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='ZNF716-SRR5197225.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='ZNF716-SRR5197225/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 ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.4187669754 s Creating peak regions... Creating peak regions took 81.7266750336 s Estimating background... Estimating background took 32.2544038296 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32398796082 s Creating peak regions... Creating peak regions took 43.2021689415 s Estimating background... Estimating background took 12.4509220123 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.25043797493 s Creating peak regions... Creating peak regions took 44.6807949543 s Estimating background... Estimating background took 11.9993700981 s Processing ZNF716-SRR5197225.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='ZNF716-SRR5197225.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='ZNF716-SRR5197225/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 ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.63087487221 s Creating peak regions... Creating peak regions took 76.0429308414 s Estimating background... Estimating background took 29.2382411957 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.36032700539 s Creating peak regions... Creating peak regions took 39.6022799015 s Estimating background... Estimating background took 11.5842609406 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.29702019691 s Creating peak regions... Creating peak regions took 41.9336881638 s Estimating background... Estimating background took 11.8570928574 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.5207221508 s Creating peak regions... Creating peak regions took 41.8541178703 s Estimating background... Estimating background took 12.9789280891 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37251496315 s Creating peak regions... Creating peak regions took 33.8405759335 s Estimating background... Estimating background took 13.6302549839 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.67010688782 s Creating peak regions... Creating peak regions took 32.9766719341 s Estimating background... Estimating background took 8.34676504135 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.56830596924 s Creating peak regions... Creating peak regions took 29.1450579166 s Estimating background... Estimating background took 8.89456295967 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.47198009491 s Creating peak regions... Creating peak regions took 24.5442240238 s Estimating background... Estimating background took 7.54001498222 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.75107192993 s Creating peak regions... Creating peak regions took 25.1464779377 s Estimating background... Estimating background took 9.84135198593 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.25125694275 s Creating peak regions... Creating peak regions took 24.4938850403 s Estimating background... Estimating background took 6.68987107277 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.09280896187 s Creating peak regions... Creating peak regions took 18.3504738808 s Estimating background... Estimating background took 5.98866391182 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.27707886696 s Creating peak regions... Creating peak regions took 75.7468180656 s Estimating background... Estimating background took 20.617358923 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.34390902519 s Creating peak regions... Creating peak regions took 18.783233881 s Estimating background... Estimating background took 7.07248806953 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.693961858749 s Creating peak regions... Creating peak regions took 14.5205788612 s Estimating background... Estimating background took 4.0787088871 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.964968919754 s Creating peak regions... Creating peak regions took 15.6205301285 s Estimating background... Estimating background took 5.58417201042 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.33332300186 s Creating peak regions... Creating peak regions took 61.7790961266 s Estimating background... Estimating background took 16.1555390358 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.0053050518 s Creating peak regions... Creating peak regions took 55.8100049496 s Estimating background... Estimating background took 13.0183591843 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.11954808235 s Creating peak regions... Creating peak regions took 56.4359881878 s Estimating background... Estimating background took 15.8264269829 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.46765995026 s Creating peak regions... Creating peak regions took 51.0026929379 s Estimating background... Estimating background took 18.4328019619 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.02856206894 s Creating peak regions... Creating peak regions took 51.004103899 s Estimating background... Estimating background took 15.5675430298 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53480005264 s Creating peak regions... Creating peak regions took 42.8327920437 s Estimating background... Estimating background took 11.4784731865 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28310799599 s Creating peak regions... Creating peak regions took 42.352848053 s Estimating background... Estimating background took 11.0000391006 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0850219726562 s Creating peak regions... Creating peak regions took 0.148958921432 s Estimating background... Estimating background took 0.710510015488 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.15908503532 s Creating peak regions... Creating peak regions took 49.3275439739 s Estimating background... Estimating background took 15.4403920174 s Processing ZNF716-SRR5197225.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0990240573883 s Creating peak regions... Creating peak regions took 16.0653510094 s Estimating background... Estimating background took 0.443905830383 s