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='ZNF571-SRR5197186.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='ZNF571-SRR5197186/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 ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.78497314453 s Creating peak regions... Creating peak regions took 75.5584430695 s Estimating background... Estimating background took 29.0037879944 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.43691515923 s Creating peak regions... Creating peak regions took 39.5631890297 s Estimating background... Estimating background took 12.1682059765 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.41823005676 s Creating peak regions... Creating peak regions took 41.8727838993 s Estimating background... Estimating background took 12.4470188618 s Processing ZNF571-SRR5197186.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='ZNF571-SRR5197186.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='ZNF571-SRR5197186/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 ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.87667608261 s Creating peak regions... Creating peak regions took 75.3235201836 s Estimating background... Estimating background took 28.0984408855 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.40729689598 s Creating peak regions... Creating peak regions took 39.1360371113 s Estimating background... Estimating background took 11.6959769726 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.3569920063 s Creating peak regions... Creating peak regions took 41.7019279003 s Estimating background... Estimating background took 12.0607428551 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.65161514282 s Creating peak regions... Creating peak regions took 39.1042568684 s Estimating background... Estimating background took 12.4798550606 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.99828600883 s Creating peak regions... Creating peak regions took 35.3543989658 s Estimating background... Estimating background took 11.7536559105 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92390012741 s Creating peak regions... Creating peak regions took 32.2156178951 s Estimating background... Estimating background took 8.4845700264 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.69543194771 s Creating peak regions... Creating peak regions took 29.1362781525 s Estimating background... Estimating background took 9.92361187935 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.81217312813 s Creating peak regions... Creating peak regions took 24.7620239258 s Estimating background... Estimating background took 8.99219608307 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.16492509842 s Creating peak regions... Creating peak regions took 26.5846889019 s Estimating background... Estimating background took 11.6168329716 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.26388907433 s Creating peak regions... Creating peak regions took 22.1897809505 s Estimating background... Estimating background took 6.06685113907 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.31735301018 s Creating peak regions... Creating peak regions took 17.9788041115 s Estimating background... Estimating background took 7.67674684525 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.17295718193 s Creating peak regions... Creating peak regions took 70.3336298466 s Estimating background... Estimating background took 19.3906731606 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.56481003761 s Creating peak regions... Creating peak regions took 20.6019802094 s Estimating background... Estimating background took 7.28289294243 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.814441919327 s Creating peak regions... Creating peak regions took 13.3357121944 s Estimating background... Estimating background took 3.97839999199 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.24341797829 s Creating peak regions... Creating peak regions took 15.800593853 s Estimating background... Estimating background took 7.45217514038 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.18959188461 s Creating peak regions... Creating peak regions took 58.0257511139 s Estimating background... Estimating background took 15.2709269524 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.57920694351 s Creating peak regions... Creating peak regions took 54.6774380207 s Estimating background... Estimating background took 12.2831339836 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.20431804657 s Creating peak regions... Creating peak regions took 52.6558578014 s Estimating background... Estimating background took 14.1334149837 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.2220158577 s Creating peak regions... Creating peak regions took 53.2370629311 s Estimating background... Estimating background took 16.3781180382 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.0794210434 s Creating peak regions... Creating peak regions took 49.8169589043 s Estimating background... Estimating background took 15.1249499321 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.76678514481 s Creating peak regions... Creating peak regions took 42.0728681087 s Estimating background... Estimating background took 11.1186611652 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.21326708794 s Creating peak regions... Creating peak regions took 40.2548561096 s Estimating background... Estimating background took 11.2618579865 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0819630622864 s Creating peak regions... Creating peak regions took 0.163661956787 s Estimating background... Estimating background took 0.572077989578 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.99259495735 s Creating peak regions... Creating peak regions took 45.2338628769 s Estimating background... Estimating background took 14.7448279858 s Processing ZNF571-SRR5197186.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0946159362793 s Creating peak regions... Creating peak regions took 14.8569509983 s Estimating background... Estimating background took 0.454593896866 s