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='ZNF846-SRR5197259.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='ZNF846-SRR5197259/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 ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.58828210831 s Creating peak regions... Creating peak regions took 78.920440197 s Estimating background... Estimating background took 49.1064350605 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.22566199303 s Creating peak regions... Creating peak regions took 41.5897021294 s Estimating background... Estimating background took 19.7161581516 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.19971013069 s Creating peak regions... Creating peak regions took 38.9978621006 s Estimating background... Estimating background took 18.0148730278 s Processing ZNF846-SRR5197259.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='ZNF846-SRR5197259.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='ZNF846-SRR5197259/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 ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.43165802956 s Creating peak regions... Creating peak regions took 79.4982230663 s Estimating background... Estimating background took 52.311316967 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.35535287857 s Creating peak regions... Creating peak regions took 43.1212849617 s Estimating background... Estimating background took 20.7427868843 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.63696098328 s Creating peak regions... Creating peak regions took 40.4096119404 s Estimating background... Estimating background took 21.5098249912 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.76986503601 s Creating peak regions... Creating peak regions took 40.9377429485 s Estimating background... Estimating background took 22.2112159729 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.9804558754 s Creating peak regions... Creating peak regions took 34.6283149719 s Estimating background... Estimating background took 20.3041329384 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32924604416 s Creating peak regions... Creating peak regions took 31.8477678299 s Estimating background... Estimating background took 14.1045570374 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.52159786224 s Creating peak regions... Creating peak regions took 30.2405838966 s Estimating background... Estimating background took 16.8013510704 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45734786987 s Creating peak regions... Creating peak regions took 27.5589339733 s Estimating background... Estimating background took 16.3705720901 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.91135692596 s Creating peak regions... Creating peak regions took 26.2695949078 s Estimating background... Estimating background took 21.2445847988 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.87056708336 s Creating peak regions... Creating peak regions took 23.9806509018 s Estimating background... Estimating background took 9.96832895279 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.07023787498 s Creating peak regions... Creating peak regions took 19.672221899 s Estimating background... Estimating background took 14.5235700607 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.40371990204 s Creating peak regions... Creating peak regions took 79.0459291935 s Estimating background... Estimating background took 34.8153779507 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.89972805977 s Creating peak regions... Creating peak regions took 21.0519049168 s Estimating background... Estimating background took 12.7409071922 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.02962708473 s Creating peak regions... Creating peak regions took 15.2324578762 s Estimating background... Estimating background took 6.49967503548 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.69432902336 s Creating peak regions... Creating peak regions took 16.3985130787 s Estimating background... Estimating background took 13.2577321529 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.45322990417 s Creating peak regions... Creating peak regions took 60.100055933 s Estimating background... Estimating background took 27.0310599804 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.72491192818 s Creating peak regions... Creating peak regions took 56.537334919 s Estimating background... Estimating background took 19.5967671871 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.25290298462 s Creating peak regions... Creating peak regions took 55.2435050011 s Estimating background... Estimating background took 25.4675159454 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.82923388481 s Creating peak regions... Creating peak regions took 52.2314200401 s Estimating background... Estimating background took 29.0192050934 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.19512104988 s Creating peak regions... Creating peak regions took 49.267952919 s Estimating background... Estimating background took 26.6426858902 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.2600941658 s Creating peak regions... Creating peak regions took 43.617087841 s Estimating background... Estimating background took 18.338821888 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85531497002 s Creating peak regions... Creating peak regions took 39.1400158405 s Estimating background... Estimating background took 19.0267810822 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.114137172699 s Creating peak regions... Creating peak regions took 0.206991910934 s Estimating background... Estimating background took 0.661988973618 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.86253499985 s Creating peak regions... Creating peak regions took 47.522135973 s Estimating background... Estimating background took 22.6893689632 s Processing ZNF846-SRR5197259.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.153377056122 s Creating peak regions... Creating peak regions took 15.4491980076 s Estimating background... Estimating background took 0.541897058487 s