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='ZNF565-SRR5197182.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='ZNF565-SRR5197182/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 ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.60999894142 s Creating peak regions... Creating peak regions took 76.2592360973 s Estimating background... Estimating background took 30.3137030602 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85720491409 s Creating peak regions... Creating peak regions took 39.912060976 s Estimating background... Estimating background took 12.2504119873 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.8933699131 s Creating peak regions... Creating peak regions took 42.2498569489 s Estimating background... Estimating background took 12.5467550755 s Processing ZNF565-SRR5197182.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='ZNF565-SRR5197182.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='ZNF565-SRR5197182/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 ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.23575019836 s Creating peak regions... Creating peak regions took 72.7822370529 s Estimating background... Estimating background took 29.8412749767 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.8691740036 s Creating peak regions... Creating peak regions took 41.7602319717 s Estimating background... Estimating background took 12.544629097 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.01159191132 s Creating peak regions... Creating peak regions took 43.9643809795 s Estimating background... Estimating background took 12.4593160152 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.90461993217 s Creating peak regions... Creating peak regions took 52.096654892 s Estimating background... Estimating background took 13.3829300404 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.36717796326 s Creating peak regions... Creating peak regions took 40.7671439648 s Estimating background... Estimating background took 12.220323801 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.96238803864 s Creating peak regions... Creating peak regions took 30.1889798641 s Estimating background... Estimating background took 8.04595804214 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.71868896484 s Creating peak regions... Creating peak regions took 28.1974790096 s Estimating background... Estimating background took 8.52848577499 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.11691999435 s Creating peak regions... Creating peak regions took 26.9694769382 s Estimating background... Estimating background took 9.56695413589 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.52641892433 s Creating peak regions... Creating peak regions took 27.3249399662 s Estimating background... Estimating background took 11.2621259689 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.61902093887 s Creating peak regions... Creating peak regions took 24.8999419212 s Estimating background... Estimating background took 6.57613611221 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92163395882 s Creating peak regions... Creating peak regions took 21.726995945 s Estimating background... Estimating background took 8.16431903839 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.94416689873 s Creating peak regions... Creating peak regions took 76.8257629871 s Estimating background... Estimating background took 20.453099966 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.73009395599 s Creating peak regions... Creating peak regions took 20.6034178734 s Estimating background... Estimating background took 8.14163994789 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.03339505196 s Creating peak regions... Creating peak regions took 15.7320628166 s Estimating background... Estimating background took 3.92956614494 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.47334599495 s Creating peak regions... Creating peak regions took 16.4885151386 s Estimating background... Estimating background took 7.88479304314 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.2858569622 s Creating peak regions... Creating peak regions took 71.5144400597 s Estimating background... Estimating background took 16.6810250282 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.72682404518 s Creating peak regions... Creating peak regions took 63.9459040165 s Estimating background... Estimating background took 13.4177968502 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.71263384819 s Creating peak regions... Creating peak regions took 63.3388609886 s Estimating background... Estimating background took 15.8132178783 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.23010206223 s Creating peak regions... Creating peak regions took 61.1038279533 s Estimating background... Estimating background took 17.410353899 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.93948483467 s Creating peak regions... Creating peak regions took 62.7830579281 s Estimating background... Estimating background took 16.9093179703 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.19147515297 s Creating peak regions... Creating peak regions took 48.4828951359 s Estimating background... Estimating background took 11.2545378208 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.67344212532 s Creating peak regions... Creating peak regions took 43.4963419437 s Estimating background... Estimating background took 11.3928558826 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.108826160431 s Creating peak regions... Creating peak regions took 0.162533998489 s Estimating background... Estimating background took 0.742879867554 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.79132890701 s Creating peak regions... Creating peak regions took 50.0443630219 s Estimating background... Estimating background took 14.7196409702 s Processing ZNF565-SRR5197182.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.124494075775 s Creating peak regions... Creating peak regions took 16.2788040638 s Estimating background... Estimating background took 0.568128108978 s