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='ZNF248-SRR5197087.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='ZNF248-SRR5197087/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 ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.50939512253 s Creating peak regions... Creating peak regions took 77.3592679501 s Estimating background... Estimating background took 33.7182919979 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.78342604637 s Creating peak regions... Creating peak regions took 40.9079868793 s Estimating background... Estimating background took 13.3559789658 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.67269015312 s Creating peak regions... Creating peak regions took 41.9812121391 s Estimating background... Estimating background took 12.0952739716 s Processing ZNF248-SRR5197087.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='ZNF248-SRR5197087.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='ZNF248-SRR5197087/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 ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.71317505836 s Creating peak regions... Creating peak regions took 92.884968996 s Estimating background... Estimating background took 36.8262200356 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.80195212364 s Creating peak regions... Creating peak regions took 48.1924331188 s Estimating background... Estimating background took 13.8926169872 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.76142096519 s Creating peak regions... Creating peak regions took 51.0958089828 s Estimating background... Estimating background took 14.4770050049 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.1186068058 s Creating peak regions... Creating peak regions took 46.9621391296 s Estimating background... Estimating background took 15.5955808163 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.83871603012 s Creating peak regions... Creating peak regions took 41.6855490208 s Estimating background... Estimating background took 20.2633039951 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.10167193413 s Creating peak regions... Creating peak regions took 39.6629099846 s Estimating background... Estimating background took 10.3550970554 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.7917330265 s Creating peak regions... Creating peak regions took 38.9443950653 s Estimating background... Estimating background took 12.4673399925 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.67642211914 s Creating peak regions... Creating peak regions took 33.8631598949 s Estimating background... Estimating background took 8.81237196922 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.09501004219 s Creating peak regions... Creating peak regions took 30.3626248837 s Estimating background... Estimating background took 10.237475872 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.52012991905 s Creating peak regions... Creating peak regions took 29.6268949509 s Estimating background... Estimating background took 8.68572282791 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.27082204819 s Creating peak regions... Creating peak regions took 21.5293149948 s Estimating background... Estimating background took 6.46121883392 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.93378996849 s Creating peak regions... Creating peak regions took 90.3352458477 s Estimating background... Estimating background took 25.1900279522 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.3471698761 s Creating peak regions... Creating peak regions took 23.9634509087 s Estimating background... Estimating background took 7.81647205353 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.984966993332 s Creating peak regions... Creating peak regions took 17.4516232014 s Estimating background... Estimating background took 4.59510397911 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.919919013977 s Creating peak regions... Creating peak regions took 18.3653490543 s Estimating background... Estimating background took 5.33061695099 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.9444899559 s Creating peak regions... Creating peak regions took 76.2190039158 s Estimating background... Estimating background took 20.920801878 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.81720399857 s Creating peak regions... Creating peak regions took 68.5511550903 s Estimating background... Estimating background took 18.0976121426 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.91269898415 s Creating peak regions... Creating peak regions took 69.9743368626 s Estimating background... Estimating background took 18.7122409344 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.10373020172 s Creating peak regions... Creating peak regions took 66.7341070175 s Estimating background... Estimating background took 22.8508379459 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.56551504135 s Creating peak regions... Creating peak regions took 56.9846701622 s Estimating background... Estimating background took 15.4702341557 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.48732686043 s Creating peak regions... Creating peak regions took 45.745246172 s Estimating background... Estimating background took 12.2776889801 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.87985491753 s Creating peak regions... Creating peak regions took 40.3568389416 s Estimating background... Estimating background took 11.174847126 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0885369777679 s Creating peak regions... Creating peak regions took 0.159981012344 s Estimating background... Estimating background took 0.522613048553 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.8997399807 s Creating peak regions... Creating peak regions took 48.3833210468 s Estimating background... Estimating background took 19.167183876 s Processing ZNF248-SRR5197087.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.128273010254 s Creating peak regions... Creating peak regions took 16.2053320408 s Estimating background... Estimating background took 0.58892583847 s