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='ZNF440-SRR5197141.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='ZNF440-SRR5197141/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 ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.85299897194 s Creating peak regions... Creating peak regions took 75.4945878983 s Estimating background... Estimating background took 26.8999559879 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.04514098167 s Creating peak regions... Creating peak regions took 39.0226240158 s Estimating background... Estimating background took 11.0584290028 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.93701601028 s Creating peak regions... Creating peak regions took 39.3955049515 s Estimating background... Estimating background took 10.501500845 s Processing ZNF440-SRR5197141.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='ZNF440-SRR5197141.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='ZNF440-SRR5197141/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 ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.49521684647 s Creating peak regions... Creating peak regions took 73.7834818363 s Estimating background... Estimating background took 28.4234449863 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.92459511757 s Creating peak regions... Creating peak regions took 40.2961349487 s Estimating background... Estimating background took 10.4892449379 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.73370599747 s Creating peak regions... Creating peak regions took 39.5400831699 s Estimating background... Estimating background took 11.3560769558 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.38046717644 s Creating peak regions... Creating peak regions took 42.4008560181 s Estimating background... Estimating background took 12.323225975 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.15127587318 s Creating peak regions... Creating peak regions took 35.9821629524 s Estimating background... Estimating background took 16.4979920387 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.15094304085 s Creating peak regions... Creating peak regions took 32.8931829929 s Estimating background... Estimating background took 7.95674705505 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.04438185692 s Creating peak regions... Creating peak regions took 29.4550361633 s Estimating background... Estimating background took 8.41198897362 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.79867911339 s Creating peak regions... Creating peak regions took 26.9757921696 s Estimating background... Estimating background took 6.00688815117 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.09572196007 s Creating peak regions... Creating peak regions took 25.4510748386 s Estimating background... Estimating background took 8.95325112343 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.62839818001 s Creating peak regions... Creating peak regions took 23.9346139431 s Estimating background... Estimating background took 7.12724113464 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.38931393623 s Creating peak regions... Creating peak regions took 18.5091228485 s Estimating background... Estimating background took 5.21175479889 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.39004087448 s Creating peak regions... Creating peak regions took 72.8301029205 s Estimating background... Estimating background took 21.36413908 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.56994700432 s Creating peak regions... Creating peak regions took 20.0458738804 s Estimating background... Estimating background took 6.1191868782 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.871647834778 s Creating peak regions... Creating peak regions took 13.8470339775 s Estimating background... Estimating background took 3.90102601051 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.03715801239 s Creating peak regions... Creating peak regions took 15.8572590351 s Estimating background... Estimating background took 4.54196095467 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.2004430294 s Creating peak regions... Creating peak regions took 61.6285288334 s Estimating background... Estimating background took 17.1795430183 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.76968789101 s Creating peak regions... Creating peak regions took 58.1130280495 s Estimating background... Estimating background took 12.8171658516 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.98005700111 s Creating peak regions... Creating peak regions took 51.8071410656 s Estimating background... Estimating background took 14.8428530693 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.76488304138 s Creating peak regions... Creating peak regions took 52.6273579597 s Estimating background... Estimating background took 18.0194540024 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.83382892609 s Creating peak regions... Creating peak regions took 47.4249870777 s Estimating background... Estimating background took 15.5644040108 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.36161589622 s Creating peak regions... Creating peak regions took 43.7559459209 s Estimating background... Estimating background took 11.39920187 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.24121618271 s Creating peak regions... Creating peak regions took 42.6960449219 s Estimating background... Estimating background took 10.2967708111 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.10004901886 s Creating peak regions... Creating peak regions took 0.166042089462 s Estimating background... Estimating background took 0.644736051559 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.18144106865 s Creating peak regions... Creating peak regions took 49.2129530907 s Estimating background... Estimating background took 15.2639050484 s Processing ZNF440-SRR5197141.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.1152780056 s Creating peak regions... Creating peak regions took 14.9056751728 s Estimating background... Estimating background took 0.442768096924 s