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='ZNF682-rep2-SRR5197216.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='ZNF682-rep2-SRR5197216/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 ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.28640294075 s Creating peak regions... Creating peak regions took 62.2028160095 s Estimating background... Estimating background took 32.211796999 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23589706421 s Creating peak regions... Creating peak regions took 34.8185379505 s Estimating background... Estimating background took 15.1776871681 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.01105189323 s Creating peak regions... Creating peak regions took 33.3631739616 s Estimating background... Estimating background took 13.4633500576 s Processing ZNF682-rep2-SRR5197216.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='ZNF682-rep2-SRR5197216.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='ZNF682-rep2-SRR5197216/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 ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.90451598167 s Creating peak regions... Creating peak regions took 73.0548448563 s Estimating background... Estimating background took 35.8249959946 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.07319998741 s Creating peak regions... Creating peak regions took 44.85795784 s Estimating background... Estimating background took 16.3730080128 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.54066610336 s Creating peak regions... Creating peak regions took 40.6164550781 s Estimating background... Estimating background took 14.0063171387 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.61485385895 s Creating peak regions... Creating peak regions took 37.8992140293 s Estimating background... Estimating background took 14.9167490005 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.26044821739 s Creating peak regions... Creating peak regions took 34.863049984 s Estimating background... Estimating background took 16.2247190475 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.75941085815 s Creating peak regions... Creating peak regions took 31.4491229057 s Estimating background... Estimating background took 10.8277950287 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.86096596718 s Creating peak regions... Creating peak regions took 34.3118240833 s Estimating background... Estimating background took 11.3084709644 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.84248709679 s Creating peak regions... Creating peak regions took 28.2722370625 s Estimating background... Estimating background took 10.7641279697 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39494395256 s Creating peak regions... Creating peak regions took 27.2953939438 s Estimating background... Estimating background took 15.4486031532 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.49475002289 s Creating peak regions... Creating peak regions took 25.0319690704 s Estimating background... Estimating background took 8.42987585068 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.59580087662 s Creating peak regions... Creating peak regions took 18.3732960224 s Estimating background... Estimating background took 10.9328241348 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.9120850563 s Creating peak regions... Creating peak regions took 78.6140110493 s Estimating background... Estimating background took 25.1747009754 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.61318588257 s Creating peak regions... Creating peak regions took 21.3075389862 s Estimating background... Estimating background took 9.80005478859 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.905781984329 s Creating peak regions... Creating peak regions took 14.7856960297 s Estimating background... Estimating background took 5.39266014099 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.22675704956 s Creating peak regions... Creating peak regions took 16.223279953 s Estimating background... Estimating background took 8.9363219738 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.94412589073 s Creating peak regions... Creating peak regions took 63.9974648952 s Estimating background... Estimating background took 20.0483310223 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.29804897308 s Creating peak regions... Creating peak regions took 60.276362896 s Estimating background... Estimating background took 16.2332341671 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.22523999214 s Creating peak regions... Creating peak regions took 55.0467810631 s Estimating background... Estimating background took 17.2990729809 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.93690919876 s Creating peak regions... Creating peak regions took 61.2135679722 s Estimating background... Estimating background took 24.5221660137 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.49962687492 s Creating peak regions... Creating peak regions took 50.4995079041 s Estimating background... Estimating background took 20.9581317902 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.82149505615 s Creating peak regions... Creating peak regions took 46.7879719734 s Estimating background... Estimating background took 13.8276741505 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.31512188911 s Creating peak regions... Creating peak regions took 40.9708809853 s Estimating background... Estimating background took 14.104820013 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0910120010376 s Creating peak regions... Creating peak regions took 0.175271987915 s Estimating background... Estimating background took 0.550518989563 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.22168111801 s Creating peak regions... Creating peak regions took 45.0788860321 s Estimating background... Estimating background took 16.444106102 s Processing ZNF682-rep2-SRR5197216.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.141842842102 s Creating peak regions... Creating peak regions took 15.3831348419 s Estimating background... Estimating background took 0.697825908661 s