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='ZNF169-SRR5197065.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='ZNF169-SRR5197065/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 ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.76734995842 s Creating peak regions... Creating peak regions took 65.3775019646 s Estimating background... Estimating background took 54.96986413 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.03777313232 s Creating peak regions... Creating peak regions took 35.5170080662 s Estimating background... Estimating background took 22.4341931343 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.17664813995 s Creating peak regions... Creating peak regions took 35.3521330357 s Estimating background... Estimating background took 22.0659070015 s Processing ZNF169-SRR5197065.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='ZNF169-SRR5197065.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='ZNF169-SRR5197065/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 ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.5119600296 s Creating peak regions... Creating peak regions took 72.5191810131 s Estimating background... Estimating background took 59.3653359413 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.32217717171 s Creating peak regions... Creating peak regions took 38.3760590553 s Estimating background... Estimating background took 23.6347661018 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.64441895485 s Creating peak regions... Creating peak regions took 38.2807030678 s Estimating background... Estimating background took 23.8792200089 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.29897594452 s Creating peak regions... Creating peak regions took 38.0029051304 s Estimating background... Estimating background took 26.4946489334 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.88625407219 s Creating peak regions... Creating peak regions took 32.8807690144 s Estimating background... Estimating background took 28.0280621052 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.35373306274 s Creating peak regions... Creating peak regions took 29.7594540119 s Estimating background... Estimating background took 16.7716038227 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.20234203339 s Creating peak regions... Creating peak regions took 27.8326108456 s Estimating background... Estimating background took 17.7144451141 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.16397404671 s Creating peak regions... Creating peak regions took 25.3795099258 s Estimating background... Estimating background took 16.2209868431 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.42892503738 s Creating peak regions... Creating peak regions took 25.9488329887 s Estimating background... Estimating background took 20.9213619232 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.96983194351 s Creating peak regions... Creating peak regions took 22.7088282108 s Estimating background... Estimating background took 12.7726299763 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.82983708382 s Creating peak regions... Creating peak regions took 17.3897099495 s Estimating background... Estimating background took 13.8133780956 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.70942687988 s Creating peak regions... Creating peak regions took 71.5497751236 s Estimating background... Estimating background took 41.6725921631 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.90073418617 s Creating peak regions... Creating peak regions took 20.6327040195 s Estimating background... Estimating background took 14.5222411156 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.04334282875 s Creating peak regions... Creating peak regions took 13.2192249298 s Estimating background... Estimating background took 8.02008104324 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.42008399963 s Creating peak regions... Creating peak regions took 14.1175661087 s Estimating background... Estimating background took 12.1188280582 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.60680794716 s Creating peak regions... Creating peak regions took 56.0410511494 s Estimating background... Estimating background took 33.1136260033 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.02335500717 s Creating peak regions... Creating peak regions took 52.5367228985 s Estimating background... Estimating background took 26.1524381638 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.43427801132 s Creating peak regions... Creating peak regions took 50.9296650887 s Estimating background... Estimating background took 31.9701399803 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.65957307816 s Creating peak regions... Creating peak regions took 49.8649389744 s Estimating background... Estimating background took 36.6109178066 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.42409181595 s Creating peak regions... Creating peak regions took 46.5170879364 s Estimating background... Estimating background took 31.682336092 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.53760004044 s Creating peak regions... Creating peak regions took 41.1886298656 s Estimating background... Estimating background took 22.4326767921 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.82568407059 s Creating peak regions... Creating peak regions took 38.0537118912 s Estimating background... Estimating background took 21.6506159306 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.134028911591 s Creating peak regions... Creating peak regions took 0.226219177246 s Estimating background... Estimating background took 0.798445940018 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.49977207184 s Creating peak regions... Creating peak regions took 43.8699359894 s Estimating background... Estimating background took 33.9867238998 s Processing ZNF169-SRR5197065.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.180925130844 s Creating peak regions... Creating peak regions took 15.0212080479 s Estimating background... Estimating background took 0.770855903625 s