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='ZNF267-SRR5197094.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='ZNF267-SRR5197094/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 ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.62749910355 s Creating peak regions... Creating peak regions took 74.6195411682 s Estimating background... Estimating background took 24.010684967 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.88521790504 s Creating peak regions... Creating peak regions took 37.4447278976 s Estimating background... Estimating background took 10.660449028 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.94749093056 s Creating peak regions... Creating peak regions took 41.0786149502 s Estimating background... Estimating background took 10.1344649792 s Processing ZNF267-SRR5197094.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='ZNF267-SRR5197094.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='ZNF267-SRR5197094/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 ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.50335884094 s Creating peak regions... Creating peak regions took 72.3746240139 s Estimating background... Estimating background took 23.847878933 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92065501213 s Creating peak regions... Creating peak regions took 40.8303480148 s Estimating background... Estimating background took 10.7404961586 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.85681891441 s Creating peak regions... Creating peak regions took 35.6983442307 s Estimating background... Estimating background took 8.86486387253 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.54602193832 s Creating peak regions... Creating peak regions took 34.7667648792 s Estimating background... Estimating background took 8.78480005264 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.29385304451 s Creating peak regions... Creating peak regions took 29.4250519276 s Estimating background... Estimating background took 8.19735002518 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.04842805862 s Creating peak regions... Creating peak regions took 27.0870699883 s Estimating background... Estimating background took 5.8146378994 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.974081039429 s Creating peak regions... Creating peak regions took 25.6897621155 s Estimating background... Estimating background took 6.46969914436 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.39179515839 s Creating peak regions... Creating peak regions took 22.3726770878 s Estimating background... Estimating background took 6.06472992897 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.1786699295 s Creating peak regions... Creating peak regions took 20.6820650101 s Estimating background... Estimating background took 7.48224377632 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.815061092377 s Creating peak regions... Creating peak regions took 19.3700220585 s Estimating background... Estimating background took 4.54205799103 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.843477010727 s Creating peak regions... Creating peak regions took 15.4041700363 s Estimating background... Estimating background took 5.29790496826 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.48338985443 s Creating peak regions... Creating peak regions took 61.9918510914 s Estimating background... Estimating background took 13.0985360146 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.859298229218 s Creating peak regions... Creating peak regions took 16.4107480049 s Estimating background... Estimating background took 5.0908510685 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.470989227295 s Creating peak regions... Creating peak regions took 12.0420939922 s Estimating background... Estimating background took 3.06353998184 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.765017032623 s Creating peak regions... Creating peak regions took 12.2579381466 s Estimating background... Estimating background took 4.84211421013 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.00023388863 s Creating peak regions... Creating peak regions took 50.7173669338 s Estimating background... Estimating background took 10.721955061 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.73062181473 s Creating peak regions... Creating peak regions took 48.6895151138 s Estimating background... Estimating background took 8.80114793777 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.80460000038 s Creating peak regions... Creating peak regions took 44.5302679539 s Estimating background... Estimating background took 10.4944238663 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.03347110748 s Creating peak regions... Creating peak regions took 45.035629034 s Estimating background... Estimating background took 11.6712889671 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.85465097427 s Creating peak regions... Creating peak regions took 39.137898922 s Estimating background... Estimating background took 10.5871651173 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.58564996719 s Creating peak regions... Creating peak regions took 35.061342001 s Estimating background... Estimating background took 8.01797199249 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.39784789085 s Creating peak regions... Creating peak regions took 33.3700580597 s Estimating background... Estimating background took 7.96643209457 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0742869377136 s Creating peak regions... Creating peak regions took 0.14932012558 s Estimating background... Estimating background took 0.530477046967 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98511600494 s Creating peak regions... Creating peak regions took 40.2714869976 s Estimating background... Estimating background took 10.2287960052 s Processing ZNF267-SRR5197094.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.077271938324 s Creating peak regions... Creating peak regions took 12.4993729591 s Estimating background... Estimating background took 0.39488697052 s