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='ZNF736-SRR5197227.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='ZNF736-SRR5197227/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 ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 15.8357400894 s Creating peak regions... Creating peak regions took 77.3028850555 s Estimating background... Estimating background took 188.163511992 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.62729096413 s Creating peak regions... Creating peak regions took 41.6902639866 s Estimating background... Estimating background took 77.8911511898 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.57895088196 s Creating peak regions... Creating peak regions took 41.4900231361 s Estimating background... Estimating background took 81.0175118446 s Processing ZNF736-SRR5197227.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='ZNF736-SRR5197227.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='ZNF736-SRR5197227/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 ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 17.2604029179 s Creating peak regions... Creating peak regions took 97.9000279903 s Estimating background... Estimating background took 218.877823114 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.86981201172 s Creating peak regions... Creating peak regions took 52.9100420475 s Estimating background... Estimating background took 91.2823650837 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.11147403717 s Creating peak regions... Creating peak regions took 53.0596301556 s Estimating background... Estimating background took 94.6341128349 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.19744801521 s Creating peak regions... Creating peak regions took 52.7838828564 s Estimating background... Estimating background took 98.1268088818 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.72265315056 s Creating peak regions... Creating peak regions took 44.8020751476 s Estimating background... Estimating background took 81.024050951 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.27368402481 s Creating peak regions... Creating peak regions took 39.8845098019 s Estimating background... Estimating background took 59.83040905 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.18935704231 s Creating peak regions... Creating peak regions took 38.3478860855 s Estimating background... Estimating background took 68.2016370296 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.22510409355 s Creating peak regions... Creating peak regions took 35.312912941 s Estimating background... Estimating background took 70.3178038597 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.19084095955 s Creating peak regions... Creating peak regions took 34.6695480347 s Estimating background... Estimating background took 86.9052579403 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.44540309906 s Creating peak regions... Creating peak regions took 30.0996949673 s Estimating background... Estimating background took 41.3810122013 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.13064599037 s Creating peak regions... Creating peak regions took 24.4026050568 s Estimating background... Estimating background took 63.2763009071 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 12.6132600307 s Creating peak regions... Creating peak regions took 83.2024149895 s Estimating background... Estimating background took 128.639304876 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.24621200562 s Creating peak regions... Creating peak regions took 24.049654007 s Estimating background... Estimating background took 44.1263661385 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.09638118744 s Creating peak regions... Creating peak regions took 14.9460391998 s Estimating background... Estimating background took 22.0695741177 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.18279194832 s Creating peak regions... Creating peak regions took 17.1625039577 s Estimating background... Estimating background took 44.0810551643 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.93686795235 s Creating peak regions... Creating peak regions took 61.671257019 s Estimating background... Estimating background took 95.272110939 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.60789585114 s Creating peak regions... Creating peak regions took 58.9588391781 s Estimating background... Estimating background took 70.601526022 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.53453397751 s Creating peak regions... Creating peak regions took 57.9152901173 s Estimating background... Estimating background took 89.7841320038 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.05534315109 s Creating peak regions... Creating peak regions took 56.1344389915 s Estimating background... Estimating background took 99.3508799076 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.62003612518 s Creating peak regions... Creating peak regions took 50.8602919579 s Estimating background... Estimating background took 92.8452689648 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.3134329319 s Creating peak regions... Creating peak regions took 44.7791180611 s Estimating background... Estimating background took 67.0035030842 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.21799612045 s Creating peak regions... Creating peak regions took 43.9745438099 s Estimating background... Estimating background took 65.2477309704 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.288253068924 s Creating peak regions... Creating peak regions took 0.364549875259 s Estimating background... Estimating background took 0.85555100441 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.4952249527 s Creating peak regions... Creating peak regions took 50.173402071 s Estimating background... Estimating background took 89.8731868267 s Processing ZNF736-SRR5197227.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.522519111633 s Creating peak regions... Creating peak regions took 14.8147909641 s Estimating background... Estimating background took 1.03390216827 s