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='ZNF626-SRR5197202.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='ZNF626-SRR5197202/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 ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.42488098145 s Creating peak regions... Creating peak regions took 75.5945699215 s Estimating background... Estimating background took 31.2657749653 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32720780373 s Creating peak regions... Creating peak regions took 39.5884690285 s Estimating background... Estimating background took 13.2917668819 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.27793884277 s Creating peak regions... Creating peak regions took 39.4051368237 s Estimating background... Estimating background took 13.1112439632 s Processing ZNF626-SRR5197202.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='ZNF626-SRR5197202.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='ZNF626-SRR5197202/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 ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.06527519226 s Creating peak regions... Creating peak regions took 73.8659460545 s Estimating background... Estimating background took 31.4370541573 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.22485995293 s Creating peak regions... Creating peak regions took 36.9404089451 s Estimating background... Estimating background took 13.0890982151 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23757505417 s Creating peak regions... Creating peak regions took 39.0246808529 s Estimating background... Estimating background took 13.6244959831 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.43453288078 s Creating peak regions... Creating peak regions took 38.4538779259 s Estimating background... Estimating background took 14.137773037 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.3616900444 s Creating peak regions... Creating peak regions took 32.8478689194 s Estimating background... Estimating background took 13.7632410526 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.45013189316 s Creating peak regions... Creating peak regions took 31.7797729969 s Estimating background... Estimating background took 9.29606819153 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.62392902374 s Creating peak regions... Creating peak regions took 28.8498771191 s Estimating background... Estimating background took 11.4324100018 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.60408496857 s Creating peak regions... Creating peak regions took 27.3944270611 s Estimating background... Estimating background took 10.0400099754 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.1857008934 s Creating peak regions... Creating peak regions took 26.3063399792 s Estimating background... Estimating background took 13.3083639145 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.47589015961 s Creating peak regions... Creating peak regions took 22.8445909023 s Estimating background... Estimating background took 7.03797793388 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.93743610382 s Creating peak regions... Creating peak regions took 18.1473710537 s Estimating background... Estimating background took 8.9087460041 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.79756522179 s Creating peak regions... Creating peak regions took 73.1999189854 s Estimating background... Estimating background took 21.9742369652 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.21789908409 s Creating peak regions... Creating peak regions took 19.4130079746 s Estimating background... Estimating background took 8.20438694954 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.767349004745 s Creating peak regions... Creating peak regions took 13.5254089832 s Estimating background... Estimating background took 4.63543796539 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.13536190987 s Creating peak regions... Creating peak regions took 14.9770181179 s Estimating background... Estimating background took 8.58053708076 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.79259800911 s Creating peak regions... Creating peak regions took 59.4671089649 s Estimating background... Estimating background took 16.6161649227 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.52101802826 s Creating peak regions... Creating peak regions took 56.9423019886 s Estimating background... Estimating background took 13.7592220306 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.69803094864 s Creating peak regions... Creating peak regions took 54.7951822281 s Estimating background... Estimating background took 16.2452008724 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.90204286575 s Creating peak regions... Creating peak regions took 49.0545659065 s Estimating background... Estimating background took 18.3912599087 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.68050599098 s Creating peak regions... Creating peak regions took 45.8566560745 s Estimating background... Estimating background took 17.4561669827 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.38606286049 s Creating peak regions... Creating peak regions took 41.9170868397 s Estimating background... Estimating background took 12.6296820641 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.99162697792 s Creating peak regions... Creating peak regions took 38.9955539703 s Estimating background... Estimating background took 12.5527198315 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0872530937195 s Creating peak regions... Creating peak regions took 0.151346921921 s Estimating background... Estimating background took 0.538954973221 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.19849395752 s Creating peak regions... Creating peak regions took 45.8671791553 s Estimating background... Estimating background took 17.3051390648 s Processing ZNF626-SRR5197202.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.110627174377 s Creating peak regions... Creating peak regions took 14.6444189548 s Estimating background... Estimating background took 2.47276997566 s