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='ZNF33A-SRR5197119.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='ZNF33A-SRR5197119/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 ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.72438621521 s Creating peak regions... Creating peak regions took 75.3212468624 s Estimating background... Estimating background took 27.814357996 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.29532289505 s Creating peak regions... Creating peak regions took 40.0235290527 s Estimating background... Estimating background took 11.6351678371 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.98648309708 s Creating peak regions... Creating peak regions took 41.9418699741 s Estimating background... Estimating background took 11.3783810139 s Processing ZNF33A-SRR5197119.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='ZNF33A-SRR5197119.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='ZNF33A-SRR5197119/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 ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.4202978611 s Creating peak regions... Creating peak regions took 72.6107378006 s Estimating background... Estimating background took 27.6037991047 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.92438697815 s Creating peak regions... Creating peak regions took 40.0905230045 s Estimating background... Estimating background took 12.0327210426 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.17778301239 s Creating peak regions... Creating peak regions took 41.2851319313 s Estimating background... Estimating background took 11.7723388672 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.34546804428 s Creating peak regions... Creating peak regions took 41.5027902126 s Estimating background... Estimating background took 12.892179966 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92073512077 s Creating peak regions... Creating peak regions took 34.5166540146 s Estimating background... Estimating background took 11.2887070179 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.47885203362 s Creating peak regions... Creating peak regions took 32.1177821159 s Estimating background... Estimating background took 8.1768591404 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.55631399155 s Creating peak regions... Creating peak regions took 29.0612277985 s Estimating background... Estimating background took 9.22596383095 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.46319890022 s Creating peak regions... Creating peak regions took 26.1162610054 s Estimating background... Estimating background took 8.8383038044 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.63248991966 s Creating peak regions... Creating peak regions took 24.3109641075 s Estimating background... Estimating background took 10.5564899445 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45152902603 s Creating peak regions... Creating peak regions took 24.0921521187 s Estimating background... Estimating background took 5.84259295464 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.87038493156 s Creating peak regions... Creating peak regions took 18.9829862118 s Estimating background... Estimating background took 8.59220695496 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.6177508831 s Creating peak regions... Creating peak regions took 70.9489359856 s Estimating background... Estimating background took 18.8807060719 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.34617996216 s Creating peak regions... Creating peak regions took 20.9953258038 s Estimating background... Estimating background took 7.83090400696 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.6641330719 s Creating peak regions... Creating peak regions took 13.1793699265 s Estimating background... Estimating background took 4.25553607941 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.74730801582 s Creating peak regions... Creating peak regions took 16.2586779594 s Estimating background... Estimating background took 8.34800195694 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.01604986191 s Creating peak regions... Creating peak regions took 56.8713519573 s Estimating background... Estimating background took 14.3609039783 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.83738613129 s Creating peak regions... Creating peak regions took 54.0542969704 s Estimating background... Estimating background took 11.7465250492 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.25252389908 s Creating peak regions... Creating peak regions took 53.790448904 s Estimating background... Estimating background took 14.1502199173 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.88017416 s Creating peak regions... Creating peak regions took 51.2812700272 s Estimating background... Estimating background took 16.2679400444 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.75693202019 s Creating peak regions... Creating peak regions took 46.5364530087 s Estimating background... Estimating background took 14.8148579597 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.02200889587 s Creating peak regions... Creating peak regions took 42.5952260494 s Estimating background... Estimating background took 10.8779320717 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.06255292892 s Creating peak regions... Creating peak regions took 40.4977140427 s Estimating background... Estimating background took 10.7812521458 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0966489315033 s Creating peak regions... Creating peak regions took 0.165853023529 s Estimating background... Estimating background took 0.64049911499 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.11170101166 s Creating peak regions... Creating peak regions took 48.2968728542 s Estimating background... Estimating background took 14.1235971451 s Processing ZNF33A-SRR5197119.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0992169380188 s Creating peak regions... Creating peak regions took 15.1245348454 s Estimating background... Estimating background took 0.548317909241 s