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='ZNF616-SRR5197198.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='ZNF616-SRR5197198/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 ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.37491512299 s Creating peak regions... Creating peak regions took 78.9485180378 s Estimating background... Estimating background took 62.8310098648 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.9403219223 s Creating peak regions... Creating peak regions took 43.272881031 s Estimating background... Estimating background took 24.3490560055 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.53620791435 s Creating peak regions... Creating peak regions took 39.4601931572 s Estimating background... Estimating background took 24.3213989735 s Processing ZNF616-SRR5197198.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='ZNF616-SRR5197198.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='ZNF616-SRR5197198/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 ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.64885807037 s Creating peak regions... Creating peak regions took 92.6656188965 s Estimating background... Estimating background took 58.2032749653 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.16182088852 s Creating peak regions... Creating peak regions took 52.1949729919 s Estimating background... Estimating background took 24.9068720341 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.592856884 s Creating peak regions... Creating peak regions took 48.4753451347 s Estimating background... Estimating background took 26.3007900715 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.51016402245 s Creating peak regions... Creating peak regions took 48.3405170441 s Estimating background... Estimating background took 28.6375639439 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.72138810158 s Creating peak regions... Creating peak regions took 38.5219841003 s Estimating background... Estimating background took 24.5490889549 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.03083086014 s Creating peak regions... Creating peak regions took 37.8122010231 s Estimating background... Estimating background took 15.5069189072 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.37981081009 s Creating peak regions... Creating peak regions took 38.8324980736 s Estimating background... Estimating background took 18.1053779125 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53052282333 s Creating peak regions... Creating peak regions took 32.0184891224 s Estimating background... Estimating background took 17.0188951492 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.2110850811 s Creating peak regions... Creating peak regions took 31.1019220352 s Estimating background... Estimating background took 20.8705248833 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.16901302338 s Creating peak regions... Creating peak regions took 29.9549348354 s Estimating background... Estimating background took 11.5676000118 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.98780012131 s Creating peak regions... Creating peak regions took 17.9147121906 s Estimating background... Estimating background took 14.0671679974 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.37485909462 s Creating peak regions... Creating peak regions took 85.7759711742 s Estimating background... Estimating background took 40.799738884 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.42099308968 s Creating peak regions... Creating peak regions took 25.9936180115 s Estimating background... Estimating background took 14.7864630222 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.20483112335 s Creating peak regions... Creating peak regions took 18.1207010746 s Estimating background... Estimating background took 7.01065587997 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.54111099243 s Creating peak regions... Creating peak regions took 16.2422959805 s Estimating background... Estimating background took 13.8915011883 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.86638402939 s Creating peak regions... Creating peak regions took 66.9623510838 s Estimating background... Estimating background took 32.874063015 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.08691310883 s Creating peak regions... Creating peak regions took 63.2508561611 s Estimating background... Estimating background took 25.9287040234 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.90743589401 s Creating peak regions... Creating peak regions took 58.3257849216 s Estimating background... Estimating background took 27.7757840157 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.09095597267 s Creating peak regions... Creating peak regions took 58.3030438423 s Estimating background... Estimating background took 34.5549650192 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.61569809914 s Creating peak regions... Creating peak regions took 52.3067119122 s Estimating background... Estimating background took 31.8908109665 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.57898902893 s Creating peak regions... Creating peak regions took 45.6763370037 s Estimating background... Estimating background took 21.8025789261 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.03383088112 s Creating peak regions... Creating peak regions took 40.8690989017 s Estimating background... Estimating background took 20.2370831966 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.203771114349 s Creating peak regions... Creating peak regions took 0.308110952377 s Estimating background... Estimating background took 0.676962137222 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.49967694283 s Creating peak regions... Creating peak regions took 49.6043109894 s Estimating background... Estimating background took 27.7060849667 s Processing ZNF616-SRR5197198.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.392124891281 s Creating peak regions... Creating peak regions took 17.9011740685 s Estimating background... Estimating background took 0.882055044174 s