INPUT PARAMETERS:
Namespace(B2=None, N4=1000, N6=1000, S4=1, UMIs=None, adapters1=None, b3=0.05, blacklist=None, center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/all_prokaryotes/2015-05-07-prokaryotes/Streptomyces_venezuelae_ATCC_10712_uid177080/sequence.chrom.sizes', e4='PeakXus', fastq='RsrR-Mutant-Rep1-GSM2138317/GSM424491.36mers.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='RsrR-Mutant-Rep1-GSM2138317/', 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 RsrR-Mutant-Rep1-GSM2138317/GSM424491.36mers.unique.bam
Reading in data... Reading data took 149.836830139 s
Creating peak regions... Creating peak regions took 40.5418541431 s
Estimating background... Estimating background took 564.199259043 s