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/female.mm10.chrom.sizes', e4='PeakXus', fastq='TAL1_G1E-ER4_0h_Rep2-GSM1689025/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='TAL1_G1E-ER4_0h_Rep2-GSM1689025/', 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='TAL1_G1E-ER4_0h_Rep2-GSM1689025/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='TAL1_G1E-ER4_0h_Rep2-GSM1689025/', 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 TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.39839887619 s Creating peak regions... Creating peak regions took 27.1825170517 s Estimating background... Estimating background took 0.201780080795 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.482151031494 s Creating peak regions... Creating peak regions took 28.2176520824 s Estimating background... Estimating background took 0.181465864182 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.435468912125 s Creating peak regions... Creating peak regions took 25.8836300373 s Estimating background... Estimating background took 0.21502494812 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.462368011475 s Creating peak regions... Creating peak regions took 27.993778944 s Estimating background... Estimating background took 0.212326049805 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.486173868179 s Creating peak regions... Creating peak regions took 27.8193449974 s Estimating background... Estimating background took 0.203149080276 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.409106969833 s Creating peak regions... Creating peak regions took 22.1142568588 s Estimating background... Estimating background took 0.202404975891 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.370307922363 s Creating peak regions... Creating peak regions took 20.6163270473 s Estimating background... Estimating background took 0.225796937943 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.374479055405 s Creating peak regions... Creating peak regions took 20.5764307976 s Estimating background... Estimating background took 0.207350969315 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.318133115768 s Creating peak regions... Creating peak regions took 23.199146986 s Estimating background... Estimating background took 0.226323127747 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.290480136871 s Creating peak regions... Creating peak regions took 13.3080160618 s Estimating background... Estimating background took 0.214872121811 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.946928977966 s Creating peak regions... Creating peak regions took 41.508223772 s Estimating background... Estimating background took 0.357106924057 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0491740703583 s Creating peak regions... Creating peak regions took 0.140016078949 s Estimating background... Estimating background took 0.246309041977 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0292899608612 s Creating peak regions... Creating peak regions took 0.165908098221 s Estimating background... Estimating background took 0.247840166092 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0421998500824 s Creating peak regions... Creating peak regions took 0.166922807693 s Estimating background... Estimating background took 0.25177192688 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.801650047302 s Creating peak regions... Creating peak regions took 37.2588379383 s Estimating background... Estimating background took 0.360064029694 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.635580778122 s Creating peak regions... Creating peak regions took 32.2954690456 s Estimating background... Estimating background took 0.262961149216 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.658821105957 s Creating peak regions... Creating peak regions took 33.4095261097 s Estimating background... Estimating background took 0.23312997818 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0561850070953 s Creating peak regions... Creating peak regions took 0.0950028896332 s Estimating background... Estimating background took 0.258110046387 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.507723093033 s Creating peak regions... Creating peak regions took 31.7975981236 s Estimating background... Estimating background took 0.380840063095 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.529658079147 s Creating peak regions... Creating peak regions took 33.8232159615 s Estimating background... Estimating background took 0.287940979004 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.648046970367 s Creating peak regions... Creating peak regions took 35.2230360508 s Estimating background... Estimating background took 0.362287044525 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.551455020905 s Creating peak regions... Creating peak regions took 27.7378380299 s Estimating background... Estimating background took 0.358645915985 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.646111965179 s Creating peak regions... Creating peak regions took 26.4347150326 s Estimating background... Estimating background took 0.361840963364 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0564839839935 s Creating peak regions... Creating peak regions took 0.0263700485229 s Estimating background... Estimating background took 0.271228075027 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0424041748047 s Creating peak regions... Creating peak regions took 0.0807001590729 s Estimating background... Estimating background took 0.274739980698 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0202388763428 s Creating peak regions... Creating peak regions took 0.0300281047821 s Estimating background... Estimating background took 0.270649194717 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0275869369507 s Creating peak regions... Creating peak regions took 0.0316531658173 s Estimating background... Estimating background took 0.273954868317 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0177659988403 s Creating peak regions... Creating peak regions took 0.00961208343506 s Estimating background... Estimating background took 0.268726110458 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0281021595001 s Creating peak regions... Creating peak regions took 0.0510149002075 s Estimating background... Estimating background took 0.259613037109 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0539000034332 s Creating peak regions... Creating peak regions took 0.0232419967651 s Estimating background... Estimating background took 0.278476953506 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0448639392853 s Creating peak regions... Creating peak regions took 0.0480828285217 s Estimating background... Estimating background took 0.272250890732 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0521621704102 s Creating peak regions... Creating peak regions took 0.0489740371704 s Estimating background... Estimating background took 0.262758016586 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0434770584106 s Creating peak regions... Creating peak regions took 0.0932359695435 s Estimating background... Estimating background took 0.258522987366 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0320019721985 s Creating peak regions... Creating peak regions took 0.030256986618 s Estimating background... Estimating background took 0.255913972855 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0581150054932 s Creating peak regions... Creating peak regions took 0.151768922806 s Estimating background... Estimating background took 0.252380132675 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.278429985046 s Creating peak regions... Creating peak regions took 35.0609059334 s Estimating background... Estimating background took 0.259055137634 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0499751567841 s Creating peak regions... Creating peak regions took 0.312767028809 s Estimating background... Estimating background took 0.248517990112 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Reading data took 0.0410959720612 s Creating peak regions... Creating peak regions took 17.7141869068 s Estimating background... Estimating background took 0.261715173721 s Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_0h_Rep2-GSM1689025/aligned.36mers.unique.bam Reading in data...