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='ZNF641-SRR5197204.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='ZNF641-SRR5197204/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 ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.38371801376 s Creating peak regions... Creating peak regions took 78.9172990322 s Estimating background... Estimating background took 65.6743550301 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.9812130928 s Creating peak regions... Creating peak regions took 42.8759481907 s Estimating background... Estimating background took 26.1527509689 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.48272800446 s Creating peak regions... Creating peak regions took 39.5021901131 s Estimating background... Estimating background took 24.8419017792 s Processing ZNF641-SRR5197204.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='ZNF641-SRR5197204.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='ZNF641-SRR5197204/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 ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.55880093575 s Creating peak regions... Creating peak regions took 76.823704958 s Estimating background... Estimating background took 62.3910119534 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.00423908234 s Creating peak regions... Creating peak regions took 41.1288120747 s Estimating background... Estimating background took 26.1768810749 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.8807079792 s Creating peak regions... Creating peak regions took 40.5500230789 s Estimating background... Estimating background took 25.7927539349 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.23351216316 s Creating peak regions... Creating peak regions took 40.4972879887 s Estimating background... Estimating background took 27.1524410248 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.17539095879 s Creating peak regions... Creating peak regions took 35.2178349495 s Estimating background... Estimating background took 25.6176650524 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.00677704811 s Creating peak regions... Creating peak regions took 31.5044310093 s Estimating background... Estimating background took 16.7501430511 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.6884469986 s Creating peak regions... Creating peak regions took 28.8615322113 s Estimating background... Estimating background took 18.8367521763 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.70601677895 s Creating peak regions... Creating peak regions took 27.2237279415 s Estimating background... Estimating background took 19.3161151409 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.32064008713 s Creating peak regions... Creating peak regions took 28.0651600361 s Estimating background... Estimating background took 25.4165329933 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.9736969471 s Creating peak regions... Creating peak regions took 24.4495489597 s Estimating background... Estimating background took 13.0682399273 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.29150509834 s Creating peak regions... Creating peak regions took 18.848304987 s Estimating background... Estimating background took 17.4680550098 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.21838784218 s Creating peak regions... Creating peak regions took 73.3909151554 s Estimating background... Estimating background took 41.7371070385 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.29900193214 s Creating peak regions... Creating peak regions took 21.1580891609 s Estimating background... Estimating background took 16.1398620605 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.1484041214 s Creating peak regions... Creating peak regions took 14.1007151604 s Estimating background... Estimating background took 8.01496696472 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.08119392395 s Creating peak regions... Creating peak regions took 15.64149189 s Estimating background... Estimating background took 16.612142086 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.41783809662 s Creating peak regions... Creating peak regions took 59.6573050022 s Estimating background... Estimating background took 33.2247040272 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.53568601608 s Creating peak regions... Creating peak regions took 57.1077539921 s Estimating background... Estimating background took 24.1634750366 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.63553595543 s Creating peak regions... Creating peak regions took 54.4099578857 s Estimating background... Estimating background took 31.2101478577 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.36113882065 s Creating peak regions... Creating peak regions took 50.6663839817 s Estimating background... Estimating background took 35.1159060001 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.75492310524 s Creating peak regions... Creating peak regions took 49.2167339325 s Estimating background... Estimating background took 32.7321100235 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.77757310867 s Creating peak regions... Creating peak regions took 44.3558149338 s Estimating background... Estimating background took 23.1953787804 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.3584010601 s Creating peak regions... Creating peak regions took 40.2105431557 s Estimating background... Estimating background took 22.4270391464 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.33699798584 s Creating peak regions... Creating peak regions took 0.261595010757 s Estimating background... Estimating background took 0.7916431427 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.59276819229 s Creating peak regions... Creating peak regions took 45.6222040653 s Estimating background... Estimating background took 30.6420371532 s Processing ZNF641-SRR5197204.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.257465839386 s Creating peak regions... Creating peak regions took 15.0220308304 s Estimating background... Estimating background took 0.773360013962 s