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='ZNF534-SRR5197167.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='ZNF534-SRR5197167/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 ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.92981100082 s Creating peak regions... Creating peak regions took 80.2685570717 s Estimating background... Estimating background took 81.1080431938 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.98158693314 s Creating peak regions... Creating peak regions took 44.296391964 s Estimating background... Estimating background took 31.8738839626 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.05959296227 s Creating peak regions... Creating peak regions took 40.202778101 s Estimating background... Estimating background took 28.8812820911 s Processing ZNF534-SRR5197167.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='ZNF534-SRR5197167.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='ZNF534-SRR5197167/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 ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.74191999435 s Creating peak regions... Creating peak regions took 79.6595449448 s Estimating background... Estimating background took 82.334980011 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.84641194344 s Creating peak regions... Creating peak regions took 43.8032710552 s Estimating background... Estimating background took 34.9551839828 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.02554297447 s Creating peak regions... Creating peak regions took 41.7015490532 s Estimating background... Estimating background took 33.3801980019 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.88342308998 s Creating peak regions... Creating peak regions took 42.1136450768 s Estimating background... Estimating background took 33.8329000473 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.15403604507 s Creating peak regions... Creating peak regions took 33.7796311378 s Estimating background... Estimating background took 28.1138107777 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.94312119484 s Creating peak regions... Creating peak regions took 33.3420250416 s Estimating background... Estimating background took 22.6054370403 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.75250506401 s Creating peak regions... Creating peak regions took 30.8996250629 s Estimating background... Estimating background took 24.416877985 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.68519592285 s Creating peak regions... Creating peak regions took 28.8133859634 s Estimating background... Estimating background took 24.1466591358 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.70086884499 s Creating peak regions... Creating peak regions took 28.5731601715 s Estimating background... Estimating background took 33.5807900429 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.96997499466 s Creating peak regions... Creating peak regions took 24.159621954 s Estimating background... Estimating background took 15.2925651073 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.44888496399 s Creating peak regions... Creating peak regions took 19.5752439499 s Estimating background... Estimating background took 23.7929029465 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.67536783218 s Creating peak regions... Creating peak regions took 74.9455080032 s Estimating background... Estimating background took 55.8554110527 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.30055904388 s Creating peak regions... Creating peak regions took 22.7972960472 s Estimating background... Estimating background took 17.0537610054 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.02041721344 s Creating peak regions... Creating peak regions took 15.0248799324 s Estimating background... Estimating background took 8.72009801865 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.63924098015 s Creating peak regions... Creating peak regions took 17.4916200638 s Estimating background... Estimating background took 18.6736149788 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.09955000877 s Creating peak regions... Creating peak regions took 61.7291178703 s Estimating background... Estimating background took 40.6353051662 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.15474009514 s Creating peak regions... Creating peak regions took 58.2191698551 s Estimating background... Estimating background took 29.6507511139 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.61298489571 s Creating peak regions... Creating peak regions took 46.7040579319 s Estimating background... Estimating background took 31.6942520142 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.24160909653 s Creating peak regions... Creating peak regions took 44.9397470951 s Estimating background... Estimating background took 36.7400150299 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.5759780407 s Creating peak regions... Creating peak regions took 41.2123041153 s Estimating background... Estimating background took 32.0188190937 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.81496906281 s Creating peak regions... Creating peak regions took 37.1786949635 s Estimating background... Estimating background took 22.0973501205 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.43051409721 s Creating peak regions... Creating peak regions took 34.7827420235 s Estimating background... Estimating background took 22.5770409107 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.107933044434 s Creating peak regions... Creating peak regions took 0.18187212944 s Estimating background... Estimating background took 0.575374126434 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.27971291542 s Creating peak regions... Creating peak regions took 39.6250109673 s Estimating background... Estimating background took 28.3749599457 s Processing ZNF534-SRR5197167.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.19584107399 s Creating peak regions... Creating peak regions took 13.5043399334 s Estimating background... Estimating background took 0.569767951965 s