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='ZNF317-SRR5197111.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='ZNF317-SRR5197111/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 ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.92708182335 s Creating peak regions... Creating peak regions took 83.9374580383 s Estimating background... Estimating background took 99.8273379803 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.8991689682 s Creating peak regions... Creating peak regions took 44.8314199448 s Estimating background... Estimating background took 37.821792841 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.95995092392 s Creating peak regions... Creating peak regions took 39.2625300884 s Estimating background... Estimating background took 34.5607309341 s Processing ZNF317-SRR5197111.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='ZNF317-SRR5197111.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='ZNF317-SRR5197111/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 ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.10066199303 s Creating peak regions... Creating peak regions took 81.8747282028 s Estimating background... Estimating background took 105.735337973 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.8541059494 s Creating peak regions... Creating peak regions took 45.7820439339 s Estimating background... Estimating background took 44.8975319862 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.9553360939 s Creating peak regions... Creating peak regions took 44.6640350819 s Estimating background... Estimating background took 41.741394043 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.22842001915 s Creating peak regions... Creating peak regions took 44.6449189186 s Estimating background... Estimating background took 44.1625318527 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.73786520958 s Creating peak regions... Creating peak regions took 39.9804968834 s Estimating background... Estimating background took 56.3537659645 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.65586185455 s Creating peak regions... Creating peak regions took 34.6020259857 s Estimating background... Estimating background took 28.6096150875 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.60201501846 s Creating peak regions... Creating peak regions took 34.0557549 s Estimating background... Estimating background took 35.9604110718 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.29738092422 s Creating peak regions... Creating peak regions took 28.3196380138 s Estimating background... Estimating background took 27.0753638744 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.6952278614 s Creating peak regions... Creating peak regions took 28.8929269314 s Estimating background... Estimating background took 36.8558578491 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.77111005783 s Creating peak regions... Creating peak regions took 25.9836080074 s Estimating background... Estimating background took 21.9214141369 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.50271105766 s Creating peak regions... Creating peak regions took 19.9004340172 s Estimating background... Estimating background took 22.1772069931 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.34032201767 s Creating peak regions... Creating peak regions took 80.3915030956 s Estimating background... Estimating background took 74.9058051109 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.90850615501 s Creating peak regions... Creating peak regions took 24.4148249626 s Estimating background... Estimating background took 23.4682559967 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.53582000732 s Creating peak regions... Creating peak regions took 15.5506699085 s Estimating background... Estimating background took 14.2091290951 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95225286484 s Creating peak regions... Creating peak regions took 17.8780200481 s Estimating background... Estimating background took 21.2550959587 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.85786795616 s Creating peak regions... Creating peak regions took 64.7760429382 s Estimating background... Estimating background took 49.0527420044 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.6525850296 s Creating peak regions... Creating peak regions took 51.9887039661 s Estimating background... Estimating background took 37.8618900776 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.00173020363 s Creating peak regions... Creating peak regions took 50.3637990952 s Estimating background... Estimating background took 44.1327290535 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.41694092751 s Creating peak regions... Creating peak regions took 48.5982851982 s Estimating background... Estimating background took 54.0319030285 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.90207791328 s Creating peak regions... Creating peak regions took 44.824048996 s Estimating background... Estimating background took 43.4495868683 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.87921214104 s Creating peak regions... Creating peak regions took 40.0688540936 s Estimating background... Estimating background took 31.9291300774 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.44929695129 s Creating peak regions... Creating peak regions took 37.7557878494 s Estimating background... Estimating background took 31.1248660088 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.187102079391 s Creating peak regions... Creating peak regions took 0.26372385025 s Estimating background... Estimating background took 2.19964385033 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.29466485977 s Creating peak regions... Creating peak regions took 41.7269229889 s Estimating background... Estimating background took 47.5472681522 s Processing ZNF317-SRR5197111.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.14456987381 s Creating peak regions... Creating peak regions took 13.1048769951 s Estimating background... Estimating background took 0.840111970901 s