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/mm10.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes', e4='PeakXus', fastq='ChIP_exo_Onecut1_day5-GSM2098377/alignments.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='ChIP_exo_Onecut1_day5-GSM2098377/peakXus/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)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/mm10.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes', e4='PeakXus', fastq='ChIP_exo_Onecut1_day5-GSM2098377/aligned.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='ChIP_exo_Onecut1_day5-GSM2098377/peakXus/', p3=1.0, p7=1, q2=20, s3=1, skip0=0, t2=1, title5='PeakXus', verbosity=1, w3=5, w4=100, wg7=None)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/mm10.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes', e4='PeakXus', fastq='ChIP_exo_Onecut1_day5-GSM2098377/aligned.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='ChIP_exo_Onecut1_day5-GSM2098377/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 ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 2.57811617851 s Creating peak regions... Creating peak regions took 31.04368186 s Estimating background... Estimating background took 5.72156190872 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 2.6217751503 s Creating peak regions... Creating peak regions took 32.2756209373 s Estimating background... Estimating background took 5.32841396332 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 2.30774307251 s Creating peak regions... Creating peak regions took 27.5218651295 s Estimating background... Estimating background took 4.950289011 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 2.16486120224 s Creating peak regions... Creating peak regions took 27.9634828568 s Estimating background... Estimating background took 5.35636997223 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 1.88354682922 s Creating peak regions... Creating peak regions took 29.6240060329 s Estimating background... Estimating background took 5.50133895874 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 2.11378407478 s Creating peak regions... Creating peak regions took 24.9980139732 s Estimating background... Estimating background took 4.86912512779 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 1.87388682365 s Creating peak regions... Creating peak regions took 24.1436421871 s Estimating background... Estimating background took 4.68848514557 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 1.733700037 s Creating peak regions... Creating peak regions took 22.3293220997 s Estimating background... Estimating background took 2.16504406929 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 1.77642393112 s Creating peak regions... Creating peak regions took 22.6482129097 s Estimating background... Estimating background took 4.51818799973 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 1.09128379822 s Creating peak regions... Creating peak regions took 15.501609087 s Estimating background... Estimating background took 3.01692414284 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 3.70652604103 s Creating peak regions... Creating peak regions took 50.9673581123 s Estimating background... Estimating background took 9.23576211929 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0375170707703 s Creating peak regions... Creating peak regions took 0.115494966507 s Estimating background... Estimating background took 0.326020002365 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0653719902039 s Creating peak regions... Creating peak regions took 0.125321865082 s Estimating background... Estimating background took 0.338734865189 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0664439201355 s Creating peak regions... Creating peak regions took 0.113256216049 s Estimating background... Estimating background took 0.327826023102 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0358588695526 s Creating peak regions... Creating peak regions took 0.118175983429 s Estimating background... Estimating background took 0.339216947556 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 3.53413105011 s Creating peak regions... Creating peak regions took 47.5762789249 s Estimating background... Estimating background took 9.00754880905 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 2.83358812332 s Creating peak regions... Creating peak regions took 39.9681708813 s Estimating background... Estimating background took 8.52441287041 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 3.16968798637 s Creating peak regions... Creating peak regions took 43.6594250202 s Estimating background... Estimating background took 7.10443902016 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0542669296265 s Creating peak regions... Creating peak regions took 0.0796091556549 s Estimating background... Estimating background took 0.32994890213 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 3.15656280518 s Creating peak regions... Creating peak regions took 42.6215250492 s Estimating background... Estimating background took 6.55569005013 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0326411724091 s Creating peak regions... Creating peak regions took 0.321427822113 s Estimating background... Estimating background took 0.342381954193 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 2.69123101234 s Creating peak regions... Creating peak regions took 40.3644869328 s Estimating background... Estimating background took 7.50607395172 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 2.09647893906 s Creating peak regions... Creating peak regions took 34.6360011101 s Estimating background... Estimating background took 5.82704401016 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 2.2336769104 s Creating peak regions... Creating peak regions took 35.3721101284 s Estimating background... Estimating background took 6.81650114059 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 2.17106580734 s Creating peak regions... Creating peak regions took 29.9934399128 s Estimating background... Estimating background took 5.71115708351 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0662400722504 s Creating peak regions... Creating peak regions took 0.0896258354187 s Estimating background... Estimating background took 0.294683933258 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0659880638123 s Creating peak regions... Creating peak regions took 0.0507128238678 s Estimating background... Estimating background took 0.332524061203 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0692009925842 s Creating peak regions... Creating peak regions took 0.0324261188507 s Estimating background... Estimating background took 0.326305866241 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0761861801147 s Creating peak regions... Creating peak regions took 0.0564758777618 s Estimating background... Estimating background took 0.312738180161 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0477290153503 s Creating peak regions... Creating peak regions took 0.0503880977631 s Estimating background... Estimating background took 0.308813810349 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0673940181732 s Creating peak regions... Creating peak regions took 0.0545220375061 s Estimating background... Estimating background took 0.307585954666 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0674650669098 s Creating peak regions... Creating peak regions took 0.0268640518188 s Estimating background... Estimating background took 0.334001064301 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0692489147186 s Creating peak regions... Creating peak regions took 0.0296139717102 s Estimating background... Estimating background took 0.337517023087 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0667059421539 s Creating peak regions... Creating peak regions took 0.0400371551514 s Estimating background... Estimating background took 0.337530136108 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0706870555878 s Creating peak regions... Creating peak regions took 0.0425379276276 s Estimating background... Estimating background took 0.352488040924 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0699632167816 s Creating peak regions... Creating peak regions took 0.092376947403 s Estimating background... Estimating background took 0.338764190674 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0682680606842 s Creating peak regions... Creating peak regions took 0.0255270004272 s Estimating background... Estimating background took 0.342705965042 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0437409877777 s Creating peak regions... Creating peak regions took 0.0610687732697 s Estimating background... Estimating background took 0.338563203812 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0692558288574 s Creating peak regions... Creating peak regions took 0.0402522087097 s Estimating background... Estimating background took 0.34799695015 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0684769153595 s Creating peak regions... Creating peak regions took 0.0290110111237 s Estimating background... Estimating background took 0.339568138123 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.122619152069 s Creating peak regions... Creating peak regions took 0.039932012558 s Estimating background... Estimating background took 0.342661857605 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0520880222321 s Creating peak regions... Creating peak regions took 0.0393388271332 s Estimating background... Estimating background took 0.33776307106 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0621120929718 s Creating peak regions... Creating peak regions took 0.0499579906464 s Estimating background... Estimating background took 0.338924884796 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0721991062164 s Creating peak regions... Creating peak regions took 0.0793199539185 s Estimating background... Estimating background took 0.338249921799 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0699541568756 s Creating peak regions... Creating peak regions took 0.0365078449249 s Estimating background... Estimating background took 0.339764118195 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0685000419617 s Creating peak regions... Creating peak regions took 0.040454864502 s Estimating background... Estimating background took 0.322329998016 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.090656042099 s Creating peak regions... Creating peak regions took 0.143568992615 s Estimating background... Estimating background took 0.312256097794 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 1.60606789589 s Creating peak regions... Creating peak regions took 40.2028768063 s Estimating background... Estimating background took 1.62638902664 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0999150276184 s Creating peak regions... Creating peak regions took 0.273952960968 s Estimating background... Estimating background took 0.317363023758 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Reading data took 0.0880718231201 s Creating peak regions... Creating peak regions took 18.7205479145 s Estimating background... Estimating background took 0.348182916641 s Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Onecut1_day5-GSM2098377/aligned.36mers.unique.bam Reading in data...