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='ZNF587-SRR5197191.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='ZNF587-SRR5197191/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 ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.31724214554 s Creating peak regions... Creating peak regions took 79.0576350689 s Estimating background... Estimating background took 45.6079130173 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.87762594223 s Creating peak regions... Creating peak regions took 41.5001199245 s Estimating background... Estimating background took 18.2543020248 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85456490517 s Creating peak regions... Creating peak regions took 40.981033802 s Estimating background... Estimating background took 17.0019900799 s Processing ZNF587-SRR5197191.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='ZNF587-SRR5197191.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='ZNF587-SRR5197191/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 ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.0696349144 s Creating peak regions... Creating peak regions took 78.8331670761 s Estimating background... Estimating background took 46.5433180332 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.20009803772 s Creating peak regions... Creating peak regions took 42.8736350536 s Estimating background... Estimating background took 18.4412100315 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.12920403481 s Creating peak regions... Creating peak regions took 41.7620520592 s Estimating background... Estimating background took 18.3377540112 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.2429921627 s Creating peak regions... Creating peak regions took 42.8993179798 s Estimating background... Estimating background took 19.8619570732 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.78466510773 s Creating peak regions... Creating peak regions took 35.431251049 s Estimating background... Estimating background took 22.0081689358 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.20883607864 s Creating peak regions... Creating peak regions took 33.9238579273 s Estimating background... Estimating background took 12.5835659504 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.07234287262 s Creating peak regions... Creating peak regions took 30.3502120972 s Estimating background... Estimating background took 13.8487930298 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95170307159 s Creating peak regions... Creating peak regions took 28.8202989101 s Estimating background... Estimating background took 12.6254720688 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.38586997986 s Creating peak regions... Creating peak regions took 25.7617869377 s Estimating background... Estimating background took 15.9988930225 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.80011487007 s Creating peak regions... Creating peak regions took 24.2545239925 s Estimating background... Estimating background took 10.0985071659 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.79208183289 s Creating peak regions... Creating peak regions took 19.3689000607 s Estimating background... Estimating background took 10.4577248096 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.097260952 s Creating peak regions... Creating peak regions took 79.3285930157 s Estimating background... Estimating background took 31.8399250507 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.76169013977 s Creating peak regions... Creating peak regions took 20.9860708714 s Estimating background... Estimating background took 11.1493358612 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.931602954865 s Creating peak regions... Creating peak regions took 15.3043069839 s Estimating background... Estimating background took 5.95261096954 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.24417996407 s Creating peak regions... Creating peak regions took 16.4178340435 s Estimating background... Estimating background took 9.71792602539 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.16241693497 s Creating peak regions... Creating peak regions took 63.9078299999 s Estimating background... Estimating background took 25.3474359512 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.50719094276 s Creating peak regions... Creating peak regions took 57.142619133 s Estimating background... Estimating background took 19.9367091656 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.95951390266 s Creating peak regions... Creating peak regions took 55.063079834 s Estimating background... Estimating background took 24.5763540268 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.01849102974 s Creating peak regions... Creating peak regions took 53.0531358719 s Estimating background... Estimating background took 27.1909821033 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.78495788574 s Creating peak regions... Creating peak regions took 49.7715117931 s Estimating background... Estimating background took 23.9325819016 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.14176893234 s Creating peak regions... Creating peak regions took 43.6543209553 s Estimating background... Estimating background took 17.3665537834 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.78876709938 s Creating peak regions... Creating peak regions took 39.4981019497 s Estimating background... Estimating background took 16.6865260601 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0973601341248 s Creating peak regions... Creating peak regions took 0.180179834366 s Estimating background... Estimating background took 0.844578027725 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.77035903931 s Creating peak regions... Creating peak regions took 47.7866649628 s Estimating background... Estimating background took 25.3691940308 s Processing ZNF587-SRR5197191.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.187561988831 s Creating peak regions... Creating peak regions took 16.347563982 s Estimating background... Estimating background took 2.76284909248 s