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='ZNF611-SRR5197194.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='ZNF611-SRR5197194/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 ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.37864208221 s Creating peak regions... Creating peak regions took 76.7403969765 s Estimating background... Estimating background took 33.8576390743 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.48035883904 s Creating peak regions... Creating peak regions took 39.8220450878 s Estimating background... Estimating background took 14.2201850414 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.52627921104 s Creating peak regions... Creating peak regions took 40.0886790752 s Estimating background... Estimating background took 14.477645874 s Processing ZNF611-SRR5197194.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='ZNF611-SRR5197194.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='ZNF611-SRR5197194/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 ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.50588798523 s Creating peak regions... Creating peak regions took 77.4582769871 s Estimating background... Estimating background took 35.3846428394 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.82550311089 s Creating peak regions... Creating peak regions took 40.3351509571 s Estimating background... Estimating background took 13.6513419151 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.5265519619 s Creating peak regions... Creating peak regions took 47.028370142 s Estimating background... Estimating background took 13.4666581154 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.45047307014 s Creating peak regions... Creating peak regions took 51.5350179672 s Estimating background... Estimating background took 15.3059980869 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.96828794479 s Creating peak regions... Creating peak regions took 35.2302839756 s Estimating background... Estimating background took 11.9290809631 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.67545104027 s Creating peak regions... Creating peak regions took 27.5895578861 s Estimating background... Estimating background took 8.86656618118 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.74852085114 s Creating peak regions... Creating peak regions took 29.2369689941 s Estimating background... Estimating background took 10.3905091286 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.90747904778 s Creating peak regions... Creating peak regions took 30.9905478954 s Estimating background... Estimating background took 10.4336218834 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.29805779457 s Creating peak regions... Creating peak regions took 26.8352630138 s Estimating background... Estimating background took 14.0377340317 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.52911496162 s Creating peak regions... Creating peak regions took 31.4358510971 s Estimating background... Estimating background took 7.6557571888 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.5157968998 s Creating peak regions... Creating peak regions took 19.7540669441 s Estimating background... Estimating background took 9.03007102013 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.48064804077 s Creating peak regions... Creating peak regions took 76.5134589672 s Estimating background... Estimating background took 22.8988158703 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.57574295998 s Creating peak regions... Creating peak regions took 23.3973560333 s Estimating background... Estimating background took 8.43756604195 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.881518125534 s Creating peak regions... Creating peak regions took 15.4644370079 s Estimating background... Estimating background took 4.921667099 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.22845292091 s Creating peak regions... Creating peak regions took 16.549626112 s Estimating background... Estimating background took 7.82909297943 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.85590291023 s Creating peak regions... Creating peak regions took 64.2786121368 s Estimating background... Estimating background took 17.8966469765 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.1065530777 s Creating peak regions... Creating peak regions took 63.0853388309 s Estimating background... Estimating background took 14.288695097 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.50643801689 s Creating peak regions... Creating peak regions took 59.5990109444 s Estimating background... Estimating background took 18.0237240791 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.66149497032 s Creating peak regions... Creating peak regions took 55.2686879635 s Estimating background... Estimating background took 19.7388350964 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.69694185257 s Creating peak regions... Creating peak regions took 53.7203478813 s Estimating background... Estimating background took 18.7215030193 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.48652291298 s Creating peak regions... Creating peak regions took 43.0127139091 s Estimating background... Estimating background took 13.2655909061 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51947283745 s Creating peak regions... Creating peak regions took 40.8125579357 s Estimating background... Estimating background took 13.28256917 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0945589542389 s Creating peak regions... Creating peak regions took 0.187658071518 s Estimating background... Estimating background took 0.697189092636 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.96560192108 s Creating peak regions... Creating peak regions took 48.9406940937 s Estimating background... Estimating background took 16.365748167 s Processing ZNF611-SRR5197194.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.165807008743 s Creating peak regions... Creating peak regions took 16.867609024 s Estimating background... Estimating background took 0.543435096741 s