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='ZNF778-SRR5197238.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='ZNF778-SRR5197238/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 ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.872590065 s Creating peak regions... Creating peak regions took 83.7704789639 s Estimating background... Estimating background took 108.670671225 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.27569913864 s Creating peak regions... Creating peak regions took 45.7726278305 s Estimating background... Estimating background took 38.4524428844 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.66061496735 s Creating peak regions... Creating peak regions took 39.4318659306 s Estimating background... Estimating background took 36.7045600414 s Processing ZNF778-SRR5197238.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='ZNF778-SRR5197238.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='ZNF778-SRR5197238/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 ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 10.2261321545 s Creating peak regions... Creating peak regions took 83.4274830818 s Estimating background... Estimating background took 107.186285019 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.41428089142 s Creating peak regions... Creating peak regions took 47.0705630779 s Estimating background... Estimating background took 42.0945310593 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.3740670681 s Creating peak regions... Creating peak regions took 44.584223032 s Estimating background... Estimating background took 43.8033978939 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.45566678047 s Creating peak regions... Creating peak regions took 44.574737072 s Estimating background... Estimating background took 46.2209770679 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.70434093475 s Creating peak regions... Creating peak regions took 37.9182190895 s Estimating background... Estimating background took 44.0589010715 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.69689488411 s Creating peak regions... Creating peak regions took 34.5588459969 s Estimating background... Estimating background took 28.0064399242 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.47744703293 s Creating peak regions... Creating peak regions took 32.5021009445 s Estimating background... Estimating background took 31.561937809 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.5712621212 s Creating peak regions... Creating peak regions took 29.5868971348 s Estimating background... Estimating background took 31.2687749863 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.35044407845 s Creating peak regions... Creating peak regions took 29.1147270203 s Estimating background... Estimating background took 44.0411369801 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.8171248436 s Creating peak regions... Creating peak regions took 26.0638740063 s Estimating background... Estimating background took 20.4077849388 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.97468185425 s Creating peak regions... Creating peak regions took 20.5192000866 s Estimating background... Estimating background took 28.3550510406 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.12270712852 s Creating peak regions... Creating peak regions took 80.197291851 s Estimating background... Estimating background took 79.5028710365 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.18756604195 s Creating peak regions... Creating peak regions took 23.8055579662 s Estimating background... Estimating background took 27.532902956 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.62508893013 s Creating peak regions... Creating peak regions took 15.1922769547 s Estimating background... Estimating background took 13.1056389809 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.38760995865 s Creating peak regions... Creating peak regions took 17.0550410748 s Estimating background... Estimating background took 26.5110120773 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.05944490433 s Creating peak regions... Creating peak regions took 64.1396961212 s Estimating background... Estimating background took 59.5946969986 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.86394000053 s Creating peak regions... Creating peak regions took 61.0271649361 s Estimating background... Estimating background took 42.3105559349 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.31787800789 s Creating peak regions... Creating peak regions took 58.8943219185 s Estimating background... Estimating background took 50.7045111656 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.95050597191 s Creating peak regions... Creating peak regions took 56.4038248062 s Estimating background... Estimating background took 58.3053569794 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.15999603271 s Creating peak regions... Creating peak regions took 47.9534640312 s Estimating background... Estimating background took 51.1415319443 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.81230187416 s Creating peak regions... Creating peak regions took 44.0518231392 s Estimating background... Estimating background took 34.6907629967 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.15352320671 s Creating peak regions... Creating peak regions took 39.538670063 s Estimating background... Estimating background took 33.9624860287 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.196265935898 s Creating peak regions... Creating peak regions took 0.270174026489 s Estimating background... Estimating background took 0.661773920059 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.16637015343 s Creating peak regions... Creating peak regions took 44.6710329056 s Estimating background... Estimating background took 45.2393651009 s Processing ZNF778-SRR5197238.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.305497169495 s Creating peak regions... Creating peak regions took 14.5791368484 s Estimating background... Estimating background took 0.806666135788 s