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='ZNF485-SRR5197155.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='ZNF485-SRR5197155/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 ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.50473213196 s Creating peak regions... Creating peak regions took 76.3460130692 s Estimating background... Estimating background took 31.5512340069 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.21340703964 s Creating peak regions... Creating peak regions took 39.7883059978 s Estimating background... Estimating background took 13.0606210232 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.17782711983 s Creating peak regions... Creating peak regions took 39.2198700905 s Estimating background... Estimating background took 13.2407410145 s Processing ZNF485-SRR5197155.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='ZNF485-SRR5197155.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='ZNF485-SRR5197155/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 ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.2348408699 s Creating peak regions... Creating peak regions took 75.117043972 s Estimating background... Estimating background took 32.8386838436 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.27192997932 s Creating peak regions... Creating peak regions took 39.7705211639 s Estimating background... Estimating background took 13.1871170998 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.13050293922 s Creating peak regions... Creating peak regions took 40.6754791737 s Estimating background... Estimating background took 14.3750920296 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.40042090416 s Creating peak regions... Creating peak regions took 40.3644721508 s Estimating background... Estimating background took 13.7239220142 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.86325407028 s Creating peak regions... Creating peak regions took 33.9024679661 s Estimating background... Estimating background took 13.6098051071 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.51815891266 s Creating peak regions... Creating peak regions took 32.6856939793 s Estimating background... Estimating background took 9.06148982048 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.36013007164 s Creating peak regions... Creating peak regions took 29.3110051155 s Estimating background... Estimating background took 9.29294300079 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.44920992851 s Creating peak regions... Creating peak regions took 25.3904409409 s Estimating background... Estimating background took 9.25282001495 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.67280602455 s Creating peak regions... Creating peak regions took 25.4985790253 s Estimating background... Estimating background took 12.4918129444 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.20884108543 s Creating peak regions... Creating peak regions took 23.9785480499 s Estimating background... Estimating background took 7.068379879 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40140390396 s Creating peak regions... Creating peak regions took 19.38570714 s Estimating background... Estimating background took 9.97209000587 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.7255461216 s Creating peak regions... Creating peak regions took 75.431114912 s Estimating background... Estimating background took 22.0400621891 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.28556704521 s Creating peak regions... Creating peak regions took 20.4491028786 s Estimating background... Estimating background took 8.15028595924 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.843881845474 s Creating peak regions... Creating peak regions took 13.9737589359 s Estimating background... Estimating background took 3.73826694489 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.755188941956 s Creating peak regions... Creating peak regions took 15.7151050568 s Estimating background... Estimating background took 7.90175890923 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.95191407204 s Creating peak regions... Creating peak regions took 58.65666008 s Estimating background... Estimating background took 16.934566021 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53249883652 s Creating peak regions... Creating peak regions took 53.9450800419 s Estimating background... Estimating background took 13.5438017845 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.8232820034 s Creating peak regions... Creating peak regions took 57.5369539261 s Estimating background... Estimating background took 17.6648430824 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.11187696457 s Creating peak regions... Creating peak regions took 53.4330039024 s Estimating background... Estimating background took 19.5030481815 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85429620743 s Creating peak regions... Creating peak regions took 49.092386961 s Estimating background... Estimating background took 18.1881399155 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.36453700066 s Creating peak regions... Creating peak regions took 42.605932951 s Estimating background... Estimating background took 11.9209649563 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.00431799889 s Creating peak regions... Creating peak regions took 40.5226778984 s Estimating background... Estimating background took 11.8150401115 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0815331935883 s Creating peak regions... Creating peak regions took 0.163145780563 s Estimating background... Estimating background took 0.539865970612 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.85275578499 s Creating peak regions... Creating peak regions took 48.4848511219 s Estimating background... Estimating background took 13.7430560589 s Processing ZNF485-SRR5197155.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.101090908051 s Creating peak regions... Creating peak regions took 13.5244600773 s Estimating background... Estimating background took 0.533525943756 s