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='ZNF224-SRR5197084.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='ZNF224-SRR5197084/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 ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.78610396385 s Creating peak regions... Creating peak regions took 74.9712479115 s Estimating background... Estimating background took 52.2136831284 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.47121191025 s Creating peak regions... Creating peak regions took 40.3121011257 s Estimating background... Estimating background took 21.0743999481 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.0281150341 s Creating peak regions... Creating peak regions took 35.5269961357 s Estimating background... Estimating background took 20.0095310211 s Processing ZNF224-SRR5197084.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='ZNF224-SRR5197084.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='ZNF224-SRR5197084/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 ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.39260005951 s Creating peak regions... Creating peak regions took 76.9154429436 s Estimating background... Estimating background took 47.9829039574 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.03784584999 s Creating peak regions... Creating peak regions took 34.8939580917 s Estimating background... Estimating background took 18.5498299599 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.8809568882 s Creating peak regions... Creating peak regions took 35.2537498474 s Estimating background... Estimating background took 19.617885828 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.01173400879 s Creating peak regions... Creating peak regions took 35.0236039162 s Estimating background... Estimating background took 20.4433290958 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.03349900246 s Creating peak regions... Creating peak regions took 30.9117779732 s Estimating background... Estimating background took 28.4701280594 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.12777495384 s Creating peak regions... Creating peak regions took 27.8623838425 s Estimating background... Estimating background took 13.6956911087 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.93622398376 s Creating peak regions... Creating peak regions took 25.6141898632 s Estimating background... Estimating background took 13.6963698864 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.04699397087 s Creating peak regions... Creating peak regions took 22.711616993 s Estimating background... Estimating background took 11.084184885 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.00176095963 s Creating peak regions... Creating peak regions took 21.6886851788 s Estimating background... Estimating background took 13.9718859196 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.80931091309 s Creating peak regions... Creating peak regions took 20.7132380009 s Estimating background... Estimating background took 11.0275938511 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.30467700958 s Creating peak regions... Creating peak regions took 15.1345260143 s Estimating background... Estimating background took 7.70800495148 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.41536688805 s Creating peak regions... Creating peak regions took 62.267553091 s Estimating background... Estimating background took 34.7438890934 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.41157507896 s Creating peak regions... Creating peak regions took 17.8383071423 s Estimating background... Estimating background took 10.3691380024 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.955116033554 s Creating peak regions... Creating peak regions took 12.9801189899 s Estimating background... Estimating background took 6.57505583763 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.26815891266 s Creating peak regions... Creating peak regions took 13.4116549492 s Estimating background... Estimating background took 7.56028199196 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.36244487762 s Creating peak regions... Creating peak regions took 54.7130389214 s Estimating background... Estimating background took 28.3508219719 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.96437096596 s Creating peak regions... Creating peak regions took 48.5450298786 s Estimating background... Estimating background took 23.5445659161 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.94627594948 s Creating peak regions... Creating peak regions took 47.6045231819 s Estimating background... Estimating background took 26.4329621792 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.64029717445 s Creating peak regions... Creating peak regions took 45.8421998024 s Estimating background... Estimating background took 31.2891449928 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.71959686279 s Creating peak regions... Creating peak regions took 42.8884518147 s Estimating background... Estimating background took 25.5051240921 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.14812111855 s Creating peak regions... Creating peak regions took 38.4338190556 s Estimating background... Estimating background took 19.5862948895 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.81588506699 s Creating peak regions... Creating peak regions took 35.8329200745 s Estimating background... Estimating background took 17.4628970623 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.111883163452 s Creating peak regions... Creating peak regions took 0.191054105759 s Estimating background... Estimating background took 0.643980979919 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.23389005661 s Creating peak regions... Creating peak regions took 42.2366518974 s Estimating background... Estimating background took 29.6145269871 s Processing ZNF224-SRR5197084.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.271696090698 s Creating peak regions... Creating peak regions took 14.3809099197 s Estimating background... Estimating background took 0.758395910263 s