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='ZNF549-SRR5197172.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='ZNF549-SRR5197172/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 ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.19676089287 s Creating peak regions... Creating peak regions took 62.6794939041 s Estimating background... Estimating background took 30.3967628479 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.31580400467 s Creating peak regions... Creating peak regions took 33.5868830681 s Estimating background... Estimating background took 13.9186050892 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.42731690407 s Creating peak regions... Creating peak regions took 33.2298548222 s Estimating background... Estimating background took 12.6394410133 s Processing ZNF549-SRR5197172.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='ZNF549-SRR5197172.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='ZNF549-SRR5197172/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 ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.42493414879 s Creating peak regions... Creating peak regions took 78.9590930939 s Estimating background... Estimating background took 34.2916579247 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.83389496803 s Creating peak regions... Creating peak regions took 46.1751317978 s Estimating background... Estimating background took 15.6239330769 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.69680786133 s Creating peak regions... Creating peak regions took 48.1173431873 s Estimating background... Estimating background took 13.0243289471 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.40561509132 s Creating peak regions... Creating peak regions took 42.0088160038 s Estimating background... Estimating background took 14.0029790401 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.27711391449 s Creating peak regions... Creating peak regions took 38.1532671452 s Estimating background... Estimating background took 13.4273059368 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.86859989166 s Creating peak regions... Creating peak regions took 30.9002659321 s Estimating background... Estimating background took 8.84272003174 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.59742212296 s Creating peak regions... Creating peak regions took 29.3482549191 s Estimating background... Estimating background took 11.4311978817 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.70860481262 s Creating peak regions... Creating peak regions took 29.5051939487 s Estimating background... Estimating background took 11.4993450642 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.11177706718 s Creating peak regions... Creating peak regions took 27.1348259449 s Estimating background... Estimating background took 13.1791620255 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.84479808807 s Creating peak regions... Creating peak regions took 34.3793618679 s Estimating background... Estimating background took 7.85748505592 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.61057186127 s Creating peak regions... Creating peak regions took 23.617347002 s Estimating background... Estimating background took 8.15281414986 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.5132958889 s Creating peak regions... Creating peak regions took 84.2852058411 s Estimating background... Estimating background took 23.1780440807 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.48865413666 s Creating peak regions... Creating peak regions took 24.6822829247 s Estimating background... Estimating background took 8.12384104729 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.798720121384 s Creating peak regions... Creating peak regions took 16.3218638897 s Estimating background... Estimating background took 4.6587638855 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.22527694702 s Creating peak regions... Creating peak regions took 21.8242900372 s Estimating background... Estimating background took 7.68996214867 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.78766298294 s Creating peak regions... Creating peak regions took 77.5092170238 s Estimating background... Estimating background took 19.3671450615 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.03545999527 s Creating peak regions... Creating peak regions took 65.2157690525 s Estimating background... Estimating background took 14.5577478409 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.53940415382 s Creating peak regions... Creating peak regions took 76.1865620613 s Estimating background... Estimating background took 19.180355072 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.36301088333 s Creating peak regions... Creating peak regions took 72.3075590134 s Estimating background... Estimating background took 18.1006729603 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.92730998993 s Creating peak regions... Creating peak regions took 61.8818919659 s Estimating background... Estimating background took 19.3520958424 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.93044018745 s Creating peak regions... Creating peak regions took 61.5464220047 s Estimating background... Estimating background took 13.2740910053 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.57674384117 s Creating peak regions... Creating peak regions took 45.6261410713 s Estimating background... Estimating background took 12.6340579987 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.258682012558 s Creating peak regions... Creating peak regions took 0.470519065857 s Estimating background... Estimating background took 0.742812156677 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.65459609032 s Creating peak regions... Creating peak regions took 59.0388040543 s Estimating background... Estimating background took 18.3737239838 s Processing ZNF549-SRR5197172.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.270223140717 s Creating peak regions... Creating peak regions took 18.6643049717 s Estimating background... Estimating background took 0.77702999115 s