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='ZNF790-SRR5197246.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='ZNF790-SRR5197246/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 ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.53097105026 s Creating peak regions... Creating peak regions took 75.5997698307 s Estimating background... Estimating background took 22.0720059872 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.76139998436 s Creating peak regions... Creating peak regions took 39.0509939194 s Estimating background... Estimating background took 9.5522608757 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.83449101448 s Creating peak regions... Creating peak regions took 38.7220289707 s Estimating background... Estimating background took 9.37377405167 s Processing ZNF790-SRR5197246.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='ZNF790-SRR5197246.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='ZNF790-SRR5197246/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 ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.41827511787 s Creating peak regions... Creating peak regions took 66.1591300964 s Estimating background... Estimating background took 19.5754208565 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.80677509308 s Creating peak regions... Creating peak regions took 35.0938439369 s Estimating background... Estimating background took 8.56979298592 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7392179966 s Creating peak regions... Creating peak regions took 35.3491191864 s Estimating background... Estimating background took 8.67551112175 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.83110618591 s Creating peak regions... Creating peak regions took 35.2143480778 s Estimating background... Estimating background took 8.78625512123 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.55158901215 s Creating peak regions... Creating peak regions took 30.1702370644 s Estimating background... Estimating background took 9.73378300667 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.18804597855 s Creating peak regions... Creating peak regions took 27.51065588 s Estimating background... Estimating background took 6.04392385483 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.09050297737 s Creating peak regions... Creating peak regions took 28.1994421482 s Estimating background... Estimating background took 6.40338993073 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.20355296135 s Creating peak regions... Creating peak regions took 25.0086259842 s Estimating background... Estimating background took 5.85338115692 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.19834303856 s Creating peak regions... Creating peak regions took 23.7241859436 s Estimating background... Estimating background took 6.74718117714 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.05250597 s Creating peak regions... Creating peak regions took 21.0379951 s Estimating background... Estimating background took 4.9822371006 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.910692930222 s Creating peak regions... Creating peak regions took 16.5801231861 s Estimating background... Estimating background took 4.42626786232 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.84427905083 s Creating peak regions... Creating peak regions took 69.011357069 s Estimating background... Estimating background took 14.9285488129 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.990023851395 s Creating peak regions... Creating peak regions took 17.6170608997 s Estimating background... Estimating background took 4.90217494965 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.546679019928 s Creating peak regions... Creating peak regions took 13.1944291592 s Estimating background... Estimating background took 1.8261449337 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.851137161255 s Creating peak regions... Creating peak regions took 13.83872509 s Estimating background... Estimating background took 4.36999893188 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.47677302361 s Creating peak regions... Creating peak regions took 55.6569280624 s Estimating background... Estimating background took 11.9703519344 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06788897514 s Creating peak regions... Creating peak regions took 52.6664128304 s Estimating background... Estimating background took 9.33632612228 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.30724406242 s Creating peak regions... Creating peak regions took 47.6762230396 s Estimating background... Estimating background took 11.2917640209 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.41082596779 s Creating peak regions... Creating peak regions took 48.4942810535 s Estimating background... Estimating background took 12.276473999 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.25756502151 s Creating peak regions... Creating peak regions took 42.6495039463 s Estimating background... Estimating background took 11.1493849754 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.74310016632 s Creating peak regions... Creating peak regions took 36.0051829815 s Estimating background... Estimating background took 8.06516289711 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.5978679657 s Creating peak regions... Creating peak regions took 38.7500879765 s Estimating background... Estimating background took 8.20627784729 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0806620121002 s Creating peak regions... Creating peak regions took 0.158144950867 s Estimating background... Estimating background took 0.54203414917 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.25956606865 s Creating peak regions... Creating peak regions took 41.7565281391 s Estimating background... Estimating background took 11.7095861435 s Processing ZNF790-SRR5197246.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0998339653015 s Creating peak regions... Creating peak regions took 13.6860351562 s Estimating background... Estimating background took 0.395061969757 s