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='ZNF621-SRR5197201.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='ZNF621-SRR5197201/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 ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.72984099388 s Creating peak regions... Creating peak regions took 73.8530979156 s Estimating background... Estimating background took 21.8356890678 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.76439094543 s Creating peak regions... Creating peak regions took 38.2883749008 s Estimating background... Estimating background took 9.5710568428 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.9490840435 s Creating peak regions... Creating peak regions took 38.7759790421 s Estimating background... Estimating background took 9.47275590897 s Processing ZNF621-SRR5197201.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='ZNF621-SRR5197201.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='ZNF621-SRR5197201/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 ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.06590390205 s Creating peak regions... Creating peak regions took 72.268157959 s Estimating background... Estimating background took 21.0534009933 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.66762900352 s Creating peak regions... Creating peak regions took 37.1677589417 s Estimating background... Estimating background took 8.93605589867 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95582103729 s Creating peak regions... Creating peak regions took 37.7897109985 s Estimating background... Estimating background took 8.87940692902 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.838586092 s Creating peak regions... Creating peak regions took 37.3612279892 s Estimating background... Estimating background took 9.52969002724 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.72435498238 s Creating peak regions... Creating peak regions took 32.153731823 s Estimating background... Estimating background took 10.695939064 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40551781654 s Creating peak regions... Creating peak regions took 29.395305872 s Estimating background... Estimating background took 6.39188909531 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.38024806976 s Creating peak regions... Creating peak regions took 29.6980061531 s Estimating background... Estimating background took 8.37013196945 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.29833912849 s Creating peak regions... Creating peak regions took 24.9081678391 s Estimating background... Estimating background took 6.39734601974 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.47179889679 s Creating peak regions... Creating peak regions took 24.7381970882 s Estimating background... Estimating background took 8.14302396774 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.976116895676 s Creating peak regions... Creating peak regions took 22.4365921021 s Estimating background... Estimating background took 5.29351997375 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.05367708206 s Creating peak regions... Creating peak regions took 17.6198179722 s Estimating background... Estimating background took 5.28269386292 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.2481470108 s Creating peak regions... Creating peak regions took 72.4801750183 s Estimating background... Estimating background took 15.43917799 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.965237140656 s Creating peak regions... Creating peak regions took 18.3590390682 s Estimating background... Estimating background took 5.47704291344 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.521514892578 s Creating peak regions... Creating peak regions took 12.2615628242 s Estimating background... Estimating background took 2.94628787041 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.850648880005 s Creating peak regions... Creating peak regions took 15.2758460045 s Estimating background... Estimating background took 5.12499403954 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.67050409317 s Creating peak regions... Creating peak regions took 59.3977620602 s Estimating background... Estimating background took 11.9147179127 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.21838998795 s Creating peak regions... Creating peak regions took 55.9593858719 s Estimating background... Estimating background took 10.3658189774 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.69843506813 s Creating peak regions... Creating peak regions took 50.4249739647 s Estimating background... Estimating background took 11.6933009624 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.54944086075 s Creating peak regions... Creating peak regions took 51.4083571434 s Estimating background... Estimating background took 12.0130908489 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.25276517868 s Creating peak regions... Creating peak regions took 47.7616991997 s Estimating background... Estimating background took 11.3861482143 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.78161287308 s Creating peak regions... Creating peak regions took 42.9325969219 s Estimating background... Estimating background took 9.30429887772 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.75763487816 s Creating peak regions... Creating peak regions took 38.4557981491 s Estimating background... Estimating background took 8.59132099152 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.106379985809 s Creating peak regions... Creating peak regions took 0.133022069931 s Estimating background... Estimating background took 0.668659925461 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.7164080143 s Creating peak regions... Creating peak regions took 47.3749802113 s Estimating background... Estimating background took 12.6126499176 s Processing ZNF621-SRR5197201.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.103596925735 s Creating peak regions... Creating peak regions took 16.7944350243 s Estimating background... Estimating background took 0.51686000824 s