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='ZNF783-SRR5197242.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='ZNF783-SRR5197242/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 ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.38055896759 s Creating peak regions... Creating peak regions took 77.5350081921 s Estimating background... Estimating background took 38.2582769394 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.81067299843 s Creating peak regions... Creating peak regions took 39.7128369808 s Estimating background... Estimating background took 15.6329779625 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.82648086548 s Creating peak regions... Creating peak regions took 39.9987418652 s Estimating background... Estimating background took 14.4890270233 s Processing ZNF783-SRR5197242.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='ZNF783-SRR5197242.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='ZNF783-SRR5197242/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 ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.4315559864 s Creating peak regions... Creating peak regions took 74.1260550022 s Estimating background... Estimating background took 35.9314789772 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.61820602417 s Creating peak regions... Creating peak regions took 38.4631512165 s Estimating background... Estimating background took 14.9443991184 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.71249103546 s Creating peak regions... Creating peak regions took 38.7477970123 s Estimating background... Estimating background took 15.1175670624 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.71190810204 s Creating peak regions... Creating peak regions took 40.8012931347 s Estimating background... Estimating background took 15.7245509624 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.269302845 s Creating peak regions... Creating peak regions took 35.5493018627 s Estimating background... Estimating background took 15.0427391529 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.72182607651 s Creating peak regions... Creating peak regions took 31.9296789169 s Estimating background... Estimating background took 10.5022850037 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.869754076 s Creating peak regions... Creating peak regions took 30.2514340878 s Estimating background... Estimating background took 12.0961971283 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95972704887 s Creating peak regions... Creating peak regions took 25.4940750599 s Estimating background... Estimating background took 11.2240979671 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.20354390144 s Creating peak regions... Creating peak regions took 24.3380279541 s Estimating background... Estimating background took 14.7348320484 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.39055299759 s Creating peak regions... Creating peak regions took 24.3688261509 s Estimating background... Estimating background took 8.13771510124 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.59286999702 s Creating peak regions... Creating peak regions took 17.1499071121 s Estimating background... Estimating background took 9.54341197014 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.2608268261 s Creating peak regions... Creating peak regions took 73.4524829388 s Estimating background... Estimating background took 25.3647840023 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.62675189972 s Creating peak regions... Creating peak regions took 19.7264268398 s Estimating background... Estimating background took 9.03599286079 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.752705097198 s Creating peak regions... Creating peak regions took 14.2770681381 s Estimating background... Estimating background took 4.91004920006 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.21179199219 s Creating peak regions... Creating peak regions took 14.9335141182 s Estimating background... Estimating background took 9.30887579918 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.55587816238 s Creating peak regions... Creating peak regions took 57.7167980671 s Estimating background... Estimating background took 20.117331028 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.01358103752 s Creating peak regions... Creating peak regions took 53.253177166 s Estimating background... Estimating background took 15.48686409 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.43007206917 s Creating peak regions... Creating peak regions took 51.7324500084 s Estimating background... Estimating background took 18.3846731186 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.55620908737 s Creating peak regions... Creating peak regions took 49.7337198257 s Estimating background... Estimating background took 21.2515559196 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.24810695648 s Creating peak regions... Creating peak regions took 46.7930669785 s Estimating background... Estimating background took 20.0129241943 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.55586194992 s Creating peak regions... Creating peak regions took 41.525124073 s Estimating background... Estimating background took 13.8971581459 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.47069716454 s Creating peak regions... Creating peak regions took 42.0360150337 s Estimating background... Estimating background took 14.0437991619 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.101204156876 s Creating peak regions... Creating peak regions took 0.18731212616 s Estimating background... Estimating background took 0.787177801132 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.24038219452 s Creating peak regions... Creating peak regions took 44.8041789532 s Estimating background... Estimating background took 17.4708888531 s Processing ZNF783-SRR5197242.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.100759029388 s Creating peak regions... Creating peak regions took 14.3332388401 s Estimating background... Estimating background took 0.662341833115 s