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='ZNF619-SRR5197199.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='ZNF619-SRR5197199/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 ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.30244207382 s Creating peak regions... Creating peak regions took 79.9238739014 s Estimating background... Estimating background took 60.1309800148 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.62031316757 s Creating peak regions... Creating peak regions took 43.7210738659 s Estimating background... Estimating background took 23.295309782 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.11360383034 s Creating peak regions... Creating peak regions took 39.4221909046 s Estimating background... Estimating background took 22.3162739277 s Processing ZNF619-SRR5197199.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='ZNF619-SRR5197199.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='ZNF619-SRR5197199/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 ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.72214698792 s Creating peak regions... Creating peak regions took 77.860460043 s Estimating background... Estimating background took 59.0975961685 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.59340596199 s Creating peak regions... Creating peak regions took 41.3447630405 s Estimating background... Estimating background took 23.6693880558 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.56211805344 s Creating peak regions... Creating peak regions took 41.2223219872 s Estimating background... Estimating background took 23.6761140823 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.65169000626 s Creating peak regions... Creating peak regions took 40.7190239429 s Estimating background... Estimating background took 26.0356068611 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.63241505623 s Creating peak regions... Creating peak regions took 35.609151125 s Estimating background... Estimating background took 31.6606500149 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.44645905495 s Creating peak regions... Creating peak regions took 32.3735511303 s Estimating background... Estimating background took 16.3022298813 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.40655612946 s Creating peak regions... Creating peak regions took 32.1768820286 s Estimating background... Estimating background took 17.4444918633 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.46713995934 s Creating peak regions... Creating peak regions took 27.1535151005 s Estimating background... Estimating background took 15.432860136 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.67099404335 s Creating peak regions... Creating peak regions took 25.6189191341 s Estimating background... Estimating background took 18.9233689308 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.00075292587 s Creating peak regions... Creating peak regions took 24.0807409286 s Estimating background... Estimating background took 13.0692000389 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.83282613754 s Creating peak regions... Creating peak regions took 17.3073079586 s Estimating background... Estimating background took 12.1211428642 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.32895708084 s Creating peak regions... Creating peak regions took 73.629971981 s Estimating background... Estimating background took 41.8365030289 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.97381210327 s Creating peak regions... Creating peak regions took 20.8944849968 s Estimating background... Estimating background took 13.4560730457 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.40092015266 s Creating peak regions... Creating peak regions took 14.143378973 s Estimating background... Estimating background took 7.56541514397 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.42074298859 s Creating peak regions... Creating peak regions took 16.0177049637 s Estimating background... Estimating background took 11.3834831715 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.0372171402 s Creating peak regions... Creating peak regions took 60.0294041634 s Estimating background... Estimating background took 34.0689759254 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.46527600288 s Creating peak regions... Creating peak regions took 57.4161610603 s Estimating background... Estimating background took 27.0617511272 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.92960190773 s Creating peak regions... Creating peak regions took 55.4018549919 s Estimating background... Estimating background took 31.8487608433 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.25223493576 s Creating peak regions... Creating peak regions took 53.1135299206 s Estimating background... Estimating background took 36.8598849773 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.65616989136 s Creating peak regions... Creating peak regions took 49.1746478081 s Estimating background... Estimating background took 31.0697340965 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.46846413612 s Creating peak regions... Creating peak regions took 44.0949029922 s Estimating background... Estimating background took 22.5780570507 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.00530195236 s Creating peak regions... Creating peak regions took 39.9190831184 s Estimating background... Estimating background took 20.5151209831 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.128575086594 s Creating peak regions... Creating peak regions took 0.219548940659 s Estimating background... Estimating background took 0.910365104675 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.50206899643 s Creating peak regions... Creating peak regions took 45.4873960018 s Estimating background... Estimating background took 32.3652210236 s Processing ZNF619-SRR5197199.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.250030994415 s Creating peak regions... Creating peak regions took 14.5039298534 s Estimating background... Estimating background took 0.658626079559 s