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='ZNF567-SRR5197184.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='ZNF567-SRR5197184/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 ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.09272408485 s Creating peak regions... Creating peak regions took 65.3066749573 s Estimating background... Estimating background took 46.0771729946 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.02979803085 s Creating peak regions... Creating peak regions took 37.5456860065 s Estimating background... Estimating background took 32.4142742157 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.89112401009 s Creating peak regions... Creating peak regions took 35.2457931042 s Estimating background... Estimating background took 18.7775890827 s Processing ZNF567-SRR5197184.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='ZNF567-SRR5197184.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='ZNF567-SRR5197184/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 ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.29291796684 s Creating peak regions... Creating peak regions took 70.8194298744 s Estimating background... Estimating background took 46.9693109989 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.10550999641 s Creating peak regions... Creating peak regions took 39.5065500736 s Estimating background... Estimating background took 32.5922029018 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.24906110764 s Creating peak regions... Creating peak regions took 38.0826449394 s Estimating background... Estimating background took 18.8051919937 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.12287592888 s Creating peak regions... Creating peak regions took 37.5948898792 s Estimating background... Estimating background took 20.549505949 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.14948797226 s Creating peak regions... Creating peak regions took 33.0339448452 s Estimating background... Estimating background took 28.9141740799 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.21898794174 s Creating peak regions... Creating peak regions took 29.664981842 s Estimating background... Estimating background took 13.4069979191 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.21707892418 s Creating peak regions... Creating peak regions took 26.9660100937 s Estimating background... Estimating background took 16.9548969269 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.81176900864 s Creating peak regions... Creating peak regions took 24.6246380806 s Estimating background... Estimating background took 11.2786328793 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.17651391029 s Creating peak regions... Creating peak regions took 23.7726020813 s Estimating background... Estimating background took 15.0194141865 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.67514610291 s Creating peak regions... Creating peak regions took 22.8957920074 s Estimating background... Estimating background took 11.3533070087 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.31686282158 s Creating peak regions... Creating peak regions took 16.8085308075 s Estimating background... Estimating background took 7.98850607872 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.24206089973 s Creating peak regions... Creating peak regions took 68.7148509026 s Estimating background... Estimating background took 34.9249839783 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.47884607315 s Creating peak regions... Creating peak regions took 19.1469449997 s Estimating background... Estimating background took 10.4071941376 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.899167060852 s Creating peak regions... Creating peak regions took 12.9425120354 s Estimating background... Estimating background took 6.32537102699 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.20644402504 s Creating peak regions... Creating peak regions took 14.7401890755 s Estimating background... Estimating background took 8.32774496078 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.09378099442 s Creating peak regions... Creating peak regions took 58.9402079582 s Estimating background... Estimating background took 27.7529051304 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.77772188187 s Creating peak regions... Creating peak regions took 50.0349421501 s Estimating background... Estimating background took 22.6973659992 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.01409602165 s Creating peak regions... Creating peak regions took 50.7728281021 s Estimating background... Estimating background took 26.0759301186 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.06529593468 s Creating peak regions... Creating peak regions took 48.2116770744 s Estimating background... Estimating background took 27.1733520031 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.7058839798 s Creating peak regions... Creating peak regions took 43.0301530361 s Estimating background... Estimating background took 24.6359829903 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.21302604675 s Creating peak regions... Creating peak regions took 40.1079301834 s Estimating background... Estimating background took 19.35115695 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28915190697 s Creating peak regions... Creating peak regions took 36.3965041637 s Estimating background... Estimating background took 13.7465970516 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.156123161316 s Creating peak regions... Creating peak regions took 0.200461864471 s Estimating background... Estimating background took 0.85697889328 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.01629209518 s Creating peak regions... Creating peak regions took 44.5319728851 s Estimating background... Estimating background took 30.4174239635 s Processing ZNF567-SRR5197184.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.211321115494 s Creating peak regions... Creating peak regions took 13.3653929234 s Estimating background... Estimating background took 0.547543048859 s