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='ZNF439-SRR5197140.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='ZNF439-SRR5197140/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 ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.86476588249 s Creating peak regions... Creating peak regions took 79.1786420345 s Estimating background... Estimating background took 53.9631659985 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.35014486313 s Creating peak regions... Creating peak regions took 42.0154409409 s Estimating background... Estimating background took 20.5728108883 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.14082694054 s Creating peak regions... Creating peak regions took 37.0846648216 s Estimating background... Estimating background took 19.1518490314 s Processing ZNF439-SRR5197140.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='ZNF439-SRR5197140.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='ZNF439-SRR5197140/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 ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.15669894218 s Creating peak regions... Creating peak regions took 77.663588047 s Estimating background... Estimating background took 57.8428888321 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.32699489594 s Creating peak regions... Creating peak regions took 41.5138170719 s Estimating background... Estimating background took 22.3246920109 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.41921186447 s Creating peak regions... Creating peak regions took 42.5113968849 s Estimating background... Estimating background took 23.2721860409 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.5964858532 s Creating peak regions... Creating peak regions took 40.8674330711 s Estimating background... Estimating background took 23.5335512161 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.01346611977 s Creating peak regions... Creating peak regions took 35.9161539078 s Estimating background... Estimating background took 23.335944891 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.2247710228 s Creating peak regions... Creating peak regions took 31.7395710945 s Estimating background... Estimating background took 14.6376981735 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.9882209301 s Creating peak regions... Creating peak regions took 30.6036179066 s Estimating background... Estimating background took 16.5765690804 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23293614388 s Creating peak regions... Creating peak regions took 28.3775479794 s Estimating background... Estimating background took 17.01749897 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.7705180645 s Creating peak regions... Creating peak regions took 27.3474040031 s Estimating background... Estimating background took 19.8763828278 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.70733094215 s Creating peak regions... Creating peak regions took 24.7157299519 s Estimating background... Estimating background took 11.6410830021 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.89702606201 s Creating peak regions... Creating peak regions took 20.2112519741 s Estimating background... Estimating background took 14.4219448566 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.71859812737 s Creating peak regions... Creating peak regions took 72.1984829903 s Estimating background... Estimating background took 36.8864219189 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.90890979767 s Creating peak regions... Creating peak regions took 21.6357450485 s Estimating background... Estimating background took 13.3370950222 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.06956601143 s Creating peak regions... Creating peak regions took 14.0244309902 s Estimating background... Estimating background took 6.85486197472 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.51404809952 s Creating peak regions... Creating peak regions took 16.0040111542 s Estimating background... Estimating background took 13.2343900204 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.37709903717 s Creating peak regions... Creating peak regions took 62.1106572151 s Estimating background... Estimating background took 29.3187170029 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.91985797882 s Creating peak regions... Creating peak regions took 57.5982270241 s Estimating background... Estimating background took 22.8491051197 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.44796395302 s Creating peak regions... Creating peak regions took 57.3835890293 s Estimating background... Estimating background took 27.761646986 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.50245285034 s Creating peak regions... Creating peak regions took 54.3431870937 s Estimating background... Estimating background took 31.3092780113 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.94120001793 s Creating peak regions... Creating peak regions took 47.3295989037 s Estimating background... Estimating background took 24.298404932 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.73630309105 s Creating peak regions... Creating peak regions took 36.8237030506 s Estimating background... Estimating background took 15.9773709774 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.1509680748 s Creating peak regions... Creating peak regions took 34.606374979 s Estimating background... Estimating background took 16.0055439472 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0896611213684 s Creating peak regions... Creating peak regions took 0.174855947495 s Estimating background... Estimating background took 0.58287191391 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.19649195671 s Creating peak regions... Creating peak regions took 40.052216053 s Estimating background... Estimating background took 24.1870758533 s Processing ZNF439-SRR5197140.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.124967098236 s Creating peak regions... Creating peak regions took 12.9807829857 s Estimating background... Estimating background took 0.688551187515 s