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='ZNF649-SRR5197205.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='ZNF649-SRR5197205/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 ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.97056102753 s Creating peak regions... Creating peak regions took 77.9633021355 s Estimating background... Estimating background took 45.0155789852 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.94707918167 s Creating peak regions... Creating peak regions took 40.724656105 s Estimating background... Estimating background took 18.3964540958 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.97579407692 s Creating peak regions... Creating peak regions took 39.1396420002 s Estimating background... Estimating background took 16.6863970757 s Processing ZNF649-SRR5197205.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='ZNF649-SRR5197205.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='ZNF649-SRR5197205/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 ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.32299995422 s Creating peak regions... Creating peak regions took 77.4928150177 s Estimating background... Estimating background took 40.3050220013 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.41510796547 s Creating peak regions... Creating peak regions took 42.3691239357 s Estimating background... Estimating background took 17.2600238323 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.26323699951 s Creating peak regions... Creating peak regions took 41.3654289246 s Estimating background... Estimating background took 17.9582328796 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.44109106064 s Creating peak regions... Creating peak regions took 45.0738370419 s Estimating background... Estimating background took 18.5317361355 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.78512001038 s Creating peak regions... Creating peak regions took 40.644053936 s Estimating background... Estimating background took 15.0485928059 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.2171561718 s Creating peak regions... Creating peak regions took 34.2275571823 s Estimating background... Estimating background took 10.1543118954 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.85001111031 s Creating peak regions... Creating peak regions took 25.9640660286 s Estimating background... Estimating background took 11.2529108524 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37144804001 s Creating peak regions... Creating peak regions took 25.9082210064 s Estimating background... Estimating background took 11.6290938854 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.68974089622 s Creating peak regions... Creating peak regions took 25.3870420456 s Estimating background... Estimating background took 15.1629729271 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40469503403 s Creating peak regions... Creating peak regions took 21.2164869308 s Estimating background... Estimating background took 7.78318500519 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.85496783257 s Creating peak regions... Creating peak regions took 17.1414148808 s Estimating background... Estimating background took 11.0625090599 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.7159819603 s Creating peak regions... Creating peak regions took 65.6527700424 s Estimating background... Estimating background took 23.8523011208 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.77521586418 s Creating peak regions... Creating peak regions took 18.6666748524 s Estimating background... Estimating background took 10.0915660858 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.14750003815 s Creating peak regions... Creating peak regions took 12.7354080677 s Estimating background... Estimating background took 5.40223288536 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.56124687195 s Creating peak regions... Creating peak regions took 15.4215919971 s Estimating background... Estimating background took 9.04625606537 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.39673709869 s Creating peak regions... Creating peak regions took 51.8252549171 s Estimating background... Estimating background took 17.9589138031 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.42766189575 s Creating peak regions... Creating peak regions took 52.1079821587 s Estimating background... Estimating background took 15.0276298523 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.20508003235 s Creating peak regions... Creating peak regions took 49.1098558903 s Estimating background... Estimating background took 18.0577659607 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.57297992706 s Creating peak regions... Creating peak regions took 45.6668729782 s Estimating background... Estimating background took 19.2146270275 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.52377200127 s Creating peak regions... Creating peak regions took 41.8349859715 s Estimating background... Estimating background took 18.9626078606 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.88409113884 s Creating peak regions... Creating peak regions took 39.1800310612 s Estimating background... Estimating background took 13.5463910103 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.5505490303 s Creating peak regions... Creating peak regions took 38.1254770756 s Estimating background... Estimating background took 14.2740130424 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.12052488327 s Creating peak regions... Creating peak regions took 0.172899961472 s Estimating background... Estimating background took 0.664333105087 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.54101610184 s Creating peak regions... Creating peak regions took 46.7866470814 s Estimating background... Estimating background took 17.6689929962 s Processing ZNF649-SRR5197205.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.199568033218 s Creating peak regions... Creating peak regions took 13.9378778934 s Estimating background... Estimating background took 0.673794031143 s