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='ZNF786-SRR5197244.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='ZNF786-SRR5197244/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 ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.1003780365 s Creating peak regions... Creating peak regions took 76.4223339558 s Estimating background... Estimating background took 32.1954979897 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.35455203056 s Creating peak regions... Creating peak regions took 39.4353637695 s Estimating background... Estimating background took 13.5103418827 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37510585785 s Creating peak regions... Creating peak regions took 39.7149679661 s Estimating background... Estimating background took 13.5197119713 s Processing ZNF786-SRR5197244.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='ZNF786-SRR5197244.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='ZNF786-SRR5197244/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 ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.68459796906 s Creating peak regions... Creating peak regions took 73.3289470673 s Estimating background... Estimating background took 30.1728758812 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.22998189926 s Creating peak regions... Creating peak regions took 37.8006179333 s Estimating background... Estimating background took 13.0076258183 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23152899742 s Creating peak regions... Creating peak regions took 37.9534430504 s Estimating background... Estimating background took 12.8836970329 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.19023990631 s Creating peak regions... Creating peak regions took 37.4704349041 s Estimating background... Estimating background took 13.5075819492 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.11018800735 s Creating peak regions... Creating peak regions took 32.0902318954 s Estimating background... Estimating background took 12.7724850178 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.58754611015 s Creating peak regions... Creating peak regions took 31.7872519493 s Estimating background... Estimating background took 9.02381515503 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40201497078 s Creating peak regions... Creating peak regions took 27.7320990562 s Estimating background... Estimating background took 9.46794080734 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.48395204544 s Creating peak regions... Creating peak regions took 27.0293841362 s Estimating background... Estimating background took 9.43649196625 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.9137339592 s Creating peak regions... Creating peak regions took 24.4986810684 s Estimating background... Estimating background took 12.0266239643 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.04680013657 s Creating peak regions... Creating peak regions took 21.6042368412 s Estimating background... Estimating background took 6.44185519218 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.36365818977 s Creating peak regions... Creating peak regions took 18.4187428951 s Estimating background... Estimating background took 10.0276179314 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.8297560215 s Creating peak regions... Creating peak regions took 72.8583409786 s Estimating background... Estimating background took 21.2422428131 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.28306794167 s Creating peak regions... Creating peak regions took 19.3645219803 s Estimating background... Estimating background took 8.26112580299 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.676114082336 s Creating peak regions... Creating peak regions took 13.338506937 s Estimating background... Estimating background took 4.34228897095 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.948626995087 s Creating peak regions... Creating peak regions took 15.5801141262 s Estimating background... Estimating background took 7.47590112686 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.70927286148 s Creating peak regions... Creating peak regions took 55.6886861324 s Estimating background... Estimating background took 16.6030800343 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45563602448 s Creating peak regions... Creating peak regions took 56.1526179314 s Estimating background... Estimating background took 14.2519278526 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.67900300026 s Creating peak regions... Creating peak regions took 50.9739689827 s Estimating background... Estimating background took 16.1809520721 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.90183806419 s Creating peak regions... Creating peak regions took 48.6214139462 s Estimating background... Estimating background took 18.0575098991 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.9439702034 s Creating peak regions... Creating peak regions took 49.024379015 s Estimating background... Estimating background took 17.4103729725 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24647593498 s Creating peak regions... Creating peak regions took 40.8917508125 s Estimating background... Estimating background took 11.5771429539 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.94501590729 s Creating peak regions... Creating peak regions took 40.7996430397 s Estimating background... Estimating background took 11.7882769108 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0737829208374 s Creating peak regions... Creating peak regions took 0.164433956146 s Estimating background... Estimating background took 0.431970119476 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.70726203918 s Creating peak regions... Creating peak regions took 46.7985100746 s Estimating background... Estimating background took 14.2171189785 s Processing ZNF786-SRR5197244.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.102592945099 s Creating peak regions... Creating peak regions took 15.3261229992 s Estimating background... Estimating background took 0.56979393959 s