peak regions took 27.3944849968 s Estimating background... Estimating background took 8.53893399239 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.78740406036 s Creating peak regions... Creating peak regions took 24.0085179806 s Estimating background... Estimating background took 10.4445319176 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.46840381622 s Creating peak regions... Creating peak regions took 24.4102141857 s Estimating background... Estimating background took 8.02087807655 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.17539620399 s Creating peak regions... Creating peak regions took 17.1419761181 s Estimating background... Estimating background took 6.20549416542 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.37474799156 s Creating peak regions... Creating peak regions took 73.6685581207 s Estimating background... Estimating background took 23.5052301884 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.35550403595 s Creating peak regions... Creating peak regions took 19.8666579723 s Estimating background... Estimating background took 7.79574990273 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.793561935425 s Creating peak regions... Creating peak regions took 13.5918619633 s Estimating background... Estimating background took 4.38750505447 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.943141937256 s Creating peak regions... Creating peak regions took 14.8787260056 s Estimating background... Estimating background took 6.30140399933 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.54742002487 s Creating peak regions... Creating peak regions took 57.4584219456 s Estimating background... Estimating background took 18.2617180347 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.24357390404 s Creating peak regions... Creating peak regions took 55.2158529758 s Estimating background... Estimating background took 15.82041502 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.31004691124 s Creating peak regions... Creating peak regions took 52.7088339329 s Estimating background... Estimating background took 18.4359171391 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.48739099503 s Creating peak regions... Creating peak regions took 50.8159959316 s Estimating background... Estimating background took 20.5076880455 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.21226215363 s Creating peak regions... Creating peak regions took 47.2255930901 s Estimating background... Estimating background took 18.0134849548 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.66818404198 s Creating peak regions... Creating peak regions took 42.4771900177 s Estimating background... Estimating background took 13.1727979183 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23901700974 s Creating peak regions... Creating peak regions took 39.4726638794 s Estimating background... Estimating background took 11.901706934 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0941691398621 s Creating peak regions... Creating peak regions took 0.177841901779 s Estimating background... Estimating background took 0.664435863495 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.4171769619 s Creating peak regions... Creating peak regions took 48.8672389984 s Estimating background... Estimating background took 20.0705699921 s Processing ZNF667-SRR5197207.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.117573976517 s Creating peak regions... Creating peak regions took 15.8052539825 s Estimating background... Estimating background took 0.566279888153 s