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='ZNF205-SRR5197077.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='ZNF205-SRR5197077/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 ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.04542183876 s Creating peak regions... Creating peak regions took 64.0645368099 s Estimating background... Estimating background took 22.8255009651 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.71364593506 s Creating peak regions... Creating peak regions took 38.4191060066 s Estimating background... Estimating background took 9.93321108818 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.78850197792 s Creating peak regions... Creating peak regions took 40.9648740292 s Estimating background... Estimating background took 9.75401091576 s Processing ZNF205-SRR5197077.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='ZNF205-SRR5197077.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='ZNF205-SRR5197077/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 ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.60062098503 s Creating peak regions... Creating peak regions took 74.6492590904 s Estimating background... Estimating background took 20.1490170956 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.88982009888 s Creating peak regions... Creating peak regions took 35.6726779938 s Estimating background... Estimating background took 10.1672859192 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.74367499352 s Creating peak regions... Creating peak regions took 38.5317518711 s Estimating background... Estimating background took 9.60257697105 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.09915184975 s Creating peak regions... Creating peak regions took 38.8685700893 s Estimating background... Estimating background took 10.0766088963 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.68403100967 s Creating peak regions... Creating peak regions took 33.4711670876 s Estimating background... Estimating background took 13.1615622044 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.57666087151 s Creating peak regions... Creating peak regions took 29.1216871738 s Estimating background... Estimating background took 6.83866906166 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.80553603172 s Creating peak regions... Creating peak regions took 30.8688900471 s Estimating background... Estimating background took 8.38675808907 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.42475104332 s Creating peak regions... Creating peak regions took 25.7867879868 s Estimating background... Estimating background took 6.41968798637 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.61647677422 s Creating peak regions... Creating peak regions took 25.3867571354 s Estimating background... Estimating background took 7.56026911736 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.07544994354 s Creating peak regions... Creating peak regions took 23.159083128 s Estimating background... Estimating background took 5.83702802658 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.60405111313 s Creating peak regions... Creating peak regions took 17.2633221149 s Estimating background... Estimating background took 4.52340507507 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.63078904152 s Creating peak regions... Creating peak regions took 74.5194129944 s Estimating background... Estimating background took 17.0779180527 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.88074302673 s Creating peak regions... Creating peak regions took 19.0594329834 s Estimating background... Estimating background took 4.9105360508 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.24661612511 s Creating peak regions... Creating peak regions took 14.2115859985 s Estimating background... Estimating background took 3.28487181664 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.34998703003 s Creating peak regions... Creating peak regions took 14.659348011 s Estimating background... Estimating background took 4.35619807243 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.56207108498 s Creating peak regions... Creating peak regions took 61.1903550625 s Estimating background... Estimating background took 13.3354480267 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.32012701035 s Creating peak regions... Creating peak regions took 57.996366024 s Estimating background... Estimating background took 11.2239279747 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.85803294182 s Creating peak regions... Creating peak regions took 55.7835400105 s Estimating background... Estimating background took 12.6187000275 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.30698513985 s Creating peak regions... Creating peak regions took 53.1640441418 s Estimating background... Estimating background took 14.231773138 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.69729614258 s Creating peak regions... Creating peak regions took 46.7780740261 s Estimating background... Estimating background took 12.2716901302 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.86746788025 s Creating peak regions... Creating peak regions took 42.5080630779 s Estimating background... Estimating background took 9.76009392738 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.23316383362 s Creating peak regions... Creating peak regions took 39.9458470345 s Estimating background... Estimating background took 9.14936089516 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0836760997772 s Creating peak regions... Creating peak regions took 0.138107061386 s Estimating background... Estimating background took 0.56346988678 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.13106608391 s Creating peak regions... Creating peak regions took 49.1635200977 s Estimating background... Estimating background took 14.6017501354 s Processing ZNF205-SRR5197077.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.13734292984 s Creating peak regions... Creating peak regions took 16.2633960247 s Estimating background... Estimating background took 0.564391851425 s