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='ZNF28-SRR5197104.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='ZNF28-SRR5197104/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 ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.05070996284 s Creating peak regions... Creating peak regions took 61.8661401272 s Estimating background... Estimating background took 27.5984179974 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.9429268837 s Creating peak regions... Creating peak regions took 32.9115691185 s Estimating background... Estimating background took 12.5263869762 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.09205198288 s Creating peak regions... Creating peak regions took 32.8846240044 s Estimating background... Estimating background took 13.4428269863 s Processing ZNF28-SRR5197104.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='ZNF28-SRR5197104.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='ZNF28-SRR5197104/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 ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 4.32379198074 s Creating peak regions... Creating peak regions took 73.445964098 s Estimating background... Estimating background took 36.293585062 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.28829979897 s Creating peak regions... Creating peak regions took 36.9629070759 s Estimating background... Estimating background took 12.7849750519 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.72216796875 s Creating peak regions... Creating peak regions took 32.7290079594 s Estimating background... Estimating background took 13.3129730225 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.87137317657 s Creating peak regions... Creating peak regions took 30.6155622005 s Estimating background... Estimating background took 13.2822728157 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.57309508324 s Creating peak regions... Creating peak regions took 27.7397930622 s Estimating background... Estimating background took 12.2072780132 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.28790402412 s Creating peak regions... Creating peak regions took 25.3151319027 s Estimating background... Estimating background took 9.00339913368 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.19642806053 s Creating peak regions... Creating peak regions took 23.8850729465 s Estimating background... Estimating background took 8.91142201424 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.32702207565 s Creating peak regions... Creating peak regions took 22.3675100803 s Estimating background... Estimating background took 9.26538991928 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.60005283356 s Creating peak regions... Creating peak regions took 21.9393258095 s Estimating background... Estimating background took 11.7119820118 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.02299308777 s Creating peak regions... Creating peak regions took 19.2624809742 s Estimating background... Estimating background took 6.22535800934 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.18518805504 s Creating peak regions... Creating peak regions took 14.8557140827 s Estimating background... Estimating background took 9.11607289314 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.89622688293 s Creating peak regions... Creating peak regions took 61.9114940166 s Estimating background... Estimating background took 20.1875030994 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.26051402092 s Creating peak regions... Creating peak regions took 16.5342409611 s Estimating background... Estimating background took 8.06470298767 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.618746042252 s Creating peak regions... Creating peak regions took 11.7574520111 s Estimating background... Estimating background took 4.46059298515 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.832830190659 s Creating peak regions... Creating peak regions took 13.2527701855 s Estimating background... Estimating background took 7.44542217255 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.51211094856 s Creating peak regions... Creating peak regions took 50.7828130722 s Estimating background... Estimating background took 16.0070509911 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.30532598495 s Creating peak regions... Creating peak regions took 45.9947161674 s Estimating background... Estimating background took 13.0534110069 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.23258709908 s Creating peak regions... Creating peak regions took 43.707955122 s Estimating background... Estimating background took 15.0070841312 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.33848905563 s Creating peak regions... Creating peak regions took 44.6836621761 s Estimating background... Estimating background took 16.6338698864 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.32699108124 s Creating peak regions... Creating peak regions took 37.2054610252 s Estimating background... Estimating background took 16.2354810238 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.89461994171 s Creating peak regions... Creating peak regions took 37.9655110836 s Estimating background... Estimating background took 11.5721130371 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 1.57023406029 s Creating peak regions... Creating peak regions took 33.1724319458 s Estimating background... Estimating background took 11.8999950886 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0750761032104 s Creating peak regions... Creating peak regions took 0.151082992554 s Estimating background... Estimating background took 0.548811912537 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 2.20586919785 s Creating peak regions... Creating peak regions took 38.9950969219 s Estimating background... Estimating background took 14.2468891144 s Processing ZNF28-SRR5197104.hg20-male.36mers.unique.bam Reading in data... Reading data took 0.0986738204956 s Creating peak regions... Creating peak regions took 12.7013599873 s Estimating background... Estimating background took 0.528696060181 s