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='ZNF133-SRR5197059.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='ZNF133-SRR5197059/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 ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.36959505081 s Creating peak regions... Creating peak regions took 76.2605450153 s Estimating background... Estimating background took 32.7659270763 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37823987007 s Creating peak regions... Creating peak regions took 40.2968070507 s Estimating background... Estimating background took 13.6283900738 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.25679397583 s Creating peak regions... Creating peak regions took 40.3379900455 s Estimating background... Estimating background took 11.5679101944 s Processing ZNF133-SRR5197059.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='ZNF133-SRR5197059.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='ZNF133-SRR5197059/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 ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.25339102745 s Creating peak regions... Creating peak regions took 66.9647810459 s Estimating background... Estimating background took 29.8284919262 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.26176691055 s Creating peak regions... Creating peak regions took 35.482049942 s Estimating background... Estimating background took 12.6139068604 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.14306497574 s Creating peak regions... Creating peak regions took 36.0419120789 s Estimating background... Estimating background took 11.3189270496 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.17168402672 s Creating peak regions... Creating peak regions took 37.3855330944 s Estimating background... Estimating background took 12.857462883 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06434202194 s Creating peak regions... Creating peak regions took 30.5185132027 s Estimating background... Estimating background took 15.8127529621 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.55371713638 s Creating peak regions... Creating peak regions took 29.307145834 s Estimating background... Estimating background took 8.57139778137 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.3979549408 s Creating peak regions... Creating peak regions took 26.0697188377 s Estimating background... Estimating background took 9.09454393387 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.27306604385 s Creating peak regions... Creating peak regions took 24.4537708759 s Estimating background... Estimating background took 7.41008687019 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.49226117134 s Creating peak regions... Creating peak regions took 21.7526409626 s Estimating background... Estimating background took 8.71329903603 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.18585205078 s Creating peak regions... Creating peak regions took 22.0818350315 s Estimating background... Estimating background took 7.09222888947 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.885465145111 s Creating peak regions... Creating peak regions took 15.3338251114 s Estimating background... Estimating background took 5.60493206978 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.54817605019 s Creating peak regions... Creating peak regions took 66.8581469059 s Estimating background... Estimating background took 20.8194642067 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.01497507095 s Creating peak regions... Creating peak regions took 17.5497689247 s Estimating background... Estimating background took 6.19646120071 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.644020080566 s Creating peak regions... Creating peak regions took 12.8902449608 s Estimating background... Estimating background took 3.94052600861 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.788192987442 s Creating peak regions... Creating peak regions took 14.042881012 s Estimating background... Estimating background took 5.10531401634 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.00515198708 s Creating peak regions... Creating peak regions took 52.6259770393 s Estimating background... Estimating background took 17.2063410282 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.60689711571 s Creating peak regions... Creating peak regions took 48.4747579098 s Estimating background... Estimating background took 14.5265159607 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.93120408058 s Creating peak regions... Creating peak regions took 50.9489319324 s Estimating background... Estimating background took 16.2166838646 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.84364104271 s Creating peak regions... Creating peak regions took 48.4106459618 s Estimating background... Estimating background took 18.551418066 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85266804695 s Creating peak regions... Creating peak regions took 42.6134970188 s Estimating background... Estimating background took 15.4984960556 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.2963719368 s Creating peak regions... Creating peak regions took 37.9482369423 s Estimating background... Estimating background took 11.3475840092 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.89090490341 s Creating peak regions... Creating peak regions took 36.9595930576 s Estimating background... Estimating background took 11.2596080303 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0880870819092 s Creating peak regions... Creating peak regions took 0.162686109543 s Estimating background... Estimating background took 0.517549037933 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53546118736 s Creating peak regions... Creating peak regions took 43.671544075 s Estimating background... Estimating background took 16.1155488491 s Processing ZNF133-SRR5197059.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.10279083252 s Creating peak regions... Creating peak regions took 13.3740060329 s Estimating background... Estimating background took 2.25201511383 s