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='ZNF708-SRR5197223.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='ZNF708-SRR5197223/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 ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.79169082642 s Creating peak regions... Creating peak regions took 84.8479218483 s Estimating background... Estimating background took 117.857581139 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.81338095665 s Creating peak regions... Creating peak regions took 44.5583879948 s Estimating background... Estimating background took 40.6916539669 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.19080591202 s Creating peak regions... Creating peak regions took 39.8412129879 s Estimating background... Estimating background took 39.6625118256 s Processing ZNF708-SRR5197223.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='ZNF708-SRR5197223.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='ZNF708-SRR5197223/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 ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 10.0082428455 s Creating peak regions... Creating peak regions took 85.295333147 s Estimating background... Estimating background took 120.547497988 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.33247089386 s Creating peak regions... Creating peak regions took 48.1519291401 s Estimating background... Estimating background took 47.5655841827 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.22716903687 s Creating peak regions... Creating peak regions took 46.006403923 s Estimating background... Estimating background took 49.7092559338 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.46950316429 s Creating peak regions... Creating peak regions took 45.4381170273 s Estimating background... Estimating background took 51.5197610855 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.55914306641 s Creating peak regions... Creating peak regions took 38.5899600983 s Estimating background... Estimating background took 44.4919219017 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.66163706779 s Creating peak regions... Creating peak regions took 34.8697509766 s Estimating background... Estimating background took 32.262814045 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.58850288391 s Creating peak regions... Creating peak regions took 33.1105499268 s Estimating background... Estimating background took 37.0493528843 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.70322704315 s Creating peak regions... Creating peak regions took 29.8125300407 s Estimating background... Estimating background took 36.9969670773 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.2353451252 s Creating peak regions... Creating peak regions took 29.3396480083 s Estimating background... Estimating background took 45.8354868889 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.6025800705 s Creating peak regions... Creating peak regions took 26.5872581005 s Estimating background... Estimating background took 22.0027630329 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.03795409203 s Creating peak regions... Creating peak regions took 21.1425819397 s Estimating background... Estimating background took 32.5969209671 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.50166392326 s Creating peak regions... Creating peak regions took 80.4443628788 s Estimating background... Estimating background took 78.1611409187 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.15030503273 s Creating peak regions... Creating peak regions took 24.23163414 s Estimating background... Estimating background took 28.9570498466 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.53097295761 s Creating peak regions... Creating peak regions took 15.2148530483 s Estimating background... Estimating background took 13.8965299129 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39274597168 s Creating peak regions... Creating peak regions took 18.3988888264 s Estimating background... Estimating background took 30.1804180145 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.63477492332 s Creating peak regions... Creating peak regions took 64.3889288902 s Estimating background... Estimating background took 62.1659290791 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.34468984604 s Creating peak regions... Creating peak regions took 60.6898219585 s Estimating background... Estimating background took 41.9984970093 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.53011894226 s Creating peak regions... Creating peak regions took 54.6886489391 s Estimating background... Estimating background took 52.9017300606 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.90196204185 s Creating peak regions... Creating peak regions took 52.2740130424 s Estimating background... Estimating background took 56.0626289845 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.93900704384 s Creating peak regions... Creating peak regions took 45.9875161648 s Estimating background... Estimating background took 50.1691799164 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.06967806816 s Creating peak regions... Creating peak regions took 40.7849190235 s Estimating background... Estimating background took 34.5714418888 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.48939800262 s Creating peak regions... Creating peak regions took 35.9388689995 s Estimating background... Estimating background took 35.5127279758 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.175840139389 s Creating peak regions... Creating peak regions took 0.239106178284 s Estimating background... Estimating background took 0.685340881348 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.94305610657 s Creating peak regions... Creating peak regions took 43.2153570652 s Estimating background... Estimating background took 49.9827568531 s Processing ZNF708-SRR5197223.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.376827955246 s Creating peak regions... Creating peak regions took 13.6940009594 s Estimating background... Estimating background took 0.767130851746 s