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='ZNF530-SRR5197166.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='ZNF530-SRR5197166/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 ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.3506770134 s Creating peak regions... Creating peak regions took 80.4329547882 s Estimating background... Estimating background took 71.3850851059 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.00842499733 s Creating peak regions... Creating peak regions took 42.5395610332 s Estimating background... Estimating background took 29.408356905 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.25836491585 s Creating peak regions... Creating peak regions took 41.1758730412 s Estimating background... Estimating background took 26.855656147 s Processing ZNF530-SRR5197166.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='ZNF530-SRR5197166.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='ZNF530-SRR5197166/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 ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.44858694077 s Creating peak regions... Creating peak regions took 84.4833369255 s Estimating background... Estimating background took 73.7856490612 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.04493689537 s Creating peak regions... Creating peak regions took 45.599768877 s Estimating background... Estimating background took 32.7957649231 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.04636693001 s Creating peak regions... Creating peak regions took 44.0224471092 s Estimating background... Estimating background took 29.8495550156 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.18364500999 s Creating peak regions... Creating peak regions took 43.8751409054 s Estimating background... Estimating background took 31.0565488338 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.28642511368 s Creating peak regions... Creating peak regions took 36.5554170609 s Estimating background... Estimating background took 32.2212278843 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.82732892036 s Creating peak regions... Creating peak regions took 35.2092170715 s Estimating background... Estimating background took 20.645761013 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.65155005455 s Creating peak regions... Creating peak regions took 31.6649339199 s Estimating background... Estimating background took 21.4259979725 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.71860599518 s Creating peak regions... Creating peak regions took 31.9194948673 s Estimating background... Estimating background took 22.6390349865 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.20048809052 s Creating peak regions... Creating peak regions took 27.9102540016 s Estimating background... Estimating background took 27.3669991493 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.20224404335 s Creating peak regions... Creating peak regions took 26.1681230068 s Estimating background... Estimating background took 14.7679860592 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.17700600624 s Creating peak regions... Creating peak regions took 20.0417749882 s Estimating background... Estimating background took 19.2076380253 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.72972488403 s Creating peak regions... Creating peak regions took 75.6369380951 s Estimating background... Estimating background took 51.2486140728 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.49597597122 s Creating peak regions... Creating peak regions took 23.6809868813 s Estimating background... Estimating background took 19.4324531555 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.28593492508 s Creating peak regions... Creating peak regions took 14.1015429497 s Estimating background... Estimating background took 10.2825279236 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.5732960701 s Creating peak regions... Creating peak regions took 17.5547637939 s Estimating background... Estimating background took 18.472730875 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.37542104721 s Creating peak regions... Creating peak regions took 67.7888782024 s Estimating background... Estimating background took 38.0709021091 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.90801000595 s Creating peak regions... Creating peak regions took 60.9659469128 s Estimating background... Estimating background took 29.6169140339 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.01494908333 s Creating peak regions... Creating peak regions took 50.9269580841 s Estimating background... Estimating background took 30.1016230583 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.08920001984 s Creating peak regions... Creating peak regions took 47.2345850468 s Estimating background... Estimating background took 35.0273900032 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.65335822105 s Creating peak regions... Creating peak regions took 43.5689761639 s Estimating background... Estimating background took 31.3598051071 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.03375291824 s Creating peak regions... Creating peak regions took 37.3204958439 s Estimating background... Estimating background took 21.8735051155 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.49249601364 s Creating peak regions... Creating peak regions took 37.1898698807 s Estimating background... Estimating background took 21.1707150936 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.135882854462 s Creating peak regions... Creating peak regions took 0.212872982025 s Estimating background... Estimating background took 0.681113004684 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.88779211044 s Creating peak regions... Creating peak regions took 42.9147880077 s Estimating background... Estimating background took 33.8031489849 s Processing ZNF530-SRR5197166.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.256417036057 s Creating peak regions... Creating peak regions took 14.344727993 s Estimating background... Estimating background took 1.26917386055 s