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='ZNF454-SRR5197147.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='ZNF454-SRR5197147/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 ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.0151181221 s Creating peak regions... Creating peak regions took 81.124119997 s Estimating background... Estimating background took 77.5267608166 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.25667285919 s Creating peak regions... Creating peak regions took 44.7470450401 s Estimating background... Estimating background took 27.4499521255 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.68175077438 s Creating peak regions... Creating peak regions took 36.4978268147 s Estimating background... Estimating background took 26.0396361351 s Processing ZNF454-SRR5197147.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='ZNF454-SRR5197147.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='ZNF454-SRR5197147/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 ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.73808002472 s Creating peak regions... Creating peak regions took 80.6853148937 s Estimating background... Estimating background took 77.8333239555 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.93126296997 s Creating peak regions... Creating peak regions took 43.5753669739 s Estimating background... Estimating background took 32.2125229836 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.07010197639 s Creating peak regions... Creating peak regions took 42.3632712364 s Estimating background... Estimating background took 30.6844918728 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.15764689445 s Creating peak regions... Creating peak regions took 43.3588180542 s Estimating background... Estimating background took 32.803951025 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.3708820343 s Creating peak regions... Creating peak regions took 35.437666893 s Estimating background... Estimating background took 31.4256498814 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.90949678421 s Creating peak regions... Creating peak regions took 32.7601139545 s Estimating background... Estimating background took 21.637111187 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.5732588768 s Creating peak regions... Creating peak regions took 32.1213331223 s Estimating background... Estimating background took 22.8334188461 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.59634995461 s Creating peak regions... Creating peak regions took 28.7784340382 s Estimating background... Estimating background took 23.3965489864 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.14388799667 s Creating peak regions... Creating peak regions took 28.4928469658 s Estimating background... Estimating background took 28.7819178104 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.27444696426 s Creating peak regions... Creating peak regions took 24.9519608021 s Estimating background... Estimating background took 15.5192558765 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.21616816521 s Creating peak regions... Creating peak regions took 20.6400771141 s Estimating background... Estimating background took 19.2355160713 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.52821993828 s Creating peak regions... Creating peak regions took 76.7233181 s Estimating background... Estimating background took 53.208493948 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.26172399521 s Creating peak regions... Creating peak regions took 23.2251160145 s Estimating background... Estimating background took 19.3440930843 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.25924396515 s Creating peak regions... Creating peak regions took 13.817522049 s Estimating background... Estimating background took 9.35927391052 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.76752901077 s Creating peak regions... Creating peak regions took 15.9723141193 s Estimating background... Estimating background took 18.6055290699 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.24299192429 s Creating peak regions... Creating peak regions took 65.1343240738 s Estimating background... Estimating background took 40.7043309212 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.42705488205 s Creating peak regions... Creating peak regions took 59.1848609447 s Estimating background... Estimating background took 29.3228628635 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.9761660099 s Creating peak regions... Creating peak regions took 50.0547790527 s Estimating background... Estimating background took 31.8737869263 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.08462023735 s Creating peak regions... Creating peak regions took 45.5634880066 s Estimating background... Estimating background took 34.4181051254 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.74122190475 s Creating peak regions... Creating peak regions took 42.1929671764 s Estimating background... Estimating background took 32.0308659077 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.97023391724 s Creating peak regions... Creating peak regions took 37.840004921 s Estimating background... Estimating background took 22.4367778301 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.57532191277 s Creating peak regions... Creating peak regions took 35.2038021088 s Estimating background... Estimating background took 22.1604890823 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.12492108345 s Creating peak regions... Creating peak regions took 0.210162878036 s Estimating background... Estimating background took 0.677467107773 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.8643848896 s Creating peak regions... Creating peak regions took 41.1044960022 s Estimating background... Estimating background took 33.7522010803 s Processing ZNF454-SRR5197147.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.192435026169 s Creating peak regions... Creating peak regions took 12.8781850338 s Estimating background... Estimating background took 0.643476009369 s