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='ZNF695-SRR5197218.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='ZNF695-SRR5197218/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 ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.87092781067 s Creating peak regions... Creating peak regions took 83.6304190159 s Estimating background... Estimating background took 105.577526093 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.80258393288 s Creating peak regions... Creating peak regions took 42.6948950291 s Estimating background... Estimating background took 35.340831995 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.89672589302 s Creating peak regions... Creating peak regions took 38.4598209858 s Estimating background... Estimating background took 33.9786539078 s Processing ZNF695-SRR5197218.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='ZNF695-SRR5197218.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='ZNF695-SRR5197218/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 ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.02261209488 s Creating peak regions... Creating peak regions took 80.1596541405 s Estimating background... Estimating background took 95.3839809895 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.43183588982 s Creating peak regions... Creating peak regions took 41.5342051983 s Estimating background... Estimating background took 37.2448179722 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.40496611595 s Creating peak regions... Creating peak regions took 44.1872050762 s Estimating background... Estimating background took 35.616204977 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.96789288521 s Creating peak regions... Creating peak regions took 47.516379118 s Estimating background... Estimating background took 44.3807389736 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.3888938427 s Creating peak regions... Creating peak regions took 41.1276941299 s Estimating background... Estimating background took 40.9094090462 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.51264095306 s Creating peak regions... Creating peak regions took 35.1870369911 s Estimating background... Estimating background took 25.7555611134 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.26987195015 s Creating peak regions... Creating peak regions took 35.851391077 s Estimating background... Estimating background took 26.8816308975 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.04121899605 s Creating peak regions... Creating peak regions took 30.4684038162 s Estimating background... Estimating background took 25.5077600479 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.93661808968 s Creating peak regions... Creating peak regions took 29.0036239624 s Estimating background... Estimating background took 34.9823701382 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.65824699402 s Creating peak regions... Creating peak regions took 27.8480529785 s Estimating background... Estimating background took 19.0809597969 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.58873295784 s Creating peak regions... Creating peak regions took 21.9774870872 s Estimating background... Estimating background took 22.4567451477 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.02965211868 s Creating peak regions... Creating peak regions took 78.5743229389 s Estimating background... Estimating background took 63.3713309765 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.83109116554 s Creating peak regions... Creating peak regions took 23.8797249794 s Estimating background... Estimating background took 22.2416319847 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.42934608459 s Creating peak regions... Creating peak regions took 15.1033890247 s Estimating background... Estimating background took 10.7936120033 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.90764784813 s Creating peak regions... Creating peak regions took 16.7341279984 s Estimating background... Estimating background took 20.959706068 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.61811113358 s Creating peak regions... Creating peak regions took 65.5123651028 s Estimating background... Estimating background took 50.825124979 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.77464103699 s Creating peak regions... Creating peak regions took 63.7704429626 s Estimating background... Estimating background took 37.5574140549 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.29268598557 s Creating peak regions... Creating peak regions took 64.0668959618 s Estimating background... Estimating background took 48.0036349297 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.92281985283 s Creating peak regions... Creating peak regions took 67.027641058 s Estimating background... Estimating background took 61.010103941 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.75272703171 s Creating peak regions... Creating peak regions took 58.2511389256 s Estimating background... Estimating background took 44.8807220459 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.76147603989 s Creating peak regions... Creating peak regions took 47.6295750141 s Estimating background... Estimating background took 34.1109900475 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.97065711021 s Creating peak regions... Creating peak regions took 47.6368460655 s Estimating background... Estimating background took 34.3023810387 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.293005943298 s Creating peak regions... Creating peak regions took 0.373709917068 s Estimating background... Estimating background took 0.700742959976 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.32657003403 s Creating peak regions... Creating peak regions took 51.3036959171 s Estimating background... Estimating background took 45.6959719658 s Processing ZNF695-SRR5197218.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.315507888794 s Creating peak regions... Creating peak regions took 16.7919681072 s Estimating background... Estimating background took 0.948718070984 s