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='ZNF257-SRR5197089.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='ZNF257-SRR5197089/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 ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.05581712723 s Creating peak regions... Creating peak regions took 76.2781569958 s Estimating background... Estimating background took 35.7428619862 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.4104309082 s Creating peak regions... Creating peak regions took 42.2033140659 s Estimating background... Estimating background took 15.9389569759 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.22234892845 s Creating peak regions... Creating peak regions took 40.7428479195 s Estimating background... Estimating background took 12.3630390167 s Processing ZNF257-SRR5197089.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='ZNF257-SRR5197089.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='ZNF257-SRR5197089/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 ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.93114209175 s Creating peak regions... Creating peak regions took 73.3438251019 s Estimating background... Estimating background took 37.5378329754 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.07129812241 s Creating peak regions... Creating peak regions took 40.9280409813 s Estimating background... Estimating background took 16.1939210892 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.22387194633 s Creating peak regions... Creating peak regions took 41.8183422089 s Estimating background... Estimating background took 14.9301719666 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.23531794548 s Creating peak regions... Creating peak regions took 40.2346138954 s Estimating background... Estimating background took 16.2435081005 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.87776899338 s Creating peak regions... Creating peak regions took 32.9181120396 s Estimating background... Estimating background took 12.3697109222 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.32640004158 s Creating peak regions... Creating peak regions took 33.0227711201 s Estimating background... Estimating background took 10.014400959 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.746571064 s Creating peak regions... Creating peak regions took 30.796900034 s Estimating background... Estimating background took 9.84403991699 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.55097484589 s Creating peak regions... Creating peak regions took 26.0465381145 s Estimating background... Estimating background took 10.3071300983 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.95972204208 s Creating peak regions... Creating peak regions took 26.4763708115 s Estimating background... Estimating background took 14.7356410027 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.25679993629 s Creating peak regions... Creating peak regions took 23.8795599937 s Estimating background... Estimating background took 7.24823403358 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.16065001488 s Creating peak regions... Creating peak regions took 19.1810419559 s Estimating background... Estimating background took 10.4288721085 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.74518990517 s Creating peak regions... Creating peak regions took 75.5885210037 s Estimating background... Estimating background took 23.9532089233 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.47070908546 s Creating peak regions... Creating peak regions took 20.5112268925 s Estimating background... Estimating background took 8.67445611954 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.25011610985 s Creating peak regions... Creating peak regions took 12.8297138214 s Estimating background... Estimating background took 4.06269097328 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.08109784126 s Creating peak regions... Creating peak regions took 14.8921740055 s Estimating background... Estimating background took 8.5699930191 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.89778995514 s Creating peak regions... Creating peak regions took 58.4252698421 s Estimating background... Estimating background took 17.5821700096 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.40110707283 s Creating peak regions... Creating peak regions took 56.3237140179 s Estimating background... Estimating background took 15.1983880997 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.01054406166 s Creating peak regions... Creating peak regions took 54.3248231411 s Estimating background... Estimating background took 17.9170789719 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.25447702408 s Creating peak regions... Creating peak regions took 49.9225549698 s Estimating background... Estimating background took 20.0317320824 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.83225488663 s Creating peak regions... Creating peak regions took 46.5337970257 s Estimating background... Estimating background took 18.6675961018 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.26085710526 s Creating peak regions... Creating peak regions took 44.9145729542 s Estimating background... Estimating background took 12.7011008263 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.86975598335 s Creating peak regions... Creating peak regions took 41.116091013 s Estimating background... Estimating background took 10.7082710266 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.079206943512 s Creating peak regions... Creating peak regions took 0.146883964539 s Estimating background... Estimating background took 0.524613142014 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.48940300941 s Creating peak regions... Creating peak regions took 43.3051240444 s Estimating background... Estimating background took 14.5622611046 s Processing ZNF257-SRR5197089.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0971200466156 s Creating peak regions... Creating peak regions took 14.9274599552 s Estimating background... Estimating background took 0.408743143082 s