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='ZNF564-SRR5197181.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='ZNF564-SRR5197181/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 ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.82479691505 s Creating peak regions... Creating peak regions took 75.2913968563 s Estimating background... Estimating background took 19.3833739758 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.81216096878 s Creating peak regions... Creating peak regions took 37.8054020405 s Estimating background... Estimating background took 8.18753600121 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.82034897804 s Creating peak regions... Creating peak regions took 38.8182239532 s Estimating background... Estimating background took 8.49838519096 s Processing ZNF564-SRR5197181.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='ZNF564-SRR5197181.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='ZNF564-SRR5197181/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 ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.09764409065 s Creating peak regions... Creating peak regions took 65.4655539989 s Estimating background... Estimating background took 17.1660439968 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.50990390778 s Creating peak regions... Creating peak regions took 34.0972049236 s Estimating background... Estimating background took 7.47767496109 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.6591501236 s Creating peak regions... Creating peak regions took 34.6534569263 s Estimating background... Estimating background took 7.77982401848 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.63933992386 s Creating peak regions... Creating peak regions took 33.1235671043 s Estimating background... Estimating background took 8.38031697273 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.51205587387 s Creating peak regions... Creating peak regions took 29.3829081059 s Estimating background... Estimating background took 8.9828209877 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.14722895622 s Creating peak regions... Creating peak regions took 26.7471530437 s Estimating background... Estimating background took 5.51414299011 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.905811071396 s Creating peak regions... Creating peak regions took 27.1327769756 s Estimating background... Estimating background took 5.59994482994 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.03305792809 s Creating peak regions... Creating peak regions took 24.0557529926 s Estimating background... Estimating background took 5.43047189713 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.23312187195 s Creating peak regions... Creating peak regions took 22.9736778736 s Estimating background... Estimating background took 6.46281909943 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.937375068665 s Creating peak regions... Creating peak regions took 20.4901371002 s Estimating background... Estimating background took 4.45164203644 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.822243928909 s Creating peak regions... Creating peak regions took 15.9631249905 s Estimating background... Estimating background took 3.94230604172 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.73604989052 s Creating peak regions... Creating peak regions took 65.6944060326 s Estimating background... Estimating background took 12.7629580498 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.925825119019 s Creating peak regions... Creating peak regions took 18.2180361748 s Estimating background... Estimating background took 4.9320371151 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.514452934265 s Creating peak regions... Creating peak regions took 12.7447729111 s Estimating background... Estimating background took 1.66769099236 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.890326023102 s Creating peak regions... Creating peak regions took 13.3682968616 s Estimating background... Estimating background took 4.42500305176 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.26591300964 s Creating peak regions... Creating peak regions took 54.5659139156 s Estimating background... Estimating background took 10.8594751358 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.97488284111 s Creating peak regions... Creating peak regions took 51.51415205 s Estimating background... Estimating background took 9.09019494057 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.97997498512 s Creating peak regions... Creating peak regions took 46.1298010349 s Estimating background... Estimating background took 10.4177057743 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.08068990707 s Creating peak regions... Creating peak regions took 43.9054369926 s Estimating background... Estimating background took 10.8280069828 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.04887104034 s Creating peak regions... Creating peak regions took 41.3377199173 s Estimating background... Estimating background took 10.1786940098 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.76861214638 s Creating peak regions... Creating peak regions took 36.9741680622 s Estimating background... Estimating background took 7.54119205475 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.52709984779 s Creating peak regions... Creating peak regions took 37.4229469299 s Estimating background... Estimating background took 7.79157495499 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0732910633087 s Creating peak regions... Creating peak regions took 0.138445138931 s Estimating background... Estimating background took 0.669862985611 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.02329707146 s Creating peak regions... Creating peak regions took 38.8096630573 s Estimating background... Estimating background took 9.48019194603 s Processing ZNF564-SRR5197181.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0833399295807 s Creating peak regions... Creating peak regions took 14.1264998913 s Estimating background... Estimating background took 0.470891952515 s