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='PRDM9-SRR5197035.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='PRDM9-SRR5197035/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 PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.80659294128 s Creating peak regions... Creating peak regions took 62.1197001934 s Estimating background... Estimating background took 17.7653388977 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.6943230629 s Creating peak regions... Creating peak regions took 32.7802288532 s Estimating background... Estimating background took 8.0481159687 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.44016909599 s Creating peak regions... Creating peak regions took 35.3078870773 s Estimating background... Estimating background took 8.31684994698 s Processing PRDM9-SRR5197035.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='PRDM9-SRR5197035.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='PRDM9-SRR5197035/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 PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.87907791138 s Creating peak regions... Creating peak regions took 58.1710410118 s Estimating background... Estimating background took 16.8642859459 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.30423903465 s Creating peak regions... Creating peak regions took 30.8277540207 s Estimating background... Estimating background took 7.65607500076 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.46626520157 s Creating peak regions... Creating peak regions took 33.096818924 s Estimating background... Estimating background took 7.78955602646 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.31913089752 s Creating peak regions... Creating peak regions took 29.0469150543 s Estimating background... Estimating background took 8.27003288269 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.64025807381 s Creating peak regions... Creating peak regions took 26.2630050182 s Estimating background... Estimating background took 7.32934093475 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.9039618969 s Creating peak regions... Creating peak regions took 25.9685740471 s Estimating background... Estimating background took 5.3971760273 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.09539794922 s Creating peak regions... Creating peak regions took 24.5083930492 s Estimating background... Estimating background took 5.66623592377 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.13323497772 s Creating peak regions... Creating peak regions took 21.9081289768 s Estimating background... Estimating background took 5.61370205879 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.56585597992 s Creating peak regions... Creating peak regions took 20.8870961666 s Estimating background... Estimating background took 7.05316591263 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.22595715523 s Creating peak regions... Creating peak regions took 18.2378780842 s Estimating background... Estimating background took 4.19744586945 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23631381989 s Creating peak regions... Creating peak regions took 14.6732571125 s Estimating background... Estimating background took 4.73804187775 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.26838493347 s Creating peak regions... Creating peak regions took 59.2851338387 s Estimating background... Estimating background took 12.1807148457 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.8099899292 s Creating peak regions... Creating peak regions took 16.567688942 s Estimating background... Estimating background took 4.8806951046 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.24622106552 s Creating peak regions... Creating peak regions took 11.4889400005 s Estimating background... Estimating background took 2.64760899544 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.2049100399 s Creating peak regions... Creating peak regions took 11.7247970104 s Estimating background... Estimating background took 4.46390604973 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.30022597313 s Creating peak regions... Creating peak regions took 48.3699851036 s Estimating background... Estimating background took 10.7196660042 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.75801587105 s Creating peak regions... Creating peak regions took 45.847992897 s Estimating background... Estimating background took 8.30748105049 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.33269309998 s Creating peak regions... Creating peak regions took 41.0095279217 s Estimating background... Estimating background took 9.57530903816 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.88372802734 s Creating peak regions... Creating peak regions took 39.4958229065 s Estimating background... Estimating background took 10.5814540386 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.4877550602 s Creating peak regions... Creating peak regions took 39.951720953 s Estimating background... Estimating background took 9.84343910217 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.29221200943 s Creating peak regions... Creating peak regions took 33.9063870907 s Estimating background... Estimating background took 7.26876521111 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.02059912682 s Creating peak regions... Creating peak regions took 33.5258131027 s Estimating background... Estimating background took 7.38852906227 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.103020906448 s Creating peak regions... Creating peak regions took 0.127106189728 s Estimating background... Estimating background took 0.539865970612 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.36632299423 s Creating peak regions... Creating peak regions took 36.0767190456 s Estimating background... Estimating background took 9.07942605019 s Processing PRDM9-SRR5197035.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.117470026016 s Creating peak regions... Creating peak regions took 11.8343508244 s Estimating background... Estimating background took 0.479057073593 s