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='ZNF214-SRR5197081.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='ZNF214-SRR5197081/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 ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.1892209053 s Creating peak regions... Creating peak regions took 72.2099728584 s Estimating background... Estimating background took 32.6024930477 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.46210408211 s Creating peak regions... Creating peak regions took 37.8656420708 s Estimating background... Estimating background took 12.5334229469 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51264691353 s Creating peak regions... Creating peak regions took 38.2358829975 s Estimating background... Estimating background took 12.9420540333 s Processing ZNF214-SRR5197081.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='ZNF214-SRR5197081.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='ZNF214-SRR5197081/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 ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.55869889259 s Creating peak regions... Creating peak regions took 76.5129039288 s Estimating background... Estimating background took 30.3733229637 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.62724089622 s Creating peak regions... Creating peak regions took 40.3998279572 s Estimating background... Estimating background took 13.0603840351 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.63551211357 s Creating peak regions... Creating peak regions took 40.3050849438 s Estimating background... Estimating background took 13.5611820221 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.86084699631 s Creating peak regions... Creating peak regions took 41.386259079 s Estimating background... Estimating background took 14.2647781372 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.44171714783 s Creating peak regions... Creating peak regions took 34.0764479637 s Estimating background... Estimating background took 14.3675038815 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.8947968483 s Creating peak regions... Creating peak regions took 31.0128810406 s Estimating background... Estimating background took 9.50649905205 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.93384408951 s Creating peak regions... Creating peak regions took 29.7373559475 s Estimating background... Estimating background took 11.2565779686 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.8759701252 s Creating peak regions... Creating peak regions took 28.061634779 s Estimating background... Estimating background took 9.48357892036 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.13722395897 s Creating peak regions... Creating peak regions took 26.7228188515 s Estimating background... Estimating background took 11.6087601185 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.45441007614 s Creating peak regions... Creating peak regions took 23.6835949421 s Estimating background... Estimating background took 6.96995186806 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.54694890976 s Creating peak regions... Creating peak regions took 18.8815500736 s Estimating background... Estimating background took 7.66734790802 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.52760791779 s Creating peak regions... Creating peak regions took 71.9783599377 s Estimating background... Estimating background took 22.8448951244 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.61624503136 s Creating peak regions... Creating peak regions took 20.0994839668 s Estimating background... Estimating background took 8.3852930069 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.933193922043 s Creating peak regions... Creating peak regions took 13.7473988533 s Estimating background... Estimating background took 4.98111605644 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.22284889221 s Creating peak regions... Creating peak regions took 16.2166469097 s Estimating background... Estimating background took 7.8853969574 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.740265131 s Creating peak regions... Creating peak regions took 58.7288479805 s Estimating background... Estimating background took 17.6739659309 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.06633901596 s Creating peak regions... Creating peak regions took 59.2785742283 s Estimating background... Estimating background took 14.3141829967 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.50874400139 s Creating peak regions... Creating peak regions took 54.1937358379 s Estimating background... Estimating background took 17.7714030743 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.88124895096 s Creating peak regions... Creating peak regions took 51.4779138565 s Estimating background... Estimating background took 19.771089077 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.37853503227 s Creating peak regions... Creating peak regions took 47.9774971008 s Estimating background... Estimating background took 17.1430311203 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.965020895 s Creating peak regions... Creating peak regions took 44.2506251335 s Estimating background... Estimating background took 13.3203082085 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.46351790428 s Creating peak regions... Creating peak regions took 41.462346077 s Estimating background... Estimating background took 12.3552689552 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0868260860443 s Creating peak regions... Creating peak regions took 0.193969011307 s Estimating background... Estimating background took 0.626695156097 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.89467906952 s Creating peak regions... Creating peak regions took 49.8437650204 s Estimating background... Estimating background took 19.8872568607 s Processing ZNF214-SRR5197081.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.13708114624 s Creating peak regions... Creating peak regions took 16.2721340656 s Estimating background... Estimating background took 0.593936920166 s