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='ZNF707-SRR5197222.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='ZNF707-SRR5197222/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 ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.48465204239 s Creating peak regions... Creating peak regions took 83.3634979725 s Estimating background... Estimating background took 98.1412220001 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.40195989609 s Creating peak regions... Creating peak regions took 46.0471420288 s Estimating background... Estimating background took 34.7439680099 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.85209393501 s Creating peak regions... Creating peak regions took 38.278990984 s Estimating background... Estimating background took 33.8153181076 s Processing ZNF707-SRR5197222.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='ZNF707-SRR5197222.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='ZNF707-SRR5197222/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 ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.66343379021 s Creating peak regions... Creating peak regions took 76.3246979713 s Estimating background... Estimating background took 78.2154409885 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.95993900299 s Creating peak regions... Creating peak regions took 43.0042228699 s Estimating background... Estimating background took 33.9771180153 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.06580591202 s Creating peak regions... Creating peak regions took 43.1418941021 s Estimating background... Estimating background took 30.5340800285 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.30921888351 s Creating peak regions... Creating peak regions took 38.8631901741 s Estimating background... Estimating background took 36.0824780464 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.13043498993 s Creating peak regions... Creating peak regions took 46.1412761211 s Estimating background... Estimating background took 31.8188939095 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.05531287193 s Creating peak regions... Creating peak regions took 33.237719059 s Estimating background... Estimating background took 21.0105998516 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51111292839 s Creating peak regions... Creating peak regions took 32.9554460049 s Estimating background... Estimating background took 22.0934388638 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.87310695648 s Creating peak regions... Creating peak regions took 27.0892419815 s Estimating background... Estimating background took 27.8163330555 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.68532896042 s Creating peak regions... Creating peak regions took 25.1958968639 s Estimating background... Estimating background took 29.1335940361 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.61765003204 s Creating peak regions... Creating peak regions took 29.3091249466 s Estimating background... Estimating background took 13.7368888855 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.82026004791 s Creating peak regions... Creating peak regions took 20.3910188675 s Estimating background... Estimating background took 26.5803351402 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.27906990051 s Creating peak regions... Creating peak regions took 78.6709358692 s Estimating background... Estimating background took 54.3459889889 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.1556699276 s Creating peak regions... Creating peak regions took 23.1271400452 s Estimating background... Estimating background took 20.6734318733 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.13023900986 s Creating peak regions... Creating peak regions took 13.318748951 s Estimating background... Estimating background took 9.77013492584 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.72647190094 s Creating peak regions... Creating peak regions took 14.6868917942 s Estimating background... Estimating background took 20.8732960224 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.76969218254 s Creating peak regions... Creating peak regions took 53.6503751278 s Estimating background... Estimating background took 39.3776068687 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.2412879467 s Creating peak regions... Creating peak regions took 48.9162039757 s Estimating background... Estimating background took 29.477615118 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.2716190815 s Creating peak regions... Creating peak regions took 51.1603240967 s Estimating background... Estimating background took 37.4244711399 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.86933898926 s Creating peak regions... Creating peak regions took 52.0151040554 s Estimating background... Estimating background took 43.7605330944 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.68775200844 s Creating peak regions... Creating peak regions took 47.0716209412 s Estimating background... Estimating background took 41.9789690971 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.90612101555 s Creating peak regions... Creating peak regions took 43.8541200161 s Estimating background... Estimating background took 29.0283539295 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.38313817978 s Creating peak regions... Creating peak regions took 38.9934699535 s Estimating background... Estimating background took 31.2430589199 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.183264970779 s Creating peak regions... Creating peak regions took 0.334300041199 s Estimating background... Estimating background took 0.636677980423 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.83213400841 s Creating peak regions... Creating peak regions took 44.6841509342 s Estimating background... Estimating background took 39.6115951538 s Processing ZNF707-SRR5197222.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.392367839813 s Creating peak regions... Creating peak regions took 16.6191029549 s Estimating background... Estimating background took 0.996281147003 s