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='ZNF570-SRR5197185.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='ZNF570-SRR5197185/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 ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.96387410164 s Creating peak regions... Creating peak regions took 61.4725430012 s Estimating background... Estimating background took 19.3816170692 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.45018482208 s Creating peak regions... Creating peak regions took 32.0065879822 s Estimating background... Estimating background took 8.48369789124 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.64095878601 s Creating peak regions... Creating peak regions took 31.4130449295 s Estimating background... Estimating background took 8.51413822174 s Processing ZNF570-SRR5197185.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='ZNF570-SRR5197185.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='ZNF570-SRR5197185/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 ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.10102701187 s Creating peak regions... Creating peak regions took 74.9310240746 s Estimating background... Estimating background took 23.2874670029 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98407697678 s Creating peak regions... Creating peak regions took 38.8465280533 s Estimating background... Estimating background took 9.53955698013 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.10765099525 s Creating peak regions... Creating peak regions took 37.1477470398 s Estimating background... Estimating background took 9.40885996819 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.19234609604 s Creating peak regions... Creating peak regions took 40.9236028194 s Estimating background... Estimating background took 10.1341519356 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.85550117493 s Creating peak regions... Creating peak regions took 33.4197409153 s Estimating background... Estimating background took 11.2763020992 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.45720791817 s Creating peak regions... Creating peak regions took 32.2555150986 s Estimating background... Estimating background took 6.84197020531 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.31396889687 s Creating peak regions... Creating peak regions took 29.2399199009 s Estimating background... Estimating background took 7.10331821442 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.38995790482 s Creating peak regions... Creating peak regions took 26.2699608803 s Estimating background... Estimating background took 6.64218187332 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.51408791542 s Creating peak regions... Creating peak regions took 25.8465938568 s Estimating background... Estimating background took 7.95594286919 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.05504393578 s Creating peak regions... Creating peak regions took 23.065279007 s Estimating background... Estimating background took 5.36888194084 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.02827000618 s Creating peak regions... Creating peak regions took 17.7811479568 s Estimating background... Estimating background took 4.93046092987 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.47867798805 s Creating peak regions... Creating peak regions took 75.1372921467 s Estimating background... Estimating background took 16.497699976 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.16668510437 s Creating peak regions... Creating peak regions took 19.2269999981 s Estimating background... Estimating background took 5.67619585991 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.677519083023 s Creating peak regions... Creating peak regions took 14.2677230835 s Estimating background... Estimating background took 3.50526285172 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.792436122894 s Creating peak regions... Creating peak regions took 14.865074873 s Estimating background... Estimating background took 5.32807087898 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.7073059082 s Creating peak regions... Creating peak regions took 61.2861669064 s Estimating background... Estimating background took 12.6949651241 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.4000878334 s Creating peak regions... Creating peak regions took 58.1722259521 s Estimating background... Estimating background took 11.2931268215 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.63611292839 s Creating peak regions... Creating peak regions took 56.0833389759 s Estimating background... Estimating background took 12.3297300339 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.88380002975 s Creating peak regions... Creating peak regions took 53.5086779594 s Estimating background... Estimating background took 13.8687591553 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.46084785461 s Creating peak regions... Creating peak regions took 47.105394125 s Estimating background... Estimating background took 12.5797379017 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.10947489738 s Creating peak regions... Creating peak regions took 42.0305178165 s Estimating background... Estimating background took 9.78621196747 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.87180900574 s Creating peak regions... Creating peak regions took 39.7550959587 s Estimating background... Estimating background took 8.86302709579 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0770001411438 s Creating peak regions... Creating peak regions took 0.142215967178 s Estimating background... Estimating background took 0.566969156265 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.76935696602 s Creating peak regions... Creating peak regions took 49.0424659252 s Estimating background... Estimating background took 13.4415149689 s Processing ZNF570-SRR5197185.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0981822013855 s Creating peak regions... Creating peak regions took 15.4438729286 s Estimating background... Estimating background took 0.558550834656 s