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='ZNF528-SRR5197164.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='ZNF528-SRR5197164/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 ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.62425589561 s Creating peak regions... Creating peak regions took 80.7524249554 s Estimating background... Estimating background took 76.842676878 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.89646410942 s Creating peak regions... Creating peak regions took 44.7223680019 s Estimating background... Estimating background took 27.4653909206 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.60689783096 s Creating peak regions... Creating peak regions took 40.9128220081 s Estimating background... Estimating background took 25.1968860626 s Processing ZNF528-SRR5197164.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='ZNF528-SRR5197164.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='ZNF528-SRR5197164/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 ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.06116294861 s Creating peak regions... Creating peak regions took 81.0921459198 s Estimating background... Estimating background took 75.6181781292 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.84916305542 s Creating peak regions... Creating peak regions took 44.2892467976 s Estimating background... Estimating background took 29.1760020256 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.89991497993 s Creating peak regions... Creating peak regions took 41.992705822 s Estimating background... Estimating background took 27.5577838421 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.95149803162 s Creating peak regions... Creating peak regions took 42.2410778999 s Estimating background... Estimating background took 30.576747179 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.13589787483 s Creating peak regions... Creating peak regions took 34.8981540203 s Estimating background... Estimating background took 26.3357999325 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.60134005547 s Creating peak regions... Creating peak regions took 31.9411709309 s Estimating background... Estimating background took 20.0103209019 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.58140206337 s Creating peak regions... Creating peak regions took 32.2496740818 s Estimating background... Estimating background took 20.8502039909 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.61971497536 s Creating peak regions... Creating peak regions took 28.1371979713 s Estimating background... Estimating background took 21.0463540554 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.0670979023 s Creating peak regions... Creating peak regions took 27.6665439606 s Estimating background... Estimating background took 26.0427961349 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28774285316 s Creating peak regions... Creating peak regions took 23.9368388653 s Estimating background... Estimating background took 13.2818050385 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.16289687157 s Creating peak regions... Creating peak regions took 19.1510281563 s Estimating background... Estimating background took 16.9233551025 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.21883893013 s Creating peak regions... Creating peak regions took 75.410171032 s Estimating background... Estimating background took 45.1090240479 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.01219892502 s Creating peak regions... Creating peak regions took 22.5552380085 s Estimating background... Estimating background took 17.1205899715 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.21231794357 s Creating peak regions... Creating peak regions took 15.0718209743 s Estimating background... Estimating background took 9.06239008904 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.82899212837 s Creating peak regions... Creating peak regions took 17.6617591381 s Estimating background... Estimating background took 16.3192369938 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.809871912 s Creating peak regions... Creating peak regions took 61.99314785 s Estimating background... Estimating background took 37.5786569118 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.52303195 s Creating peak regions... Creating peak regions took 56.4296441078 s Estimating background... Estimating background took 29.161262989 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.71609401703 s Creating peak regions... Creating peak regions took 56.5499150753 s Estimating background... Estimating background took 33.3095719814 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.46512889862 s Creating peak regions... Creating peak regions took 45.4858181477 s Estimating background... Estimating background took 31.0117149353 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.63957691193 s Creating peak regions... Creating peak regions took 42.1955449581 s Estimating background... Estimating background took 29.3981759548 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.86810684204 s Creating peak regions... Creating peak regions took 37.6707489491 s Estimating background... Estimating background took 20.9848949909 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.39387989044 s Creating peak regions... Creating peak regions took 34.9298970699 s Estimating background... Estimating background took 19.4504230022 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.106851816177 s Creating peak regions... Creating peak regions took 0.192432880402 s Estimating background... Estimating background took 0.536144971848 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.64778518677 s Creating peak regions... Creating peak regions took 41.0328450203 s Estimating background... Estimating background took 30.7064847946 s Processing ZNF528-SRR5197164.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.238897800446 s Creating peak regions... Creating peak regions took 12.9697999954 s Estimating background... Estimating background took 0.702766895294 s