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='ZNF284-SRR5197101.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='ZNF284-SRR5197101/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 ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.22310400009 s Creating peak regions... Creating peak regions took 62.1805639267 s Estimating background... Estimating background took 28.0623910427 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92980194092 s Creating peak regions... Creating peak regions took 33.0851550102 s Estimating background... Estimating background took 12.0263118744 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.97296500206 s Creating peak regions... Creating peak regions took 32.8373739719 s Estimating background... Estimating background took 12.6615889072 s Processing ZNF284-SRR5197101.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='ZNF284-SRR5197101.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='ZNF284-SRR5197101/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 ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.01538801193 s Creating peak regions... Creating peak regions took 79.1216890812 s Estimating background... Estimating background took 36.3184659481 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.91666984558 s Creating peak regions... Creating peak regions took 37.904943943 s Estimating background... Estimating background took 14.5366079807 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.64758586884 s Creating peak regions... Creating peak regions took 42.3330748081 s Estimating background... Estimating background took 14.0093381405 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.14669513702 s Creating peak regions... Creating peak regions took 42.7691059113 s Estimating background... Estimating background took 15.4246919155 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.19113898277 s Creating peak regions... Creating peak regions took 36.1093070507 s Estimating background... Estimating background took 14.7051811218 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.75591516495 s Creating peak regions... Creating peak regions took 33.0601620674 s Estimating background... Estimating background took 9.94362807274 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.6572060585 s Creating peak regions... Creating peak regions took 33.0864930153 s Estimating background... Estimating background took 10.4020500183 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.8915708065 s Creating peak regions... Creating peak regions took 29.8807039261 s Estimating background... Estimating background took 10.4275398254 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.08134794235 s Creating peak regions... Creating peak regions took 28.2601959705 s Estimating background... Estimating background took 13.1829841137 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40377688408 s Creating peak regions... Creating peak regions took 24.9964430332 s Estimating background... Estimating background took 7.28045606613 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.44563603401 s Creating peak regions... Creating peak regions took 19.3551828861 s Estimating background... Estimating background took 9.48701786995 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.16233110428 s Creating peak regions... Creating peak regions took 81.8846759796 s Estimating background... Estimating background took 23.60496521 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.41920685768 s Creating peak regions... Creating peak regions took 22.7459871769 s Estimating background... Estimating background took 8.68204689026 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.855087041855 s Creating peak regions... Creating peak regions took 14.62966609 s Estimating background... Estimating background took 4.76455783844 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.07629513741 s Creating peak regions... Creating peak regions took 17.106523037 s Estimating background... Estimating background took 8.28525185585 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.38587093353 s Creating peak regions... Creating peak regions took 63.315787077 s Estimating background... Estimating background took 18.8979928493 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.86089491844 s Creating peak regions... Creating peak regions took 59.3897120953 s Estimating background... Estimating background took 14.859498024 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.34001398087 s Creating peak regions... Creating peak regions took 58.6892271042 s Estimating background... Estimating background took 17.8686549664 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.50183105469 s Creating peak regions... Creating peak regions took 57.9851410389 s Estimating background... Estimating background took 20.3215458393 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.20503020287 s Creating peak regions... Creating peak regions took 51.4300029278 s Estimating background... Estimating background took 18.59075284 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.77240777016 s Creating peak regions... Creating peak regions took 48.1769869328 s Estimating background... Estimating background took 12.9522531033 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53431391716 s Creating peak regions... Creating peak regions took 45.6951789856 s Estimating background... Estimating background took 13.1061859131 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0845749378204 s Creating peak regions... Creating peak regions took 0.343476057053 s Estimating background... Estimating background took 0.696555137634 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.92617821693 s Creating peak regions... Creating peak regions took 49.2971179485 s Estimating background... Estimating background took 17.8445599079 s Processing ZNF284-SRR5197101.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0999431610107 s Creating peak regions... Creating peak regions took 15.4159789085 s Estimating background... Estimating background took 0.683919906616 s