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='ZNF334-SRR5197117.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='ZNF334-SRR5197117/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 ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.11315393448 s Creating peak regions... Creating peak regions took 71.0601270199 s Estimating background... Estimating background took 12.9584069252 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.91181397438 s Creating peak regions... Creating peak regions took 38.8436610699 s Estimating background... Estimating background took 6.207062006 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.83351588249 s Creating peak regions... Creating peak regions took 39.7693920135 s Estimating background... Estimating background took 6.39314889908 s Processing ZNF334-SRR5197117.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='ZNF334-SRR5197117.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='ZNF334-SRR5197117/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 ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 9.71832895279 s Creating peak regions... Creating peak regions took 69.2004730701 s Estimating background... Estimating background took 12.8918068409 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.6198451519 s Creating peak regions... Creating peak regions took 39.5040650368 s Estimating background... Estimating background took 6.57472515106 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.97625803947 s Creating peak regions... Creating peak regions took 41.1092638969 s Estimating background... Estimating background took 6.95479512215 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.70144701004 s Creating peak regions... Creating peak regions took 39.3588168621 s Estimating background... Estimating background took 6.68391799927 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.97485899925 s Creating peak regions... Creating peak regions took 34.3169682026 s Estimating background... Estimating background took 6.04121685028 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.25108504295 s Creating peak regions... Creating peak regions took 31.954846859 s Estimating background... Estimating background took 4.94184994698 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.36541199684 s Creating peak regions... Creating peak regions took 28.8198049068 s Estimating background... Estimating background took 5.0717420578 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.56366014481 s Creating peak regions... Creating peak regions took 26.5765841007 s Estimating background... Estimating background took 5.04128694534 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.38940000534 s Creating peak regions... Creating peak regions took 25.0471599102 s Estimating background... Estimating background took 6.22665405273 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.47694921494 s Creating peak regions... Creating peak regions took 22.9414801598 s Estimating background... Estimating background took 3.29602503777 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.98308396339 s Creating peak regions... Creating peak regions took 16.1763660908 s Estimating background... Estimating background took 4.34477901459 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.87623596191 s Creating peak regions... Creating peak regions took 72.9770240784 s Estimating background... Estimating background took 10.6109101772 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.16174483299 s Creating peak regions... Creating peak regions took 20.2885909081 s Estimating background... Estimating background took 4.44881701469 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.37854099274 s Creating peak regions... Creating peak regions took 12.7168068886 s Estimating background... Estimating background took 1.48604106903 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45635485649 s Creating peak regions... Creating peak regions took 14.9797680378 s Estimating background... Estimating background took 4.14647603035 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.21853613853 s Creating peak regions... Creating peak regions took 56.8335080147 s Estimating background... Estimating background took 8.66046309471 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.18825316429 s Creating peak regions... Creating peak regions took 55.3288559914 s Estimating background... Estimating background took 6.98669981956 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.2249610424 s Creating peak regions... Creating peak regions took 53.72706604 s Estimating background... Estimating background took 7.71476387978 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.14640188217 s Creating peak regions... Creating peak regions took 49.5556759834 s Estimating background... Estimating background took 8.0710849762 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.81225514412 s Creating peak regions... Creating peak regions took 47.1109130383 s Estimating background... Estimating background took 8.53551697731 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.66532206535 s Creating peak regions... Creating peak regions took 43.9566838741 s Estimating background... Estimating background took 6.3259241581 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.13606905937 s Creating peak regions... Creating peak regions took 40.3802568913 s Estimating background... Estimating background took 6.58796310425 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0902881622314 s Creating peak regions... Creating peak regions took 0.139971971512 s Estimating background... Estimating background took 0.427683830261 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.43347907066 s Creating peak regions... Creating peak regions took 47.3154149055 s Estimating background... Estimating background took 7.39637899399 s Processing ZNF334-SRR5197117.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.124802112579 s Creating peak regions... Creating peak regions took 15.0257251263 s Estimating background... Estimating background took 0.488173961639 s