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='ZNF197-SRR5197074.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='ZNF197-SRR5197074/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 ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.21216487885 s Creating peak regions... Creating peak regions took 63.8527522087 s Estimating background... Estimating background took 39.1755268574 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.27786898613 s Creating peak regions... Creating peak regions took 34.135684967 s Estimating background... Estimating background took 16.1698799133 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.3770210743 s Creating peak regions... Creating peak regions took 33.6044919491 s Estimating background... Estimating background took 15.7496030331 s Processing ZNF197-SRR5197074.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='ZNF197-SRR5197074.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='ZNF197-SRR5197074/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 ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.82704997063 s Creating peak regions... Creating peak regions took 77.2653150558 s Estimating background... Estimating background took 47.1123518944 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.81904411316 s Creating peak regions... Creating peak regions took 42.1176600456 s Estimating background... Estimating background took 20.2433731556 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.04151296616 s Creating peak regions... Creating peak regions took 41.0342121124 s Estimating background... Estimating background took 19.0419549942 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.00311112404 s Creating peak regions... Creating peak regions took 44.8558049202 s Estimating background... Estimating background took 21.608590126 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.92113280296 s Creating peak regions... Creating peak regions took 35.2027709484 s Estimating background... Estimating background took 22.6429309845 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.07713317871 s Creating peak regions... Creating peak regions took 32.2818250656 s Estimating background... Estimating background took 13.3397140503 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.03961801529 s Creating peak regions... Creating peak regions took 30.2938899994 s Estimating background... Estimating background took 14.9850988388 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.96977710724 s Creating peak regions... Creating peak regions took 26.4361228943 s Estimating background... Estimating background took 13.4369549751 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.15972709656 s Creating peak regions... Creating peak regions took 25.9216811657 s Estimating background... Estimating background took 18.3609099388 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.71807813644 s Creating peak regions... Creating peak regions took 23.5810530186 s Estimating background... Estimating background took 10.911481142 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.6470220089 s Creating peak regions... Creating peak regions took 19.8525471687 s Estimating background... Estimating background took 12.3131551743 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.34519505501 s Creating peak regions... Creating peak regions took 74.072655201 s Estimating background... Estimating background took 34.5282809734 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.60279393196 s Creating peak regions... Creating peak regions took 21.1570880413 s Estimating background... Estimating background took 10.7232921124 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.843398809433 s Creating peak regions... Creating peak regions took 13.9272921085 s Estimating background... Estimating background took 6.41672205925 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.35105204582 s Creating peak regions... Creating peak regions took 16.4107580185 s Estimating background... Estimating background took 11.4163250923 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.87604403496 s Creating peak regions... Creating peak regions took 58.6275248528 s Estimating background... Estimating background took 24.6706459522 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.51266598701 s Creating peak regions... Creating peak regions took 56.5203509331 s Estimating background... Estimating background took 21.0191180706 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.87592697144 s Creating peak regions... Creating peak regions took 55.4122810364 s Estimating background... Estimating background took 24.3871262074 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.01059699059 s Creating peak regions... Creating peak regions took 53.5906400681 s Estimating background... Estimating background took 29.0698759556 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.99919986725 s Creating peak regions... Creating peak regions took 49.2686080933 s Estimating background... Estimating background took 25.1528110504 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.20771503448 s Creating peak regions... Creating peak regions took 44.1902780533 s Estimating background... Estimating background took 18.0767030716 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.69598484039 s Creating peak regions... Creating peak regions took 37.7457671165 s Estimating background... Estimating background took 14.5318861008 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0884921550751 s Creating peak regions... Creating peak regions took 0.141819953918 s Estimating background... Estimating background took 0.658087015152 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.02615189552 s Creating peak regions... Creating peak regions took 47.0224120617 s Estimating background... Estimating background took 25.9128210545 s Processing ZNF197-SRR5197074.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.203190088272 s Creating peak regions... Creating peak regions took 16.2244710922 s Estimating background... Estimating background took 0.552277088165 s