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='ZNF805-SRR5197254.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='ZNF805-SRR5197254/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 ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.30315589905 s Creating peak regions... Creating peak regions took 78.9853579998 s Estimating background... Estimating background took 42.7634429932 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.15271711349 s Creating peak regions... Creating peak regions took 41.1389939785 s Estimating background... Estimating background took 16.8428111076 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.04393696785 s Creating peak regions... Creating peak regions took 42.5307300091 s Estimating background... Estimating background took 15.9509019852 s Processing ZNF805-SRR5197254.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='ZNF805-SRR5197254.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='ZNF805-SRR5197254/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 ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.26687502861 s Creating peak regions... Creating peak regions took 79.6065449715 s Estimating background... Estimating background took 44.4929311275 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.19418382645 s Creating peak regions... Creating peak regions took 42.7025580406 s Estimating background... Estimating background took 17.4597837925 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.15051102638 s Creating peak regions... Creating peak regions took 44.5368471146 s Estimating background... Estimating background took 17.4440438747 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.45093894005 s Creating peak regions... Creating peak regions took 41.1802039146 s Estimating background... Estimating background took 19.1273829937 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.22903299332 s Creating peak regions... Creating peak regions took 35.6628739834 s Estimating background... Estimating background took 23.1988019943 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.31938195229 s Creating peak regions... Creating peak regions took 32.5169739723 s Estimating background... Estimating background took 12.4465780258 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.03941392899 s Creating peak regions... Creating peak regions took 30.2578771114 s Estimating background... Estimating background took 12.3769109249 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.13822984695 s Creating peak regions... Creating peak regions took 28.6559150219 s Estimating background... Estimating background took 11.3595061302 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32271504402 s Creating peak regions... Creating peak regions took 27.5517258644 s Estimating background... Estimating background took 13.5487248898 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.85772109032 s Creating peak regions... Creating peak regions took 24.2106490135 s Estimating background... Estimating background took 9.8527200222 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.56247591972 s Creating peak regions... Creating peak regions took 17.7126178741 s Estimating background... Estimating background took 7.97772502899 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.62189912796 s Creating peak regions... Creating peak regions took 75.5066139698 s Estimating background... Estimating background took 31.7290740013 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.83066892624 s Creating peak regions... Creating peak regions took 21.1785240173 s Estimating background... Estimating background took 9.666877985 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.04189801216 s Creating peak regions... Creating peak regions took 14.9940350056 s Estimating background... Estimating background took 5.72200703621 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.18097496033 s Creating peak regions... Creating peak regions took 16.2847759724 s Estimating background... Estimating background took 8.26843094826 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.58584284782 s Creating peak regions... Creating peak regions took 65.0101327896 s Estimating background... Estimating background took 27.4079859257 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.11562013626 s Creating peak regions... Creating peak regions took 57.5435769558 s Estimating background... Estimating background took 21.3942408562 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.49709606171 s Creating peak regions... Creating peak regions took 56.4499459267 s Estimating background... Estimating background took 24.5461969376 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.73304605484 s Creating peak regions... Creating peak regions took 54.2793438435 s Estimating background... Estimating background took 29.005461216 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.0822198391 s Creating peak regions... Creating peak regions took 50.2165009975 s Estimating background... Estimating background took 22.4897241592 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.41737604141 s Creating peak regions... Creating peak regions took 47.5216071606 s Estimating background... Estimating background took 17.5755710602 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.87309384346 s Creating peak regions... Creating peak regions took 43.9300181866 s Estimating background... Estimating background took 16.5195701122 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.110687017441 s Creating peak regions... Creating peak regions took 0.190191030502 s Estimating background... Estimating background took 0.652670145035 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.39133000374 s Creating peak regions... Creating peak regions took 51.318418026 s Estimating background... Estimating background took 28.6793999672 s Processing ZNF805-SRR5197254.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.209125995636 s Creating peak regions... Creating peak regions took 16.5260870457 s Estimating background... Estimating background took 0.652851104736 s