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='ZNF354A-SRR5197123.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='ZNF354A-SRR5197123/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 ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 8.14677095413 s Creating peak regions... Creating peak regions took 80.52906394 s Estimating background... Estimating background took 71.341176033 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.20970702171 s Creating peak regions... Creating peak regions took 43.4075279236 s Estimating background... Estimating background took 24.4587860107 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.32262396812 s Creating peak regions... Creating peak regions took 35.2920820713 s Estimating background... Estimating background took 22.9623661041 s Processing ZNF354A-SRR5197123.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='ZNF354A-SRR5197123.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='ZNF354A-SRR5197123/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 ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 7.90620017052 s Creating peak regions... Creating peak regions took 78.8902180195 s Estimating background... Estimating background took 74.7955429554 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.09302401543 s Creating peak regions... Creating peak regions took 42.7441618443 s Estimating background... Estimating background took 28.0235230923 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.2660369873 s Creating peak regions... Creating peak regions took 43.5692901611 s Estimating background... Estimating background took 29.433300972 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.31504201889 s Creating peak regions... Creating peak regions took 42.7292897701 s Estimating background... Estimating background took 30.823679924 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.00602078438 s Creating peak regions... Creating peak regions took 35.8207008839 s Estimating background... Estimating background took 36.4993290901 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.74751782417 s Creating peak regions... Creating peak regions took 32.1153681278 s Estimating background... Estimating background took 18.740306139 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.42212104797 s Creating peak regions... Creating peak regions took 34.0483751297 s Estimating background... Estimating background took 21.1185178757 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.59203100204 s Creating peak regions... Creating peak regions took 28.8777611256 s Estimating background... Estimating background took 17.9461658001 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.84476590157 s Creating peak regions... Creating peak regions took 26.3413438797 s Estimating background... Estimating background took 23.3697109222 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.34332990646 s Creating peak regions... Creating peak regions took 25.8797008991 s Estimating background... Estimating background took 16.248180151 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.00806689262 s Creating peak regions... Creating peak regions took 20.6181440353 s Estimating background... Estimating background took 14.8640289307 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 6.10463404655 s Creating peak regions... Creating peak regions took 81.6100461483 s Estimating background... Estimating background took 49.6668560505 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23398900032 s Creating peak regions... Creating peak regions took 21.5618758202 s Estimating background... Estimating background took 15.4543199539 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.18340492249 s Creating peak regions... Creating peak regions took 15.5170691013 s Estimating background... Estimating background took 9.20748901367 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.60490989685 s Creating peak regions... Creating peak regions took 17.26684618 s Estimating background... Estimating background took 14.2331671715 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.58795881271 s Creating peak regions... Creating peak regions took 62.1535890102 s Estimating background... Estimating background took 40.3017640114 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.26225209236 s Creating peak regions... Creating peak regions took 59.0725531578 s Estimating background... Estimating background took 32.2567298412 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.65357995033 s Creating peak regions... Creating peak regions took 59.4669809341 s Estimating background... Estimating background took 38.7092819214 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 5.50375914574 s Creating peak regions... Creating peak regions took 51.3287680149 s Estimating background... Estimating background took 35.9919240475 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.84715294838 s Creating peak regions... Creating peak regions took 43.8423070908 s Estimating background... Estimating background took 31.2959580421 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 3.14240288734 s Creating peak regions... Creating peak regions took 38.6210420132 s Estimating background... Estimating background took 22.4140820503 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.70428180695 s Creating peak regions... Creating peak regions took 36.0524160862 s Estimating background... Estimating background took 21.3110721111 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.120517015457 s Creating peak regions... Creating peak regions took 0.207776069641 s Estimating background... Estimating background took 0.700441122055 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.0344889164 s Creating peak regions... Creating peak regions took 39.8373541832 s Estimating background... Estimating background took 33.5943808556 s Processing ZNF354A-SRR5197123.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.204010009766 s Creating peak regions... Creating peak regions took 14.0400161743 s Estimating background... Estimating background took 0.776822090149 s