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='ZNF430-SRR5197136.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='ZNF430-SRR5197136/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 ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.99755811691 s Creating peak regions... Creating peak regions took 84.5092859268 s Estimating background... Estimating background took 97.3034949303 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.63893985748 s Creating peak regions... Creating peak regions took 46.5441970825 s Estimating background... Estimating background took 35.1177799702 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.36634302139 s Creating peak regions... Creating peak regions took 41.4279639721 s Estimating background... Estimating background took 33.1318659782 s Processing ZNF430-SRR5197136.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='ZNF430-SRR5197136.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='ZNF430-SRR5197136/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 ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.88386583328 s Creating peak regions... Creating peak regions took 83.6607730389 s Estimating background... Estimating background took 97.487942934 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.98588705063 s Creating peak regions... Creating peak regions took 45.9479129314 s Estimating background... Estimating background took 38.1169950962 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.31206488609 s Creating peak regions... Creating peak regions took 46.9899771214 s Estimating background... Estimating background took 38.4935400486 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.95489597321 s Creating peak regions... Creating peak regions took 44.3824810982 s Estimating background... Estimating background took 40.1096799374 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.69261884689 s Creating peak regions... Creating peak regions took 38.3345007896 s Estimating background... Estimating background took 53.1802530289 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.67898702621 s Creating peak regions... Creating peak regions took 34.77917099 s Estimating background... Estimating background took 27.1304931641 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.18223714828 s Creating peak regions... Creating peak regions took 33.7288348675 s Estimating background... Estimating background took 29.2331209183 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.30708289146 s Creating peak regions... Creating peak regions took 27.2233929634 s Estimating background... Estimating background took 24.3606262207 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.51158499718 s Creating peak regions... Creating peak regions took 28.334872961 s Estimating background... Estimating background took 32.2097129822 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.77707695961 s Creating peak regions... Creating peak regions took 25.8204109669 s Estimating background... Estimating background took 20.6362330914 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.80566000938 s Creating peak regions... Creating peak regions took 19.3115670681 s Estimating background... Estimating background took 17.3325259686 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.30889606476 s Creating peak regions... Creating peak regions took 79.316767931 s Estimating background... Estimating background took 68.9481658936 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.60545516014 s Creating peak regions... Creating peak regions took 24.3413040638 s Estimating background... Estimating background took 22.596834898 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.66359400749 s Creating peak regions... Creating peak regions took 15.321420908 s Estimating background... Estimating background took 11.4223399162 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.57335495949 s Creating peak regions... Creating peak regions took 16.796077013 s Estimating background... Estimating background took 18.5015950203 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.66005277634 s Creating peak regions... Creating peak regions took 65.512444973 s Estimating background... Estimating background took 49.1584579945 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.03829789162 s Creating peak regions... Creating peak regions took 52.1354780197 s Estimating background... Estimating background took 35.5548930168 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.94937205315 s Creating peak regions... Creating peak regions took 51.1355879307 s Estimating background... Estimating background took 43.1255970001 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.26366996765 s Creating peak regions... Creating peak regions took 46.7218921185 s Estimating background... Estimating background took 48.9512658119 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.63578796387 s Creating peak regions... Creating peak regions took 45.3654899597 s Estimating background... Estimating background took 40.9371778965 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.91480183601 s Creating peak regions... Creating peak regions took 40.2513320446 s Estimating background... Estimating background took 30.8135938644 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.13873910904 s Creating peak regions... Creating peak regions took 36.6660559177 s Estimating background... Estimating background took 26.8287987709 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.144104003906 s Creating peak regions... Creating peak regions took 0.21710395813 s Estimating background... Estimating background took 0.887912988663 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.61527705193 s Creating peak regions... Creating peak regions took 42.8413171768 s Estimating background... Estimating background took 43.56549716 s Processing ZNF430-SRR5197136.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.273617982864 s Creating peak regions... Creating peak regions took 14.2846040726 s Estimating background... Estimating background took 0.972811937332 s