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='ZNF445-SRR5197145.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='ZNF445-SRR5197145/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 ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.51081395149 s Creating peak regions... Creating peak regions took 81.2812941074 s Estimating background... Estimating background took 83.3517382145 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.20192289352 s Creating peak regions... Creating peak regions took 44.1979811192 s Estimating background... Estimating background took 28.4850959778 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.03076696396 s Creating peak regions... Creating peak regions took 38.259196043 s Estimating background... Estimating background took 28.413487196 s Processing ZNF445-SRR5197145.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='ZNF445-SRR5197145.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='ZNF445-SRR5197145/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 ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.05094385147 s Creating peak regions... Creating peak regions took 80.6612808704 s Estimating background... Estimating background took 83.7132689953 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.00014090538 s Creating peak regions... Creating peak regions took 44.9918630123 s Estimating background... Estimating background took 33.7055230141 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.22284603119 s Creating peak regions... Creating peak regions took 41.4806449413 s Estimating background... Estimating background took 34.5722250938 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.46712994576 s Creating peak regions... Creating peak regions took 43.287484169 s Estimating background... Estimating background took 36.8967981339 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.71190500259 s Creating peak regions... Creating peak regions took 35.8186869621 s Estimating background... Estimating background took 36.292773962 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.10340094566 s Creating peak regions... Creating peak regions took 34.7384121418 s Estimating background... Estimating background took 23.6321790218 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.87233400345 s Creating peak regions... Creating peak regions took 31.026157856 s Estimating background... Estimating background took 25.2275269032 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.06860184669 s Creating peak regions... Creating peak regions took 30.0211470127 s Estimating background... Estimating background took 28.029818058 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.66825795174 s Creating peak regions... Creating peak regions took 27.3679959774 s Estimating background... Estimating background took 37.1643569469 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.82430911064 s Creating peak regions... Creating peak regions took 25.8409211636 s Estimating background... Estimating background took 17.0431990623 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.58695292473 s Creating peak regions... Creating peak regions took 21.2168619633 s Estimating background... Estimating background took 27.5345141888 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.03015995026 s Creating peak regions... Creating peak regions took 75.9902591705 s Estimating background... Estimating background took 57.4233269691 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.34613800049 s Creating peak regions... Creating peak regions took 22.5204310417 s Estimating background... Estimating background took 22.1287539005 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40297293663 s Creating peak regions... Creating peak regions took 15.2856361866 s Estimating background... Estimating background took 11.1341760159 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.09910392761 s Creating peak regions... Creating peak regions took 18.2366631031 s Estimating background... Estimating background took 22.7796001434 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.50795197487 s Creating peak regions... Creating peak regions took 63.3196148872 s Estimating background... Estimating background took 42.2900359631 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.41636800766 s Creating peak regions... Creating peak regions took 58.3193290234 s Estimating background... Estimating background took 27.5165967941 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.37131690979 s Creating peak regions... Creating peak regions took 47.8416879177 s Estimating background... Estimating background took 34.2688469887 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.64802384377 s Creating peak regions... Creating peak regions took 46.318392992 s Estimating background... Estimating background took 39.4564089775 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.92408204079 s Creating peak regions... Creating peak regions took 42.7311439514 s Estimating background... Estimating background took 36.3085000515 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.37227582932 s Creating peak regions... Creating peak regions took 36.4938950539 s Estimating background... Estimating background took 25.1692042351 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.86887001991 s Creating peak regions... Creating peak regions took 35.6879680157 s Estimating background... Estimating background took 25.6849789619 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.119336843491 s Creating peak regions... Creating peak regions took 0.194602966309 s Estimating background... Estimating background took 0.699282884598 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.79760885239 s Creating peak regions... Creating peak regions took 39.2461509705 s Estimating background... Estimating background took 33.4513659477 s Processing ZNF445-SRR5197145.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.197270154953 s Creating peak regions... Creating peak regions took 14.0589020252 s Estimating background... Estimating background took 0.64385008812 s