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='ZNF484-SRR5197154.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='ZNF484-SRR5197154/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 ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.57006692886 s Creating peak regions... Creating peak regions took 82.1757190228 s Estimating background... Estimating background took 84.1402430534 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.48801398277 s Creating peak regions... Creating peak regions took 44.0195040703 s Estimating background... Estimating background took 26.9998030663 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.83771586418 s Creating peak regions... Creating peak regions took 38.0441920757 s Estimating background... Estimating background took 27.5817949772 s Processing ZNF484-SRR5197154.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='ZNF484-SRR5197154.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='ZNF484-SRR5197154/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 ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.70800304413 s Creating peak regions... Creating peak regions took 81.4635820389 s Estimating background... Estimating background took 84.5798530579 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.52874088287 s Creating peak regions... Creating peak regions took 44.5637021065 s Estimating background... Estimating background took 33.0843818188 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.65601491928 s Creating peak regions... Creating peak regions took 43.3258779049 s Estimating background... Estimating background took 33.3489701748 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.64331007004 s Creating peak regions... Creating peak regions took 43.3733718395 s Estimating background... Estimating background took 35.6245748997 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.1730799675 s Creating peak regions... Creating peak regions took 36.1615600586 s Estimating background... Estimating background took 40.3014230728 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.27578091621 s Creating peak regions... Creating peak regions took 35.0683319569 s Estimating background... Estimating background took 23.2881071568 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.17894601822 s Creating peak regions... Creating peak regions took 31.5305020809 s Estimating background... Estimating background took 25.9735269547 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.13762187958 s Creating peak regions... Creating peak regions took 29.3987398148 s Estimating background... Estimating background took 22.89965415 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.44553899765 s Creating peak regions... Creating peak regions took 27.4211728573 s Estimating background... Estimating background took 28.7885007858 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.54577112198 s Creating peak regions... Creating peak regions took 25.8400139809 s Estimating background... Estimating background took 17.9760820866 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.25877594948 s Creating peak regions... Creating peak regions took 19.2950520515 s Estimating background... Estimating background took 17.2827539444 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.58407020569 s Creating peak regions... Creating peak regions took 80.2336959839 s Estimating background... Estimating background took 59.5255880356 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51373100281 s Creating peak regions... Creating peak regions took 21.6758592129 s Estimating background... Estimating background took 18.3977530003 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.32979011536 s Creating peak regions... Creating peak regions took 15.706441164 s Estimating background... Estimating background took 10.4581201077 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.8024790287 s Creating peak regions... Creating peak regions took 17.762387991 s Estimating background... Estimating background took 17.7488160133 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.01902198792 s Creating peak regions... Creating peak regions took 62.5602328777 s Estimating background... Estimating background took 43.8298230171 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.37392091751 s Creating peak regions... Creating peak regions took 59.3051860332 s Estimating background... Estimating background took 30.0385661125 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.04285097122 s Creating peak regions... Creating peak regions took 47.9526410103 s Estimating background... Estimating background took 34.1922380924 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.70069694519 s Creating peak regions... Creating peak regions took 45.9016211033 s Estimating background... Estimating background took 39.0616970062 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.19680094719 s Creating peak regions... Creating peak regions took 40.9827859402 s Estimating background... Estimating background took 34.2073531151 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.53960299492 s Creating peak regions... Creating peak regions took 38.7228279114 s Estimating background... Estimating background took 25.8320109844 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.04620099068 s Creating peak regions... Creating peak regions took 36.0379850864 s Estimating background... Estimating background took 23.4887390137 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.143782138824 s Creating peak regions... Creating peak regions took 0.225690126419 s Estimating background... Estimating background took 0.66338801384 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.4360640049 s Creating peak regions... Creating peak regions took 42.1599550247 s Estimating background... Estimating background took 38.6611881256 s Processing ZNF484-SRR5197154.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.336842060089 s Creating peak regions... Creating peak regions took 14.3621048927 s Estimating background... Estimating background took 0.987114906311 s