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='ZNF548-SRR5197171.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='ZNF548-SRR5197171/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 ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.83997702599 s Creating peak regions... Creating peak regions took 80.9375939369 s Estimating background... Estimating background took 73.9864518642 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.58157682419 s Creating peak regions... Creating peak regions took 44.6693990231 s Estimating background... Estimating background took 28.7221539021 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.34304499626 s Creating peak regions... Creating peak regions took 41.3931670189 s Estimating background... Estimating background took 27.6199719906 s Processing ZNF548-SRR5197171.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='ZNF548-SRR5197171.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='ZNF548-SRR5197171/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 ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.04861211777 s Creating peak regions... Creating peak regions took 80.3920230865 s Estimating background... Estimating background took 76.5355470181 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.44007015228 s Creating peak regions... Creating peak regions took 46.6511001587 s Estimating background... Estimating background took 30.0853700638 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.34506106377 s Creating peak regions... Creating peak regions took 41.260972023 s Estimating background... Estimating background took 30.4744238853 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.36035609245 s Creating peak regions... Creating peak regions took 42.7192661762 s Estimating background... Estimating background took 31.5413069725 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.59843111038 s Creating peak regions... Creating peak regions took 36.6059191227 s Estimating background... Estimating background took 28.1696410179 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.07203507423 s Creating peak regions... Creating peak regions took 33.3321511745 s Estimating background... Estimating background took 19.8787820339 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.75795602798 s Creating peak regions... Creating peak regions took 31.5439181328 s Estimating background... Estimating background took 22.7570579052 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.10693502426 s Creating peak regions... Creating peak regions took 28.6978170872 s Estimating background... Estimating background took 22.1573610306 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.53494787216 s Creating peak regions... Creating peak regions took 27.6486570835 s Estimating background... Estimating background took 28.2471358776 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.27383303642 s Creating peak regions... Creating peak regions took 25.2690091133 s Estimating background... Estimating background took 14.1280548573 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39799213409 s Creating peak regions... Creating peak regions took 19.2067019939 s Estimating background... Estimating background took 19.2974069118 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.88112998009 s Creating peak regions... Creating peak regions took 77.2591328621 s Estimating background... Estimating background took 48.691546917 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.00824999809 s Creating peak regions... Creating peak regions took 21.3073611259 s Estimating background... Estimating background took 17.7760050297 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.33482098579 s Creating peak regions... Creating peak regions took 14.7709820271 s Estimating background... Estimating background took 8.89823412895 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.0123488903 s Creating peak regions... Creating peak regions took 16.9926290512 s Estimating background... Estimating background took 18.4601299763 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.60745096207 s Creating peak regions... Creating peak regions took 62.7541708946 s Estimating background... Estimating background took 37.9837768078 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.93613004684 s Creating peak regions... Creating peak regions took 59.6409709454 s Estimating background... Estimating background took 28.1595520973 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.4861869812 s Creating peak regions... Creating peak regions took 57.1077160835 s Estimating background... Estimating background took 36.2079079151 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.62633395195 s Creating peak regions... Creating peak regions took 55.2280130386 s Estimating background... Estimating background took 41.2362520695 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.97436714172 s Creating peak regions... Creating peak regions took 51.1906998158 s Estimating background... Estimating background took 36.7320039272 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.84044218063 s Creating peak regions... Creating peak regions took 43.7294328213 s Estimating background... Estimating background took 25.0597469807 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.48551607132 s Creating peak regions... Creating peak regions took 39.5292179585 s Estimating background... Estimating background took 23.9134230614 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.200849056244 s Creating peak regions... Creating peak regions took 0.197237968445 s Estimating background... Estimating background took 0.796178102493 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.22132897377 s Creating peak regions... Creating peak regions took 44.2653958797 s Estimating background... Estimating background took 33.2130529881 s Processing ZNF548-SRR5197171.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.195121049881 s Creating peak regions... Creating peak regions took 15.0072758198 s Estimating background... Estimating background took 0.774930953979 s