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='ZNF479-SRR5197151.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='ZNF479-SRR5197151/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 ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.56395316124 s Creating peak regions... Creating peak regions took 80.113558054 s Estimating background... Estimating background took 78.3018958569 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.73334503174 s Creating peak regions... Creating peak regions took 42.5537838936 s Estimating background... Estimating background took 28.4231748581 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.17693901062 s Creating peak regions... Creating peak regions took 36.4181470871 s Estimating background... Estimating background took 27.5872280598 s Processing ZNF479-SRR5197151.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='ZNF479-SRR5197151.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='ZNF479-SRR5197151/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 ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.05493211746 s Creating peak regions... Creating peak regions took 67.3440270424 s Estimating background... Estimating background took 68.6987788677 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.45006990433 s Creating peak regions... Creating peak regions took 36.0797300339 s Estimating background... Estimating background took 28.5810070038 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.54033303261 s Creating peak regions... Creating peak regions took 35.8753669262 s Estimating background... Estimating background took 28.8179740906 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.72136211395 s Creating peak regions... Creating peak regions took 34.2636520863 s Estimating background... Estimating background took 30.6508920193 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.10828495026 s Creating peak regions... Creating peak regions took 30.7395319939 s Estimating background... Estimating background took 27.9678339958 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.36419796944 s Creating peak regions... Creating peak regions took 26.3910219669 s Estimating background... Estimating background took 19.3494400978 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.50157308578 s Creating peak regions... Creating peak regions took 26.646794796 s Estimating background... Estimating background took 23.1625299454 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.40161514282 s Creating peak regions... Creating peak regions took 23.8266170025 s Estimating background... Estimating background took 21.2465009689 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.01790904999 s Creating peak regions... Creating peak regions took 23.5112161636 s Estimating background... Estimating background took 30.1722381115 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.83494091034 s Creating peak regions... Creating peak regions took 21.2657279968 s Estimating background... Estimating background took 13.9668080807 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.36756801605 s Creating peak regions... Creating peak regions took 16.5897388458 s Estimating background... Estimating background took 22.5658769608 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.84748101234 s Creating peak regions... Creating peak regions took 59.0886111259 s Estimating background... Estimating background took 46.8645098209 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.92496490479 s Creating peak regions... Creating peak regions took 17.9750568867 s Estimating background... Estimating background took 16.3977370262 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.03239393234 s Creating peak regions... Creating peak regions took 12.6660449505 s Estimating background... Estimating background took 8.41404294968 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.55676794052 s Creating peak regions... Creating peak regions took 14.2209038734 s Estimating background... Estimating background took 16.4112827778 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.28969311714 s Creating peak regions... Creating peak regions took 49.4367759228 s Estimating background... Estimating background took 34.8293521404 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.82213187218 s Creating peak regions... Creating peak regions took 48.2123699188 s Estimating background... Estimating background took 27.4071419239 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.10362696648 s Creating peak regions... Creating peak regions took 46.3645141125 s Estimating background... Estimating background took 33.1043920517 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.60208201408 s Creating peak regions... Creating peak regions took 44.3692061901 s Estimating background... Estimating background took 39.6309771538 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.12078213692 s Creating peak regions... Creating peak regions took 42.99340415 s Estimating background... Estimating background took 37.7024300098 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.60105514526 s Creating peak regions... Creating peak regions took 39.5380079746 s Estimating background... Estimating background took 25.8002090454 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.13814401627 s Creating peak regions... Creating peak regions took 36.3890469074 s Estimating background... Estimating background took 26.0862760544 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.124144077301 s Creating peak regions... Creating peak regions took 0.195266962051 s Estimating background... Estimating background took 0.532212018967 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.8684990406 s Creating peak regions... Creating peak regions took 40.1512980461 s Estimating background... Estimating background took 30.5885009766 s Processing ZNF479-SRR5197151.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.148493051529 s Creating peak regions... Creating peak regions took 13.4302451611 s Estimating background... Estimating background took 0.531349182129 s