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='ZNF460-SRR5197149.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='ZNF460-SRR5197149/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 ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.16560792923 s Creating peak regions... Creating peak regions took 76.715430975 s Estimating background... Estimating background took 34.4561839104 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.66292691231 s Creating peak regions... Creating peak regions took 40.1524078846 s Estimating background... Estimating background took 13.602533102 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.17393684387 s Creating peak regions... Creating peak regions took 39.0445978642 s Estimating background... Estimating background took 12.8312649727 s Processing ZNF460-SRR5197149.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='ZNF460-SRR5197149.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='ZNF460-SRR5197149/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 ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.51491189003 s Creating peak regions... Creating peak regions took 65.7726578712 s Estimating background... Estimating background took 29.5986800194 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.22905111313 s Creating peak regions... Creating peak regions took 34.9696199894 s Estimating background... Estimating background took 11.9987738132 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.46684503555 s Creating peak regions... Creating peak regions took 34.9696390629 s Estimating background... Estimating background took 12.0336170197 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.4113612175 s Creating peak regions... Creating peak regions took 36.8812580109 s Estimating background... Estimating background took 13.3255138397 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.0189230442 s Creating peak regions... Creating peak regions took 29.4912350178 s Estimating background... Estimating background took 11.1037290096 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7052359581 s Creating peak regions... Creating peak regions took 26.5541768074 s Estimating background... Estimating background took 8.62242698669 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.48696494102 s Creating peak regions... Creating peak regions took 25.8581709862 s Estimating background... Estimating background took 9.5154030323 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.62131500244 s Creating peak regions... Creating peak regions took 25.345042944 s Estimating background... Estimating background took 9.6113910675 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.85393500328 s Creating peak regions... Creating peak regions took 23.6451568604 s Estimating background... Estimating background took 12.0073750019 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.11267805099 s Creating peak regions... Creating peak regions took 20.6885149479 s Estimating background... Estimating background took 5.85161685944 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.5024561882 s Creating peak regions... Creating peak regions took 17.2202250957 s Estimating background... Estimating background took 8.99325609207 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.80115604401 s Creating peak regions... Creating peak regions took 66.6179111004 s Estimating background... Estimating background took 19.5510880947 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.5009059906 s Creating peak regions... Creating peak regions took 17.7660601139 s Estimating background... Estimating background took 7.71138191223 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.716819047928 s Creating peak regions... Creating peak regions took 11.3831949234 s Estimating background... Estimating background took 3.8533449173 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.05998182297 s Creating peak regions... Creating peak regions took 13.4256370068 s Estimating background... Estimating background took 8.13968205452 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85862112045 s Creating peak regions... Creating peak regions took 52.1580178738 s Estimating background... Estimating background took 15.5557570457 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.33756399155 s Creating peak regions... Creating peak regions took 51.7628479004 s Estimating background... Estimating background took 12.1496229172 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.68073892593 s Creating peak regions... Creating peak regions took 50.2793970108 s Estimating background... Estimating background took 14.440130949 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.98130917549 s Creating peak regions... Creating peak regions took 44.1295249462 s Estimating background... Estimating background took 16.2559030056 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.87484693527 s Creating peak regions... Creating peak regions took 41.3503110409 s Estimating background... Estimating background took 15.5123260021 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37113404274 s Creating peak regions... Creating peak regions took 37.5476229191 s Estimating background... Estimating background took 11.384968996 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.44240403175 s Creating peak regions... Creating peak regions took 35.1945488453 s Estimating background... Estimating background took 11.2799911499 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0792880058289 s Creating peak regions... Creating peak regions took 0.166965961456 s Estimating background... Estimating background took 0.572626113892 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.71640086174 s Creating peak regions... Creating peak regions took 43.1873049736 s Estimating background... Estimating background took 14.3623359203 s Processing ZNF460-SRR5197149.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0997610092163 s Creating peak regions... Creating peak regions took 13.1803629398 s Estimating background... Estimating background took 0.468523979187 s