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='ZNF605-SRR5197192.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='ZNF605-SRR5197192/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 ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.54513597488 s Creating peak regions... Creating peak regions took 76.7056350708 s Estimating background... Estimating background took 41.4513480663 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.90401291847 s Creating peak regions... Creating peak regions took 41.4346959591 s Estimating background... Estimating background took 17.3467290401 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.90330505371 s Creating peak regions... Creating peak regions took 40.4874768257 s Estimating background... Estimating background took 16.5401389599 s Processing ZNF605-SRR5197192.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='ZNF605-SRR5197192.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='ZNF605-SRR5197192/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 ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.93110918999 s Creating peak regions... Creating peak regions took 76.8653509617 s Estimating background... Estimating background took 41.2773940563 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.92921805382 s Creating peak regions... Creating peak regions took 39.4171361923 s Estimating background... Estimating background took 17.2808589935 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.15576100349 s Creating peak regions... Creating peak regions took 39.8733959198 s Estimating background... Estimating background took 17.7840919495 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.0530090332 s Creating peak regions... Creating peak regions took 39.7284488678 s Estimating background... Estimating background took 18.1721229553 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32745194435 s Creating peak regions... Creating peak regions took 33.6889679432 s Estimating background... Estimating background took 14.7326939106 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.95004606247 s Creating peak regions... Creating peak regions took 31.0517058372 s Estimating background... Estimating background took 11.682502985 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06756901741 s Creating peak regions... Creating peak regions took 29.5452611446 s Estimating background... Estimating background took 13.8001201153 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24739003181 s Creating peak regions... Creating peak regions took 26.7435097694 s Estimating background... Estimating background took 13.9313819408 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.5568010807 s Creating peak regions... Creating peak regions took 25.6515631676 s Estimating background... Estimating background took 17.6447238922 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.64339900017 s Creating peak regions... Creating peak regions took 23.3252460957 s Estimating background... Estimating background took 8.05945420265 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06396698952 s Creating peak regions... Creating peak regions took 19.1652181149 s Estimating background... Estimating background took 13.40279603 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.86633992195 s Creating peak regions... Creating peak regions took 73.2546930313 s Estimating background... Estimating background took 27.9764459133 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.79251003265 s Creating peak regions... Creating peak regions took 20.6302678585 s Estimating background... Estimating background took 10.5720150471 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.985350131989 s Creating peak regions... Creating peak regions took 14.9908549786 s Estimating background... Estimating background took 5.63244700432 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.44702291489 s Creating peak regions... Creating peak regions took 16.3061490059 s Estimating background... Estimating background took 11.8636460304 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.83349013329 s Creating peak regions... Creating peak regions took 58.5813188553 s Estimating background... Estimating background took 21.0688140392 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.06579494476 s Creating peak regions... Creating peak regions took 55.6195960045 s Estimating background... Estimating background took 15.7723038197 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.57381510735 s Creating peak regions... Creating peak regions took 56.6794748306 s Estimating background... Estimating background took 20.3696420193 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.75823307037 s Creating peak regions... Creating peak regions took 51.6302509308 s Estimating background... Estimating background took 22.8829100132 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.63533711433 s Creating peak regions... Creating peak regions took 47.7973008156 s Estimating background... Estimating background took 22.0024209023 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.89638495445 s Creating peak regions... Creating peak regions took 43.0086820126 s Estimating background... Estimating background took 14.6977789402 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.52430009842 s Creating peak regions... Creating peak regions took 40.2244691849 s Estimating background... Estimating background took 16.3386039734 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0921759605408 s Creating peak regions... Creating peak regions took 0.159398078918 s Estimating background... Estimating background took 0.57958984375 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.44760513306 s Creating peak regions... Creating peak regions took 46.5159451962 s Estimating background... Estimating background took 19.5647139549 s Processing ZNF605-SRR5197192.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.138246059418 s Creating peak regions... Creating peak regions took 15.8304998875 s Estimating background... Estimating background took 2.40885305405 s