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='ZNF283-SRR5197100.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='ZNF283-SRR5197100/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 ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.99214696884 s Creating peak regions... Creating peak regions took 70.5856618881 s Estimating background... Estimating background took 54.6725440025 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.44676804543 s Creating peak regions... Creating peak regions took 43.0187969208 s Estimating background... Estimating background took 21.2897260189 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.33236098289 s Creating peak regions... Creating peak regions took 41.9061141014 s Estimating background... Estimating background took 22.6639409065 s Processing ZNF283-SRR5197100.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='ZNF283-SRR5197100.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='ZNF283-SRR5197100/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 ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.2726688385 s Creating peak regions... Creating peak regions took 75.492221117 s Estimating background... Estimating background took 58.9055659771 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.25946688652 s Creating peak regions... Creating peak regions took 34.6312868595 s Estimating background... Estimating background took 18.7149949074 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.33770489693 s Creating peak regions... Creating peak regions took 34.5411779881 s Estimating background... Estimating background took 19.0476658344 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.524944067 s Creating peak regions... Creating peak regions took 34.5055248737 s Estimating background... Estimating background took 20.7795228958 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.71329498291 s Creating peak regions... Creating peak regions took 27.7989659309 s Estimating background... Estimating background took 17.7988171577 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.40515398979 s Creating peak regions... Creating peak regions took 26.6199169159 s Estimating background... Estimating background took 13.3004040718 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.15893793106 s Creating peak regions... Creating peak regions took 27.1514728069 s Estimating background... Estimating background took 13.6845490932 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32913708687 s Creating peak regions... Creating peak regions took 24.2442309856 s Estimating background... Estimating background took 14.9068479538 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.74359917641 s Creating peak regions... Creating peak regions took 22.1055691242 s Estimating background... Estimating background took 19.0808620453 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.77676486969 s Creating peak regions... Creating peak regions took 20.2156260014 s Estimating background... Estimating background took 8.81622409821 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.96086716652 s Creating peak regions... Creating peak regions took 16.4046661854 s Estimating background... Estimating background took 13.1466360092 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.70013308525 s Creating peak regions... Creating peak regions took 65.5202209949 s Estimating background... Estimating background took 31.7886040211 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.066644907 s Creating peak regions... Creating peak regions took 18.150001049 s Estimating background... Estimating background took 12.9033381939 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.11271715164 s Creating peak regions... Creating peak regions took 12.5203580856 s Estimating background... Estimating background took 5.8962290287 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.53324508667 s Creating peak regions... Creating peak regions took 13.9206221104 s Estimating background... Estimating background took 12.1139531136 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.5101211071 s Creating peak regions... Creating peak regions took 53.0125808716 s Estimating background... Estimating background took 23.679710865 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.08606696129 s Creating peak regions... Creating peak regions took 47.3977091312 s Estimating background... Estimating background took 19.4334068298 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.38491487503 s Creating peak regions... Creating peak regions took 43.3645207882 s Estimating background... Estimating background took 23.7501559258 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.65062785149 s Creating peak regions... Creating peak regions took 44.3740429878 s Estimating background... Estimating background took 26.28439188 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.35297703743 s Creating peak regions... Creating peak regions took 41.2144839764 s Estimating background... Estimating background took 24.0904128551 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.51384115219 s Creating peak regions... Creating peak regions took 36.3970499039 s Estimating background... Estimating background took 17.2164359093 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.11484384537 s Creating peak regions... Creating peak regions took 34.6689829826 s Estimating background... Estimating background took 17.3074431419 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.117641925812 s Creating peak regions... Creating peak regions took 0.165307044983 s Estimating background... Estimating background took 0.622830867767 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.17304897308 s Creating peak regions... Creating peak regions took 38.0821049213 s Estimating background... Estimating background took 22.8376169205 s Processing ZNF283-SRR5197100.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.128191947937 s Creating peak regions... Creating peak regions took 13.5272710323 s Estimating background... Estimating background took 0.53627705574 s