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='ZNF681-SRR5197214.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='ZNF681-SRR5197214/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 ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.07841897011 s Creating peak regions... Creating peak regions took 75.5407011509 s Estimating background... Estimating background took 18.5469930172 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.74521303177 s Creating peak regions... Creating peak regions took 40.1926579475 s Estimating background... Estimating background took 7.96792507172 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.82196903229 s Creating peak regions... Creating peak regions took 40.772012949 s Estimating background... Estimating background took 8.20616292953 s Processing ZNF681-SRR5197214.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='ZNF681-SRR5197214.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='ZNF681-SRR5197214/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 ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.62279891968 s Creating peak regions... Creating peak regions took 78.747385025 s Estimating background... Estimating background took 18.8669850826 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.88702607155 s Creating peak regions... Creating peak regions took 44.9762299061 s Estimating background... Estimating background took 7.76489210129 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.09293317795 s Creating peak regions... Creating peak regions took 46.257076025 s Estimating background... Estimating background took 8.18151211739 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.00617313385 s Creating peak regions... Creating peak regions took 42.1952021122 s Estimating background... Estimating background took 8.54908299446 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98276591301 s Creating peak regions... Creating peak regions took 33.4943749905 s Estimating background... Estimating background took 9.23063993454 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.48425292969 s Creating peak regions... Creating peak regions took 33.3331019878 s Estimating background... Estimating background took 5.98354697227 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.45443701744 s Creating peak regions... Creating peak regions took 34.5984270573 s Estimating background... Estimating background took 6.77929806709 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.35682797432 s Creating peak regions... Creating peak regions took 28.378262043 s Estimating background... Estimating background took 5.65342402458 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.3958439827 s Creating peak regions... Creating peak regions took 26.5762481689 s Estimating background... Estimating background took 6.47316884995 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.15918207169 s Creating peak regions... Creating peak regions took 25.1130099297 s Estimating background... Estimating background took 4.63752198219 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.916478872299 s Creating peak regions... Creating peak regions took 20.1685290337 s Estimating background... Estimating background took 4.39140200615 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.3294301033 s Creating peak regions... Creating peak regions took 77.3595950603 s Estimating background... Estimating background took 14.2613539696 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.0399210453 s Creating peak regions... Creating peak regions took 21.3674929142 s Estimating background... Estimating background took 4.3716609478 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.684380054474 s Creating peak regions... Creating peak regions took 14.812322855 s Estimating background... Estimating background took 1.5983338356 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.986628055573 s Creating peak regions... Creating peak regions took 16.2799229622 s Estimating background... Estimating background took 3.60707712173 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.80565786362 s Creating peak regions... Creating peak regions took 62.8285698891 s Estimating background... Estimating background took 11.4622898102 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28017115593 s Creating peak regions... Creating peak regions took 58.0076720715 s Estimating background... Estimating background took 9.34811997414 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.58594202995 s Creating peak regions... Creating peak regions took 51.0363149643 s Estimating background... Estimating background took 10.6666719913 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.95785093307 s Creating peak regions... Creating peak regions took 54.7788658142 s Estimating background... Estimating background took 12.0174050331 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.46355414391 s Creating peak regions... Creating peak regions took 51.5099351406 s Estimating background... Estimating background took 10.6574840546 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.01855397224 s Creating peak regions... Creating peak regions took 43.4847941399 s Estimating background... Estimating background took 8.1531560421 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.776720047 s Creating peak regions... Creating peak regions took 43.5019199848 s Estimating background... Estimating background took 7.5185508728 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.121175050735 s Creating peak regions... Creating peak regions took 0.165796041489 s Estimating background... Estimating background took 0.668318033218 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.61266493797 s Creating peak regions... Creating peak regions took 49.4118690491 s Estimating background... Estimating background took 11.7432050705 s Processing ZNF681-SRR5197214.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.107886075974 s Creating peak regions... Creating peak regions took 15.1414148808 s Estimating background... Estimating background took 0.459597110748 s