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='ZNF132-SRR5197058.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='ZNF132-SRR5197058/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 ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.33020210266 s Creating peak regions... Creating peak regions took 75.0561418533 s Estimating background... Estimating background took 21.222630024 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.77074313164 s Creating peak regions... Creating peak regions took 38.5706110001 s Estimating background... Estimating background took 9.14458703995 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.84687399864 s Creating peak regions... Creating peak regions took 40.6852579117 s Estimating background... Estimating background took 9.32096886635 s Processing ZNF132-SRR5197058.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='ZNF132-SRR5197058.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='ZNF132-SRR5197058/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 ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.39562487602 s Creating peak regions... Creating peak regions took 66.1481919289 s Estimating background... Estimating background took 19.1208589077 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.69809103012 s Creating peak regions... Creating peak regions took 34.1067941189 s Estimating background... Estimating background took 8.29448986053 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.56541180611 s Creating peak regions... Creating peak regions took 36.8288788795 s Estimating background... Estimating background took 8.459608078 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.78303909302 s Creating peak regions... Creating peak regions took 34.251855135 s Estimating background... Estimating background took 8.79435896873 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.49295806885 s Creating peak regions... Creating peak regions took 29.6034469604 s Estimating background... Estimating background took 8.78354787827 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.12442302704 s Creating peak regions... Creating peak regions took 25.5384731293 s Estimating background... Estimating background took 5.88669395447 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.07996797562 s Creating peak regions... Creating peak regions took 27.1541719437 s Estimating background... Estimating background took 6.57292890549 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.04611611366 s Creating peak regions... Creating peak regions took 23.8969798088 s Estimating background... Estimating background took 6.20952987671 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.23326015472 s Creating peak regions... Creating peak regions took 22.8231790066 s Estimating background... Estimating background took 7.74310302734 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.966990947723 s Creating peak regions... Creating peak regions took 20.1535208225 s Estimating background... Estimating background took 4.83838105202 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.928442955017 s Creating peak regions... Creating peak regions took 16.1020669937 s Estimating background... Estimating background took 4.99491596222 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.63397216797 s Creating peak regions... Creating peak regions took 65.4662680626 s Estimating background... Estimating background took 13.813585043 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.858230829239 s Creating peak regions... Creating peak regions took 16.9982790947 s Estimating background... Estimating background took 5.1200170517 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.448400974274 s Creating peak regions... Creating peak regions took 12.7160050869 s Estimating background... Estimating background took 1.87059092522 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.838268995285 s Creating peak regions... Creating peak regions took 13.9977250099 s Estimating background... Estimating background took 4.53277206421 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.04271292686 s Creating peak regions... Creating peak regions took 54.9168450832 s Estimating background... Estimating background took 10.6145021915 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.77218723297 s Creating peak regions... Creating peak regions took 50.8149330616 s Estimating background... Estimating background took 9.14257407188 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95543909073 s Creating peak regions... Creating peak regions took 46.2446269989 s Estimating background... Estimating background took 10.7972760201 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24212598801 s Creating peak regions... Creating peak regions took 44.5983071327 s Estimating background... Estimating background took 11.7041900158 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.02266192436 s Creating peak regions... Creating peak regions took 43.7211232185 s Estimating background... Estimating background took 10.8729510307 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.65409898758 s Creating peak regions... Creating peak regions took 39.1341810226 s Estimating background... Estimating background took 8.25456190109 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.38103508949 s Creating peak regions... Creating peak regions took 34.6662790775 s Estimating background... Estimating background took 8.02593302727 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0699801445007 s Creating peak regions... Creating peak regions took 0.124889135361 s Estimating background... Estimating background took 0.578936100006 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.93477797508 s Creating peak regions... Creating peak regions took 42.7146089077 s Estimating background... Estimating background took 10.0996730328 s Processing ZNF132-SRR5197058.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0908350944519 s Creating peak regions... Creating peak regions took 14.0286450386 s Estimating background... Estimating background took 0.439913988113 s