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='ZNF680-rep2-SRR5197213.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='ZNF680-rep2-SRR5197213/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 ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.78454303741 s Creating peak regions... Creating peak regions took 76.6973741055 s Estimating background... Estimating background took 36.7554168701 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.66001200676 s Creating peak regions... Creating peak regions took 41.9352080822 s Estimating background... Estimating background took 14.4467120171 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.52412486076 s Creating peak regions... Creating peak regions took 39.7785739899 s Estimating background... Estimating background took 13.3346028328 s Processing ZNF680-rep2-SRR5197213.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='ZNF680-rep2-SRR5197213.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='ZNF680-rep2-SRR5197213/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 ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.10692381859 s Creating peak regions... Creating peak regions took 78.0392711163 s Estimating background... Estimating background took 37.5395829678 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45556712151 s Creating peak regions... Creating peak regions took 40.6538078785 s Estimating background... Estimating background took 14.6702330112 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39543509483 s Creating peak regions... Creating peak regions took 43.8098988533 s Estimating background... Estimating background took 14.4370789528 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.00321602821 s Creating peak regions... Creating peak regions took 41.1083579063 s Estimating background... Estimating background took 16.5062799454 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.34323906898 s Creating peak regions... Creating peak regions took 36.506551981 s Estimating background... Estimating background took 17.1264870167 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95780110359 s Creating peak regions... Creating peak regions took 36.0173268318 s Estimating background... Estimating background took 9.93883299828 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.77845692635 s Creating peak regions... Creating peak regions took 33.4290201664 s Estimating background... Estimating background took 11.0896801949 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.62966585159 s Creating peak regions... Creating peak regions took 29.3708870411 s Estimating background... Estimating background took 9.28892278671 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.86467909813 s Creating peak regions... Creating peak regions took 27.6488888264 s Estimating background... Estimating background took 10.7112360001 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.61941099167 s Creating peak regions... Creating peak regions took 26.5650072098 s Estimating background... Estimating background took 8.46159791946 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.21448016167 s Creating peak regions... Creating peak regions took 17.312084198 s Estimating background... Estimating background took 7.6589679718 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.06750607491 s Creating peak regions... Creating peak regions took 76.1913890839 s Estimating background... Estimating background took 26.7589430809 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.41412401199 s Creating peak regions... Creating peak regions took 21.1662960052 s Estimating background... Estimating background took 8.40502285957 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.01331114769 s Creating peak regions... Creating peak regions took 14.4530160427 s Estimating background... Estimating background took 4.6731710434 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.0432100296 s Creating peak regions... Creating peak regions took 16.9947090149 s Estimating background... Estimating background took 6.80355811119 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.81082201004 s Creating peak regions... Creating peak regions took 66.9070720673 s Estimating background... Estimating background took 22.030755043 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.20913100243 s Creating peak regions... Creating peak regions took 59.2223439217 s Estimating background... Estimating background took 17.8673429489 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.64149904251 s Creating peak regions... Creating peak regions took 56.5326159 s Estimating background... Estimating background took 19.5153710842 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.68280506134 s Creating peak regions... Creating peak regions took 59.3165459633 s Estimating background... Estimating background took 22.8401100636 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.59203004837 s Creating peak regions... Creating peak regions took 58.8834180832 s Estimating background... Estimating background took 18.8233268261 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.74856114388 s Creating peak regions... Creating peak regions took 45.1032118797 s Estimating background... Estimating background took 13.489178896 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.58851599693 s Creating peak regions... Creating peak regions took 46.9416952133 s Estimating background... Estimating background took 13.4625959396 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.22552895546 s Creating peak regions... Creating peak regions took 0.197201967239 s Estimating background... Estimating background took 0.660397052765 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.1252579689 s Creating peak regions... Creating peak regions took 47.2382690907 s Estimating background... Estimating background took 18.9305429459 s Processing ZNF680-rep2-SRR5197213.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.137061834335 s Creating peak regions... Creating peak regions took 15.8662428856 s Estimating background... Estimating background took 2.63295984268 s