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='ZNF730-SRR5197226.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='ZNF730-SRR5197226/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 ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.76387286186 s Creating peak regions... Creating peak regions took 78.9796469212 s Estimating background... Estimating background took 56.2736999989 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.99608612061 s Creating peak regions... Creating peak regions took 43.7248499393 s Estimating background... Estimating background took 22.4851338863 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.00740408897 s Creating peak regions... Creating peak regions took 39.3100299835 s Estimating background... Estimating background took 20.5720989704 s Processing ZNF730-SRR5197226.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='ZNF730-SRR5197226.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='ZNF730-SRR5197226/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 ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.65070700645 s Creating peak regions... Creating peak regions took 78.8147799969 s Estimating background... Estimating background took 51.8287181854 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.99833798409 s Creating peak regions... Creating peak regions took 42.5230538845 s Estimating background... Estimating background took 20.8547170162 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.08226203918 s Creating peak regions... Creating peak regions took 41.260956049 s Estimating background... Estimating background took 21.6907629967 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.43188619614 s Creating peak regions... Creating peak regions took 40.5922000408 s Estimating background... Estimating background took 22.8390009403 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.70724606514 s Creating peak regions... Creating peak regions took 34.6798319817 s Estimating background... Estimating background took 19.3043949604 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98677897453 s Creating peak regions... Creating peak regions took 32.0948560238 s Estimating background... Estimating background took 14.2026259899 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.16717290878 s Creating peak regions... Creating peak regions took 32.7058370113 s Estimating background... Estimating background took 17.7880589962 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.20787000656 s Creating peak regions... Creating peak regions took 27.573731184 s Estimating background... Estimating background took 17.1497118473 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.62451601028 s Creating peak regions... Creating peak regions took 26.5380861759 s Estimating background... Estimating background took 22.5373251438 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.55563902855 s Creating peak regions... Creating peak regions took 24.0206291676 s Estimating background... Estimating background took 9.80720901489 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98024296761 s Creating peak regions... Creating peak regions took 19.7757787704 s Estimating background... Estimating background took 16.1440370083 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.7552959919 s Creating peak regions... Creating peak regions took 74.1360650063 s Estimating background... Estimating background took 33.4467799664 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.80870699883 s Creating peak regions... Creating peak regions took 20.9092919827 s Estimating background... Estimating background took 13.2857260704 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.961282968521 s Creating peak regions... Creating peak regions took 14.1549060345 s Estimating background... Estimating background took 6.69907188416 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.57426810265 s Creating peak regions... Creating peak regions took 17.1682169437 s Estimating background... Estimating background took 15.4523391724 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.83589506149 s Creating peak regions... Creating peak regions took 59.3396990299 s Estimating background... Estimating background took 25.5826950073 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.31992793083 s Creating peak regions... Creating peak regions took 56.4214789867 s Estimating background... Estimating background took 19.8370480537 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.57006311417 s Creating peak regions... Creating peak regions took 58.0842969418 s Estimating background... Estimating background took 25.1448259354 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.87434601784 s Creating peak regions... Creating peak regions took 52.4783949852 s Estimating background... Estimating background took 28.5441000462 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.87015295029 s Creating peak regions... Creating peak regions took 49.1787641048 s Estimating background... Estimating background took 27.7416899204 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.91780900955 s Creating peak regions... Creating peak regions took 43.980812788 s Estimating background... Estimating background took 18.4123721123 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.5378370285 s Creating peak regions... Creating peak regions took 40.925896883 s Estimating background... Estimating background took 19.7911510468 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0998520851135 s Creating peak regions... Creating peak regions took 0.197874069214 s Estimating background... Estimating background took 0.564225912094 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.18679714203 s Creating peak regions... Creating peak regions took 46.6879479885 s Estimating background... Estimating background took 22.2401981354 s Processing ZNF730-SRR5197226.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.109614849091 s Creating peak regions... Creating peak regions took 14.8181929588 s Estimating background... Estimating background took 2.63035392761 s