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='ZNF18-SRR5197073.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='ZNF18-SRR5197073/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 ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.2446000576 s Creating peak regions... Creating peak regions took 68.5873579979 s Estimating background... Estimating background took 44.5786190033 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.28649497032 s Creating peak regions... Creating peak regions took 41.613268137 s Estimating background... Estimating background took 17.4181661606 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.04789495468 s Creating peak regions... Creating peak regions took 40.885381937 s Estimating background... Estimating background took 18.1204838753 s Processing ZNF18-SRR5197073.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='ZNF18-SRR5197073.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='ZNF18-SRR5197073/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 ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.12145805359 s Creating peak regions... Creating peak regions took 77.6051659584 s Estimating background... Estimating background took 44.6655509472 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.95395803452 s Creating peak regions... Creating peak regions took 43.0521168709 s Estimating background... Estimating background took 18.9886550903 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.10867094994 s Creating peak regions... Creating peak regions took 41.8287780285 s Estimating background... Estimating background took 18.3403530121 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.4569439888 s Creating peak regions... Creating peak regions took 40.442127943 s Estimating background... Estimating background took 19.9681949615 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.02623105049 s Creating peak regions... Creating peak regions took 36.4503040314 s Estimating background... Estimating background took 22.9693310261 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.17497706413 s Creating peak regions... Creating peak regions took 32.3325769901 s Estimating background... Estimating background took 12.8878288269 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.02757000923 s Creating peak regions... Creating peak regions took 30.5295679569 s Estimating background... Estimating background took 13.4765250683 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.84889984131 s Creating peak regions... Creating peak regions took 26.5232930183 s Estimating background... Estimating background took 11.2241930962 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.04957890511 s Creating peak regions... Creating peak regions took 26.7256801128 s Estimating background... Estimating background took 14.6550769806 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.83269882202 s Creating peak regions... Creating peak regions took 24.997469902 s Estimating background... Estimating background took 10.9136891365 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.54454517365 s Creating peak regions... Creating peak regions took 19.517950058 s Estimating background... Estimating background took 9.21882200241 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.34261107445 s Creating peak regions... Creating peak regions took 78.9252021313 s Estimating background... Estimating background took 32.7600190639 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.64011096954 s Creating peak regions... Creating peak regions took 21.3747241497 s Estimating background... Estimating background took 9.90779304504 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.06524586678 s Creating peak regions... Creating peak regions took 14.4846699238 s Estimating background... Estimating background took 6.05596709251 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.11378622055 s Creating peak regions... Creating peak regions took 16.2277469635 s Estimating background... Estimating background took 8.44387984276 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.22171497345 s Creating peak regions... Creating peak regions took 63.8872659206 s Estimating background... Estimating background took 25.0082960129 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.50708293915 s Creating peak regions... Creating peak regions took 56.2259480953 s Estimating background... Estimating background took 20.3443820477 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.17112398148 s Creating peak regions... Creating peak regions took 57.1311600208 s Estimating background... Estimating background took 24.5459170341 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.11410593987 s Creating peak regions... Creating peak regions took 51.5801920891 s Estimating background... Estimating background took 29.0201640129 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.08135795593 s Creating peak regions... Creating peak regions took 50.0482521057 s Estimating background... Estimating background took 24.6496210098 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.24027991295 s Creating peak regions... Creating peak regions took 45.2580399513 s Estimating background... Estimating background took 17.2736730576 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.64634418488 s Creating peak regions... Creating peak regions took 39.8291220665 s Estimating background... Estimating background took 13.9470739365 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.088700056076 s Creating peak regions... Creating peak regions took 0.183198213577 s Estimating background... Estimating background took 0.644260883331 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.28235793114 s Creating peak regions... Creating peak regions took 47.4888181686 s Estimating background... Estimating background took 28.0634121895 s Processing ZNF18-SRR5197073.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.206197977066 s Creating peak regions... Creating peak regions took 16.3980100155 s Estimating background... Estimating background took 0.647141933441 s