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='ZNF302-SRR5197107.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='ZNF302-SRR5197107/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 ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.55633497238 s Creating peak regions... Creating peak regions took 79.6838240623 s Estimating background... Estimating background took 58.361276865 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.31921505928 s Creating peak regions... Creating peak regions took 41.1088740826 s Estimating background... Estimating background took 23.6094079018 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.47470116615 s Creating peak regions... Creating peak regions took 39.2317018509 s Estimating background... Estimating background took 22.941491127 s Processing ZNF302-SRR5197107.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='ZNF302-SRR5197107.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='ZNF302-SRR5197107/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 ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.38524484634 s Creating peak regions... Creating peak regions took 76.499063015 s Estimating background... Estimating background took 59.2385389805 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.37041091919 s Creating peak regions... Creating peak regions took 42.7128140926 s Estimating background... Estimating background took 22.9540300369 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.25333094597 s Creating peak regions... Creating peak regions took 41.2362539768 s Estimating background... Estimating background took 26.0670161247 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.72462582588 s Creating peak regions... Creating peak regions took 42.1308319569 s Estimating background... Estimating background took 24.3148231506 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.9236741066 s Creating peak regions... Creating peak regions took 35.2214958668 s Estimating background... Estimating background took 22.3688831329 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.43768000603 s Creating peak regions... Creating peak regions took 32.4077968597 s Estimating background... Estimating background took 15.7635011673 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28370690346 s Creating peak regions... Creating peak regions took 31.4084188938 s Estimating background... Estimating background took 18.6605949402 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.42751002312 s Creating peak regions... Creating peak regions took 27.5712440014 s Estimating background... Estimating background took 20.0027618408 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.0891430378 s Creating peak regions... Creating peak regions took 27.3709259033 s Estimating background... Estimating background took 26.0692839622 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.99565815926 s Creating peak regions... Creating peak regions took 23.8441970348 s Estimating background... Estimating background took 11.3532190323 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.14032196999 s Creating peak regions... Creating peak regions took 18.9618330002 s Estimating background... Estimating background took 18.7464499474 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.61923599243 s Creating peak regions... Creating peak regions took 75.2931730747 s Estimating background... Estimating background took 39.117552042 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.17652106285 s Creating peak regions... Creating peak regions took 21.7405788898 s Estimating background... Estimating background took 16.2105739117 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.23638701439 s Creating peak regions... Creating peak regions took 14.5574159622 s Estimating background... Estimating background took 8.46644997597 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.62658309937 s Creating peak regions... Creating peak regions took 15.631816864 s Estimating background... Estimating background took 15.4012751579 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.83463788033 s Creating peak regions... Creating peak regions took 63.1918840408 s Estimating background... Estimating background took 31.5045790672 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.66031908989 s Creating peak regions... Creating peak regions took 56.4195199013 s Estimating background... Estimating background took 21.7246508598 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.22798085213 s Creating peak regions... Creating peak regions took 57.4754559994 s Estimating background... Estimating background took 29.3779859543 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.97553014755 s Creating peak regions... Creating peak regions took 53.3333079815 s Estimating background... Estimating background took 33.0517849922 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.25614118576 s Creating peak regions... Creating peak regions took 49.3845369816 s Estimating background... Estimating background took 26.3938269615 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.56238389015 s Creating peak regions... Creating peak regions took 36.9533889294 s Estimating background... Estimating background took 17.4614140987 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.18871688843 s Creating peak regions... Creating peak regions took 34.2941401005 s Estimating background... Estimating background took 17.5390439034 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.111975193024 s Creating peak regions... Creating peak regions took 0.167762994766 s Estimating background... Estimating background took 0.680665016174 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.15976190567 s Creating peak regions... Creating peak regions took 38.8417730331 s Estimating background... Estimating background took 23.9705090523 s Processing ZNF302-SRR5197107.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.188071966171 s Creating peak regions... Creating peak regions took 12.4040849209 s Estimating background... Estimating background took 0.679666042328 s