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='ZNF417-SRR5197130.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='ZNF417-SRR5197130/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 ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.25018382072 s Creating peak regions... Creating peak regions took 85.4942409992 s Estimating background... Estimating background took 113.880580902 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.98327302933 s Creating peak regions... Creating peak regions took 46.2381789684 s Estimating background... Estimating background took 39.4147620201 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.4464931488 s Creating peak regions... Creating peak regions took 40.1834049225 s Estimating background... Estimating background took 36.9456689358 s Processing ZNF417-SRR5197130.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='ZNF417-SRR5197130.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='ZNF417-SRR5197130/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 ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.85594391823 s Creating peak regions... Creating peak regions took 83.4547359943 s Estimating background... Estimating background took 111.292896986 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.04568505287 s Creating peak regions... Creating peak regions took 46.5666518211 s Estimating background... Estimating background took 41.5367758274 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.81736803055 s Creating peak regions... Creating peak regions took 45.0717270374 s Estimating background... Estimating background took 44.6020190716 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.11044096947 s Creating peak regions... Creating peak regions took 43.9136691093 s Estimating background... Estimating background took 45.4312810898 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.31001210213 s Creating peak regions... Creating peak regions took 39.4170720577 s Estimating background... Estimating background took 43.4540169239 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.48142385483 s Creating peak regions... Creating peak regions took 33.6351370811 s Estimating background... Estimating background took 30.1494407654 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.36065888405 s Creating peak regions... Creating peak regions took 33.8115429878 s Estimating background... Estimating background took 32.6943900585 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.24607896805 s Creating peak regions... Creating peak regions took 29.3011109829 s Estimating background... Estimating background took 32.3796589375 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.99351215363 s Creating peak regions... Creating peak regions took 28.5896580219 s Estimating background... Estimating background took 37.9259221554 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45685887337 s Creating peak regions... Creating peak regions took 24.8784167767 s Estimating background... Estimating background took 18.7751400471 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.68295097351 s Creating peak regions... Creating peak regions took 21.1104309559 s Estimating background... Estimating background took 30.8425750732 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.38257694244 s Creating peak regions... Creating peak regions took 78.7613618374 s Estimating background... Estimating background took 75.9765341282 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.06753993034 s Creating peak regions... Creating peak regions took 23.7935619354 s Estimating background... Estimating background took 27.2644271851 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40494918823 s Creating peak regions... Creating peak regions took 14.6079099178 s Estimating background... Estimating background took 12.1520149708 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.26923298836 s Creating peak regions... Creating peak regions took 17.1476662159 s Estimating background... Estimating background took 25.5745120049 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.40762495995 s Creating peak regions... Creating peak regions took 58.2993011475 s Estimating background... Estimating background took 42.4838140011 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.35792207718 s Creating peak regions... Creating peak regions took 51.0343880653 s Estimating background... Estimating background took 35.1602201462 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.97182679176 s Creating peak regions... Creating peak regions took 49.745059967 s Estimating background... Estimating background took 44.2838070393 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.20948600769 s Creating peak regions... Creating peak regions took 48.2769470215 s Estimating background... Estimating background took 48.8234689236 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.77638697624 s Creating peak regions... Creating peak regions took 45.1380250454 s Estimating background... Estimating background took 44.4082500935 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.99331903458 s Creating peak regions... Creating peak regions took 40.0232310295 s Estimating background... Estimating background took 32.7210590839 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.36860799789 s Creating peak regions... Creating peak regions took 37.2950379848 s Estimating background... Estimating background took 31.6160361767 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.171984910965 s Creating peak regions... Creating peak regions took 0.21600818634 s Estimating background... Estimating background took 0.805531978607 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.68774104118 s Creating peak regions... Creating peak regions took 41.3635208607 s Estimating background... Estimating background took 45.6353449821 s Processing ZNF417-SRR5197130.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.300266027451 s Creating peak regions... Creating peak regions took 13.5814759731 s Estimating background... Estimating background took 0.881888151169 s