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='ZNF101-SRR5197053.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='ZNF101-SRR5197053/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 ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.76779103279 s Creating peak regions... Creating peak regions took 69.4088609219 s Estimating background... Estimating background took 24.2098860741 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.86945390701 s Creating peak regions... Creating peak regions took 36.8618059158 s Estimating background... Estimating background took 10.5920248032 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.82607698441 s Creating peak regions... Creating peak regions took 36.6012179852 s Estimating background... Estimating background took 10.5068590641 s Processing ZNF101-SRR5197053.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='ZNF101-SRR5197053.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='ZNF101-SRR5197053/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 ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.99364304543 s Creating peak regions... Creating peak regions took 72.7554678917 s Estimating background... Estimating background took 25.0388050079 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.07324099541 s Creating peak regions... Creating peak regions took 38.7233729362 s Estimating background... Estimating background took 11.0240440369 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.03184103966 s Creating peak regions... Creating peak regions took 38.5611450672 s Estimating background... Estimating background took 10.7445440292 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.17363500595 s Creating peak regions... Creating peak regions took 40.919383049 s Estimating background... Estimating background took 11.3102960587 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.86755084991 s Creating peak regions... Creating peak regions took 35.2076499462 s Estimating background... Estimating background took 11.9214701653 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.50135493279 s Creating peak regions... Creating peak regions took 32.1850969791 s Estimating background... Estimating background took 7.62433815002 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.36223888397 s Creating peak regions... Creating peak regions took 30.6260199547 s Estimating background... Estimating background took 8.75893998146 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.34119415283 s Creating peak regions... Creating peak regions took 25.7241740227 s Estimating background... Estimating background took 8.159760952 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.67943501472 s Creating peak regions... Creating peak regions took 23.6009860039 s Estimating background... Estimating background took 9.55910801888 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.16533684731 s Creating peak regions... Creating peak regions took 24.2433171272 s Estimating background... Estimating background took 6.1089618206 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.19490385056 s Creating peak regions... Creating peak regions took 18.2556321621 s Estimating background... Estimating background took 6.59253621101 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.45458817482 s Creating peak regions... Creating peak regions took 70.4030060768 s Estimating background... Estimating background took 18.0861449242 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.21885204315 s Creating peak regions... Creating peak regions took 20.6997168064 s Estimating background... Estimating background took 6.36978602409 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.726592063904 s Creating peak regions... Creating peak regions took 14.2563459873 s Estimating background... Estimating background took 3.97307896614 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.942364931107 s Creating peak regions... Creating peak regions took 15.6242189407 s Estimating background... Estimating background took 6.04873108864 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.88508582115 s Creating peak regions... Creating peak regions took 60.3592209816 s Estimating background... Estimating background took 14.8098409176 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.52073383331 s Creating peak regions... Creating peak regions took 54.2456719875 s Estimating background... Estimating background took 12.093968153 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.8650097847 s Creating peak regions... Creating peak regions took 52.4368739128 s Estimating background... Estimating background took 14.0706369877 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.94518303871 s Creating peak regions... Creating peak regions took 53.1675591469 s Estimating background... Estimating background took 15.6867730618 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.78766489029 s Creating peak regions... Creating peak regions took 46.7024211884 s Estimating background... Estimating background took 14.6342420578 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.21646595001 s Creating peak regions... Creating peak regions took 41.8799328804 s Estimating background... Estimating background took 10.4092531204 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.09083986282 s Creating peak regions... Creating peak regions took 42.0760569572 s Estimating background... Estimating background took 10.4174690247 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0849359035492 s Creating peak regions... Creating peak regions took 0.15967297554 s Estimating background... Estimating background took 0.522994995117 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.52496409416 s Creating peak regions... Creating peak regions took 46.007791996 s Estimating background... Estimating background took 14.0650169849 s Processing ZNF101-SRR5197053.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.11602306366 s Creating peak regions... Creating peak regions took 16.2687239647 s Estimating background... Estimating background took 0.561373949051 s