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='ZNF189-SRR5197072.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='ZNF189-SRR5197072/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 ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.3837749958 s Creating peak regions... Creating peak regions took 66.7317390442 s Estimating background... Estimating background took 40.3053860664 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.77373218536 s Creating peak regions... Creating peak regions took 40.6742150784 s Estimating background... Estimating background took 17.3302788734 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.55974006653 s Creating peak regions... Creating peak regions took 40.8569331169 s Estimating background... Estimating background took 16.1149470806 s Processing ZNF189-SRR5197072.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='ZNF189-SRR5197072.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='ZNF189-SRR5197072/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 ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.32401680946 s Creating peak regions... Creating peak regions took 72.6053431034 s Estimating background... Estimating background took 38.9717288017 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.53899908066 s Creating peak regions... Creating peak regions took 38.0913000107 s Estimating background... Estimating background took 17.0255539417 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.47654390335 s Creating peak regions... Creating peak regions took 38.2609379292 s Estimating background... Estimating background took 15.6697888374 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.64785313606 s Creating peak regions... Creating peak regions took 40.1637699604 s Estimating background... Estimating background took 17.0040428638 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.06965088844 s Creating peak regions... Creating peak regions took 31.8947958946 s Estimating background... Estimating background took 16.322614193 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.78571581841 s Creating peak regions... Creating peak regions took 29.4682102203 s Estimating background... Estimating background took 10.4914290905 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.71118378639 s Creating peak regions... Creating peak regions took 29.4307749271 s Estimating background... Estimating background took 13.4708249569 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.05950808525 s Creating peak regions... Creating peak regions took 24.740489006 s Estimating background... Estimating background took 10.7875230312 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.38833403587 s Creating peak regions... Creating peak regions took 25.8232810497 s Estimating background... Estimating background took 15.2937719822 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.29632592201 s Creating peak regions... Creating peak regions took 24.0560629368 s Estimating background... Estimating background took 8.51266908646 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.27403783798 s Creating peak regions... Creating peak regions took 17.0132551193 s Estimating background... Estimating background took 9.95034313202 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.27037501335 s Creating peak regions... Creating peak regions took 71.805357933 s Estimating background... Estimating background took 26.161509037 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.57059693336 s Creating peak regions... Creating peak regions took 18.8410658836 s Estimating background... Estimating background took 9.53409409523 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.98775100708 s Creating peak regions... Creating peak regions took 12.9327590466 s Estimating background... Estimating background took 6.04782891273 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.948749065399 s Creating peak regions... Creating peak regions took 15.1642549038 s Estimating background... Estimating background took 8.601115942 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.31401705742 s Creating peak regions... Creating peak regions took 59.5105600357 s Estimating background... Estimating background took 20.1635019779 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.84524488449 s Creating peak regions... Creating peak regions took 51.7997059822 s Estimating background... Estimating background took 16.9694838524 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.42543888092 s Creating peak regions... Creating peak regions took 50.5017199516 s Estimating background... Estimating background took 20.2799949646 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.61739611626 s Creating peak regions... Creating peak regions took 49.2022619247 s Estimating background... Estimating background took 22.9478130341 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.14864301682 s Creating peak regions... Creating peak regions took 43.6354420185 s Estimating background... Estimating background took 20.0362241268 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.58285784721 s Creating peak regions... Creating peak regions took 41.0305998325 s Estimating background... Estimating background took 14.9600670338 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23438096046 s Creating peak regions... Creating peak regions took 38.7874138355 s Estimating background... Estimating background took 14.2931990623 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0829319953918 s Creating peak regions... Creating peak regions took 0.166771888733 s Estimating background... Estimating background took 0.542124032974 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.31568098068 s Creating peak regions... Creating peak regions took 48.004390955 s Estimating background... Estimating background took 20.7662780285 s Processing ZNF189-SRR5197072.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.246909141541 s Creating peak regions... Creating peak regions took 15.9132688046 s Estimating background... Estimating background took 1.69048309326 s