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='ZNF519-SRR5197161.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='ZNF519-SRR5197161/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 ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.74070096016 s Creating peak regions... Creating peak regions took 75.1758389473 s Estimating background... Estimating background took 33.283203125 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.22268009186 s Creating peak regions... Creating peak regions took 39.9733641148 s Estimating background... Estimating background took 13.1812880039 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.14969301224 s Creating peak regions... Creating peak regions took 41.8345718384 s Estimating background... Estimating background took 12.3553128242 s Processing ZNF519-SRR5197161.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='ZNF519-SRR5197161.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='ZNF519-SRR5197161/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 ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.38441491127 s Creating peak regions... Creating peak regions took 74.9451608658 s Estimating background... Estimating background took 34.9855809212 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.16216111183 s Creating peak regions... Creating peak regions took 38.7436540127 s Estimating background... Estimating background took 13.3372650146 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.2608590126 s Creating peak regions... Creating peak regions took 43.6518039703 s Estimating background... Estimating background took 13.516835928 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32579612732 s Creating peak regions... Creating peak regions took 38.8595190048 s Estimating background... Estimating background took 14.1246409416 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.88804006577 s Creating peak regions... Creating peak regions took 35.3071639538 s Estimating background... Estimating background took 12.3732478619 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.53170609474 s Creating peak regions... Creating peak regions took 32.1513447762 s Estimating background... Estimating background took 8.60348200798 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.587266922 s Creating peak regions... Creating peak regions took 28.9691998959 s Estimating background... Estimating background took 11.6687829494 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.60696196556 s Creating peak regions... Creating peak regions took 26.0554299355 s Estimating background... Estimating background took 11.2035820484 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98811602592 s Creating peak regions... Creating peak regions took 24.6458330154 s Estimating background... Estimating background took 15.0075500011 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.22401285172 s Creating peak regions... Creating peak regions took 23.6683988571 s Estimating background... Estimating background took 6.96079015732 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.46949696541 s Creating peak regions... Creating peak regions took 18.5005378723 s Estimating background... Estimating background took 10.1706540585 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.47646212578 s Creating peak regions... Creating peak regions took 76.1753249168 s Estimating background... Estimating background took 22.7583501339 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.3091340065 s Creating peak regions... Creating peak regions took 17.7225599289 s Estimating background... Estimating background took 7.59315013885 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.612100839615 s Creating peak regions... Creating peak regions took 13.6191959381 s Estimating background... Estimating background took 4.09258818626 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.07700800896 s Creating peak regions... Creating peak regions took 15.8903241158 s Estimating background... Estimating background took 8.02168989182 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.83099508286 s Creating peak regions... Creating peak regions took 60.9657289982 s Estimating background... Estimating background took 15.9337890148 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.20085096359 s Creating peak regions... Creating peak regions took 50.2650661469 s Estimating background... Estimating background took 13.6718049049 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.66242218018 s Creating peak regions... Creating peak regions took 57.0160300732 s Estimating background... Estimating background took 15.6805479527 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.81154990196 s Creating peak regions... Creating peak regions took 50.123707056 s Estimating background... Estimating background took 19.2684791088 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.74826788902 s Creating peak regions... Creating peak regions took 47.725536108 s Estimating background... Estimating background took 17.8661739826 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.2378718853 s Creating peak regions... Creating peak regions took 43.9160940647 s Estimating background... Estimating background took 11.4860510826 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.87173199654 s Creating peak regions... Creating peak regions took 42.0969800949 s Estimating background... Estimating background took 12.7605779171 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0756988525391 s Creating peak regions... Creating peak regions took 0.139241933823 s Estimating background... Estimating background took 0.559333086014 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.434871912 s Creating peak regions... Creating peak regions took 47.3350930214 s Estimating background... Estimating background took 11.6553778648 s Processing ZNF519-SRR5197161.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0873379707336 s Creating peak regions... Creating peak regions took 12.1048438549 s Estimating background... Estimating background took 0.471144914627 s