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='ZNF212-SRR5197080.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='ZNF212-SRR5197080/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 ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.24243783951 s Creating peak regions... Creating peak regions took 70.9806950092 s Estimating background... Estimating background took 25.5937550068 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.59498381615 s Creating peak regions... Creating peak regions took 37.1351909637 s Estimating background... Estimating background took 10.7303640842 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51650309563 s Creating peak regions... Creating peak regions took 37.3360829353 s Estimating background... Estimating background took 10.0248880386 s Processing ZNF212-SRR5197080.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='ZNF212-SRR5197080.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='ZNF212-SRR5197080/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 ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.31528186798 s Creating peak regions... Creating peak regions took 68.3810031414 s Estimating background... Estimating background took 23.079349041 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.94881892204 s Creating peak regions... Creating peak regions took 32.2811291218 s Estimating background... Estimating background took 9.17687296867 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.93102216721 s Creating peak regions... Creating peak regions took 32.9278731346 s Estimating background... Estimating background took 9.39651417732 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.25000214577 s Creating peak regions... Creating peak regions took 34.2574880123 s Estimating background... Estimating background took 9.67234897614 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.02984404564 s Creating peak regions... Creating peak regions took 28.4994118214 s Estimating background... Estimating background took 11.4788639545 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.56000900269 s Creating peak regions... Creating peak regions took 25.3956129551 s Estimating background... Estimating background took 6.60604906082 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.31013679504 s Creating peak regions... Creating peak regions took 25.6062421799 s Estimating background... Estimating background took 6.82887911797 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.32247710228 s Creating peak regions... Creating peak regions took 21.6588189602 s Estimating background... Estimating background took 6.42493200302 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.31782793999 s Creating peak regions... Creating peak regions took 21.5891010761 s Estimating background... Estimating background took 7.62613081932 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.29299902916 s Creating peak regions... Creating peak regions took 19.4124908447 s Estimating background... Estimating background took 5.38532590866 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.18685388565 s Creating peak regions... Creating peak regions took 15.2972919941 s Estimating background... Estimating background took 4.85272407532 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.63225698471 s Creating peak regions... Creating peak regions took 62.2588410378 s Estimating background... Estimating background took 15.4003651142 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.11046218872 s Creating peak regions... Creating peak regions took 17.4879560471 s Estimating background... Estimating background took 5.51390194893 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.814604997635 s Creating peak regions... Creating peak regions took 12.0330939293 s Estimating background... Estimating background took 3.76079416275 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.867264032364 s Creating peak regions... Creating peak regions took 12.9522349834 s Estimating background... Estimating background took 4.81583404541 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.89458203316 s Creating peak regions... Creating peak regions took 51.3929998875 s Estimating background... Estimating background took 12.5973749161 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.89242601395 s Creating peak regions... Creating peak regions took 45.4437561035 s Estimating background... Estimating background took 10.6749761105 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.80128407478 s Creating peak regions... Creating peak regions took 44.7677810192 s Estimating background... Estimating background took 12.389097929 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.23340702057 s Creating peak regions... Creating peak regions took 42.2563488483 s Estimating background... Estimating background took 13.6523940563 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.17297291756 s Creating peak regions... Creating peak regions took 39.2349998951 s Estimating background... Estimating background took 11.7874498367 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.26631999016 s Creating peak regions... Creating peak regions took 37.6937580109 s Estimating background... Estimating background took 8.95025396347 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.79410600662 s Creating peak regions... Creating peak regions took 33.1036419868 s Estimating background... Estimating background took 8.6338660717 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.080769777298 s Creating peak regions... Creating peak regions took 0.151734113693 s Estimating background... Estimating background took 0.594715833664 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.48377490044 s Creating peak regions... Creating peak regions took 41.0931200981 s Estimating background... Estimating background took 13.0785899162 s Processing ZNF212-SRR5197080.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.118597984314 s Creating peak regions... Creating peak regions took 12.7228338718 s Estimating background... Estimating background took 0.680712938309 s