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='ZNF557-SRR5197177.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='ZNF557-SRR5197177/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 ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.15969395638 s Creating peak regions... Creating peak regions took 77.2125689983 s Estimating background... Estimating background took 38.1083710194 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.72506284714 s Creating peak regions... Creating peak regions took 42.3296039104 s Estimating background... Estimating background took 14.8125419617 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.5633020401 s Creating peak regions... Creating peak regions took 40.2118990421 s Estimating background... Estimating background took 13.2308840752 s Processing ZNF557-SRR5197177.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='ZNF557-SRR5197177.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='ZNF557-SRR5197177/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 ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.1072268486 s Creating peak regions... Creating peak regions took 76.9997620583 s Estimating background... Estimating background took 37.4177260399 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.82022809982 s Creating peak regions... Creating peak regions took 40.0241880417 s Estimating background... Estimating background took 14.5039288998 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.72444701195 s Creating peak regions... Creating peak regions took 40.7112119198 s Estimating background... Estimating background took 14.423871994 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.7618701458 s Creating peak regions... Creating peak regions took 42.1072649956 s Estimating background... Estimating background took 15.9156899452 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53305983543 s Creating peak regions... Creating peak regions took 36.8430800438 s Estimating background... Estimating background took 17.7284450531 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.84660577774 s Creating peak regions... Creating peak regions took 31.3925979137 s Estimating background... Estimating background took 10.0537469387 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.69480800629 s Creating peak regions... Creating peak regions took 31.5701229572 s Estimating background... Estimating background took 10.2506639957 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.6652700901 s Creating peak regions... Creating peak regions took 27.8466920853 s Estimating background... Estimating background took 9.18850803375 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.12790799141 s Creating peak regions... Creating peak regions took 26.2716729641 s Estimating background... Estimating background took 11.7898240089 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.5050110817 s Creating peak regions... Creating peak regions took 23.9759979248 s Estimating background... Estimating background took 7.79584407806 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.37588906288 s Creating peak regions... Creating peak regions took 19.0495369434 s Estimating background... Estimating background took 8.91482305527 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.44573402405 s Creating peak regions... Creating peak regions took 76.5956089497 s Estimating background... Estimating background took 24.8773570061 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.3991920948 s Creating peak regions... Creating peak regions took 20.3270680904 s Estimating background... Estimating background took 8.3702890873 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.88209104538 s Creating peak regions... Creating peak regions took 13.907679081 s Estimating background... Estimating background took 4.84838104248 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.16357302666 s Creating peak regions... Creating peak regions took 15.9201250076 s Estimating background... Estimating background took 7.40533590317 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.74105501175 s Creating peak regions... Creating peak regions took 57.2676720619 s Estimating background... Estimating background took 19.8024449348 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.1565220356 s Creating peak regions... Creating peak regions took 56.3906550407 s Estimating background... Estimating background took 16.7127430439 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.56924009323 s Creating peak regions... Creating peak regions took 53.827491045 s Estimating background... Estimating background took 19.300866127 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.75066995621 s Creating peak regions... Creating peak regions took 49.8287119865 s Estimating background... Estimating background took 22.4437291622 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.64596509933 s Creating peak regions... Creating peak regions took 48.4746918678 s Estimating background... Estimating background took 20.0975120068 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.73859381676 s Creating peak regions... Creating peak regions took 42.9836359024 s Estimating background... Estimating background took 13.735473156 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.30053114891 s Creating peak regions... Creating peak regions took 38.7078330517 s Estimating background... Estimating background took 13.1138761044 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0918660163879 s Creating peak regions... Creating peak regions took 0.167695999146 s Estimating background... Estimating background took 0.668203830719 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.33815097809 s Creating peak regions... Creating peak regions took 49.2121119499 s Estimating background... Estimating background took 17.7533910275 s Processing ZNF557-SRR5197177.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.12916302681 s Creating peak regions... Creating peak regions took 17.4811940193 s Estimating background... Estimating background took 0.564774990082 s