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='ZNF81-SRR5197257.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='ZNF81-SRR5197257/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 ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.2823009491 s Creating peak regions... Creating peak regions took 81.5286169052 s Estimating background... Estimating background took 78.8739750385 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.26892805099 s Creating peak regions... Creating peak regions took 43.2011210918 s Estimating background... Estimating background took 29.1226511002 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.6102540493 s Creating peak regions... Creating peak regions took 36.4977860451 s Estimating background... Estimating background took 26.222299099 s Processing ZNF81-SRR5197257.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='ZNF81-SRR5197257.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='ZNF81-SRR5197257/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 ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.13429403305 s Creating peak regions... Creating peak regions took 81.9894349575 s Estimating background... Estimating background took 82.3155200481 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.45141410828 s Creating peak regions... Creating peak regions took 47.0865459442 s Estimating background... Estimating background took 32.3095338345 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.33676815033 s Creating peak regions... Creating peak regions took 43.9231951237 s Estimating background... Estimating background took 31.9968659878 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.48025393486 s Creating peak regions... Creating peak regions took 43.2952878475 s Estimating background... Estimating background took 34.2351708412 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.98201704025 s Creating peak regions... Creating peak regions took 37.1597759724 s Estimating background... Estimating background took 36.584777832 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.06023192406 s Creating peak regions... Creating peak regions took 34.1980540752 s Estimating background... Estimating background took 21.802423954 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.8213121891 s Creating peak regions... Creating peak regions took 31.5588128567 s Estimating background... Estimating background took 23.1245989799 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.78846001625 s Creating peak regions... Creating peak regions took 28.6768698692 s Estimating background... Estimating background took 21.7750239372 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.17412090302 s Creating peak regions... Creating peak regions took 27.8377981186 s Estimating background... Estimating background took 27.704720974 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37593197823 s Creating peak regions... Creating peak regions took 25.6893007755 s Estimating background... Estimating background took 16.7513179779 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.11622810364 s Creating peak regions... Creating peak regions took 19.0914549828 s Estimating background... Estimating background took 17.2841160297 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.01008605957 s Creating peak regions... Creating peak regions took 78.7878022194 s Estimating background... Estimating background took 54.5245149136 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.34627580643 s Creating peak regions... Creating peak regions took 22.49563694 s Estimating background... Estimating background took 18.7803709507 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.19366812706 s Creating peak regions... Creating peak regions took 14.456485033 s Estimating background... Estimating background took 9.80431509018 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.91506886482 s Creating peak regions... Creating peak regions took 16.063699007 s Estimating background... Estimating background took 16.6468570232 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.80189490318 s Creating peak regions... Creating peak regions took 62.80448699 s Estimating background... Estimating background took 43.3692951202 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.22900795937 s Creating peak regions... Creating peak regions took 59.8673398495 s Estimating background... Estimating background took 33.2085649967 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.40464401245 s Creating peak regions... Creating peak regions took 58.3445570469 s Estimating background... Estimating background took 41.4472720623 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.62976789474 s Creating peak regions... Creating peak regions took 55.9300789833 s Estimating background... Estimating background took 47.3427209854 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.24685907364 s Creating peak regions... Creating peak regions took 52.0241241455 s Estimating background... Estimating background took 39.6565549374 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.93528318405 s Creating peak regions... Creating peak regions took 43.2818369865 s Estimating background... Estimating background took 26.3698608875 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.53005003929 s Creating peak regions... Creating peak regions took 39.4425630569 s Estimating background... Estimating background took 25.7121288776 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.114231109619 s Creating peak regions... Creating peak regions took 0.200294017792 s Estimating background... Estimating background took 0.786174058914 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.48243308067 s Creating peak regions... Creating peak regions took 45.2904958725 s Estimating background... Estimating background took 38.9702548981 s Processing ZNF81-SRR5197257.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.200797080994 s Creating peak regions... Creating peak regions took 14.7270600796 s Estimating background... Estimating background took 0.729387044907 s