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='ZNF776-SRR5197236.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='ZNF776-SRR5197236/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 ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.17910695076 s Creating peak regions... Creating peak regions took 78.4559118748 s Estimating background... Estimating background took 45.3919308186 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.1044588089 s Creating peak regions... Creating peak regions took 40.6339268684 s Estimating background... Estimating background took 17.7283210754 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.11931800842 s Creating peak regions... Creating peak regions took 40.8431069851 s Estimating background... Estimating background took 17.7520811558 s Processing ZNF776-SRR5197236.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='ZNF776-SRR5197236.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='ZNF776-SRR5197236/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 ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.32093787193 s Creating peak regions... Creating peak regions took 78.8660058975 s Estimating background... Estimating background took 44.6256110668 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.09481811523 s Creating peak regions... Creating peak regions took 41.0403518677 s Estimating background... Estimating background took 17.5866560936 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.1653649807 s Creating peak regions... Creating peak regions took 41.1802301407 s Estimating background... Estimating background took 18.311768055 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.17530012131 s Creating peak regions... Creating peak regions took 40.4190011024 s Estimating background... Estimating background took 19.1252930164 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.88332295418 s Creating peak regions... Creating peak regions took 34.3587150574 s Estimating background... Estimating background took 18.0910010338 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.1465010643 s Creating peak regions... Creating peak regions took 31.8137559891 s Estimating background... Estimating background took 11.9526441097 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.96264100075 s Creating peak regions... Creating peak regions took 29.7613499165 s Estimating background... Estimating background took 12.1426751614 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.10921788216 s Creating peak regions... Creating peak regions took 28.4443399906 s Estimating background... Estimating background took 13.066546917 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.46317195892 s Creating peak regions... Creating peak regions took 25.7815349102 s Estimating background... Estimating background took 16.8175208569 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.61519312859 s Creating peak regions... Creating peak regions took 25.6890029907 s Estimating background... Estimating background took 9.32997393608 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.68345189095 s Creating peak regions... Creating peak regions took 19.3352730274 s Estimating background... Estimating background took 11.2702620029 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.95602297783 s Creating peak regions... Creating peak regions took 73.0358290672 s Estimating background... Estimating background took 29.3616631031 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.68764019012 s Creating peak regions... Creating peak regions took 20.5756599903 s Estimating background... Estimating background took 10.6432869434 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.01133203506 s Creating peak regions... Creating peak regions took 14.0026698112 s Estimating background... Estimating background took 5.92581105232 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.35853695869 s Creating peak regions... Creating peak regions took 16.4493041039 s Estimating background... Estimating background took 10.9097869396 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.18860316277 s Creating peak regions... Creating peak regions took 59.2655510902 s Estimating background... Estimating background took 22.986125946 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.65485692024 s Creating peak regions... Creating peak regions took 56.5354750156 s Estimating background... Estimating background took 18.6893680096 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.85230398178 s Creating peak regions... Creating peak regions took 54.5508859158 s Estimating background... Estimating background took 22.6397500038 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.15988993645 s Creating peak regions... Creating peak regions took 52.3383438587 s Estimating background... Estimating background took 25.5870280266 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.82843399048 s Creating peak regions... Creating peak regions took 48.7518010139 s Estimating background... Estimating background took 23.2870490551 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.01931095123 s Creating peak regions... Creating peak regions took 43.7896540165 s Estimating background... Estimating background took 16.0612919331 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.7911131382 s Creating peak regions... Creating peak regions took 39.3264830112 s Estimating background... Estimating background took 16.0880389214 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0998299121857 s Creating peak regions... Creating peak regions took 0.173913955688 s Estimating background... Estimating background took 0.647149085999 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.41771292686 s Creating peak regions... Creating peak regions took 47.4148008823 s Estimating background... Estimating background took 20.6485350132 s Processing ZNF776-SRR5197236.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.139534950256 s Creating peak regions... Creating peak regions took 16.334831953 s Estimating background... Estimating background took 0.573677062988 s