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='ZNF343-SRR5197122.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='ZNF343-SRR5197122/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 ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.96495604515 s Creating peak regions... Creating peak regions took 76.8804140091 s Estimating background... Estimating background took 39.1192400455 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53321504593 s Creating peak regions... Creating peak regions took 41.0271499157 s Estimating background... Estimating background took 16.1024551392 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.63159704208 s Creating peak regions... Creating peak regions took 39.2178418636 s Estimating background... Estimating background took 14.2037630081 s Processing ZNF343-SRR5197122.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='ZNF343-SRR5197122.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='ZNF343-SRR5197122/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 ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.00798106194 s Creating peak regions... Creating peak regions took 74.8059811592 s Estimating background... Estimating background took 38.9380719662 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.7453558445 s Creating peak regions... Creating peak regions took 40.6363799572 s Estimating background... Estimating background took 16.4775631428 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.76534891129 s Creating peak regions... Creating peak regions took 37.8138170242 s Estimating background... Estimating background took 16.1396539211 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.76345205307 s Creating peak regions... Creating peak regions took 43.5615639687 s Estimating background... Estimating background took 17.572521925 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.36594986916 s Creating peak regions... Creating peak regions took 35.6791710854 s Estimating background... Estimating background took 14.9035489559 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.83474802971 s Creating peak regions... Creating peak regions took 31.230009079 s Estimating background... Estimating background took 11.0701239109 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92424511909 s Creating peak regions... Creating peak regions took 31.3091418743 s Estimating background... Estimating background took 12.6576070786 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.72731494904 s Creating peak regions... Creating peak regions took 26.2992818356 s Estimating background... Estimating background took 11.7473700047 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.2583990097 s Creating peak regions... Creating peak regions took 25.9601809978 s Estimating background... Estimating background took 15.779927969 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.39525413513 s Creating peak regions... Creating peak regions took 24.2020800114 s Estimating background... Estimating background took 8.01733398438 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.50804018974 s Creating peak regions... Creating peak regions took 19.3042628765 s Estimating background... Estimating background took 10.8938610554 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.26905107498 s Creating peak regions... Creating peak regions took 76.8156061172 s Estimating background... Estimating background took 27.2746219635 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.5891289711 s Creating peak regions... Creating peak regions took 20.8128950596 s Estimating background... Estimating background took 9.75363397598 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.8114361763 s Creating peak regions... Creating peak regions took 14.9653749466 s Estimating background... Estimating background took 5.32190704346 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.23607206345 s Creating peak regions... Creating peak regions took 15.4381971359 s Estimating background... Estimating background took 9.43673801422 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.4518430233 s Creating peak regions... Creating peak regions took 62.4546210766 s Estimating background... Estimating background took 20.4281270504 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.98929095268 s Creating peak regions... Creating peak regions took 54.5224969387 s Estimating background... Estimating background took 15.2020320892 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.18773603439 s Creating peak regions... Creating peak regions took 57.0121688843 s Estimating background... Estimating background took 20.0214600563 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.71805214882 s Creating peak regions... Creating peak regions took 51.1354920864 s Estimating background... Estimating background took 21.9556450844 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.26046085358 s Creating peak regions... Creating peak regions took 49.2394940853 s Estimating background... Estimating background took 20.724132061 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.82362794876 s Creating peak regions... Creating peak regions took 42.4502170086 s Estimating background... Estimating background took 14.7197628021 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.42055797577 s Creating peak regions... Creating peak regions took 41.2934310436 s Estimating background... Estimating background took 13.9257388115 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0892901420593 s Creating peak regions... Creating peak regions took 0.157682180405 s Estimating background... Estimating background took 0.625147104263 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.23528695107 s Creating peak regions... Creating peak regions took 48.4797899723 s Estimating background... Estimating background took 15.158894062 s Processing ZNF343-SRR5197122.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0955111980438 s Creating peak regions... Creating peak regions took 13.6425659657 s Estimating background... Estimating background took 0.408000946045 s