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_24h_Rep1-GSM1689032/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_24h_Rep1-GSM1689032/', 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_24h_Rep1-GSM1689032/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_24h_Rep1-GSM1689032/', 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_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.908103942871 s Creating peak regions... Creating peak regions took 32.8584399223 s Estimating background... Estimating background took 0.244877099991 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.88415312767 s Creating peak regions... Creating peak regions took 29.6038730145 s Estimating background... Estimating background took 0.351438045502 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.821330070496 s Creating peak regions... Creating peak regions took 28.8458960056 s Estimating background... Estimating background took 0.339591026306 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.751581907272 s Creating peak regions... Creating peak regions took 28.2594518661 s Estimating background... Estimating background took 0.229543209076 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.694409132004 s Creating peak regions... Creating peak regions took 30.7464778423 s Estimating background... Estimating background took 0.332734823227 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.795283079147 s Creating peak regions... Creating peak regions took 26.2037501335 s Estimating background... Estimating background took 0.232961893082 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.645534992218 s Creating peak regions... Creating peak regions took 24.1969211102 s Estimating background... Estimating background took 0.249871015549 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.582189083099 s Creating peak regions... Creating peak regions took 23.8852579594 s Estimating background... Estimating background took 0.24321103096 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.51468205452 s Creating peak regions... Creating peak regions took 21.6432800293 s Estimating background... Estimating background took 0.239648103714 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.352454900742 s Creating peak regions... Creating peak regions took 13.9425499439 s Estimating background... Estimating background took 0.248466014862 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 1.34352302551 s Creating peak regions... Creating peak regions took 45.610806942 s Estimating background... Estimating background took 0.399312973022 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0684449672699 s Creating peak regions... Creating peak regions took 0.201453924179 s Estimating background... Estimating background took 0.268526077271 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0303161144257 s Creating peak regions... Creating peak regions took 0.228556871414 s Estimating background... Estimating background took 0.270340919495 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0296239852905 s Creating peak regions... Creating peak regions took 0.197903871536 s Estimating background... Estimating background took 0.271878957748 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0325629711151 s Creating peak regions... Creating peak regions took 0.200731039047 s Estimating background... Estimating background took 0.272344112396 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 1.71888017654 s Creating peak regions... Creating peak regions took 38.0924401283 s Estimating background... Estimating background took 0.399369001389 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.88009595871 s Creating peak regions... Creating peak regions took 36.0320048332 s Estimating background... Estimating background took 0.26930308342 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 1.03399205208 s Creating peak regions... Creating peak regions took 35.256788969 s Estimating background... Estimating background took 0.40371799469 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0620830059052 s Creating peak regions... Creating peak regions took 0.0788400173187 s Estimating background... Estimating background took 0.292441129684 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.963090896606 s Creating peak regions... Creating peak regions took 38.7480559349 s Estimating background... Estimating background took 0.411873102188 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0245170593262 s Creating peak regions... Creating peak regions took 0.470710039139 s Estimating background... Estimating background took 0.307945966721 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 1.0625398159 s Creating peak regions... Creating peak regions took 37.6522269249 s Estimating background... Estimating background took 0.417796850204 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 1.30455994606 s Creating peak regions... Creating peak regions took 36.649037838 s Estimating background... Estimating background took 0.406682014465 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.724488019943 s Creating peak regions... Creating peak regions took 30.7556869984 s Estimating background... Estimating background took 0.386913061142 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.953325033188 s Creating peak regions... Creating peak regions took 29.5751011372 s Estimating background... Estimating background took 0.379653930664 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0637137889862 s Creating peak regions... Creating peak regions took 0.02747797966 s Estimating background... Estimating background took 0.271280050278 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0451350212097 s Creating peak regions... Creating peak regions took 0.0386760234833 s Estimating background... Estimating background took 0.270549058914 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0322780609131 s Creating peak regions... Creating peak regions took 0.034658908844 s Estimating background... Estimating background took 0.2774310112 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0328130722046 s Creating peak regions... Creating peak regions took 0.0300798416138 s Estimating background... Estimating background took 0.270159006119 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0289869308472 s Creating peak regions... Creating peak regions took 0.0589880943298 s Estimating background... Estimating background took 0.271920204163 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.025267124176 s Creating peak regions... Creating peak regions took 0.030562877655 s Estimating background... Estimating background took 0.275702953339 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0959270000458 s Creating peak regions... Creating peak regions took 0.0375709533691 s Estimating background... Estimating background took 0.280888795853 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0305740833282 s Creating peak regions... Creating peak regions took 0.0351641178131 s Estimating background... Estimating background took 0.266525030136 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0364887714386 s Creating peak regions... Creating peak regions took 0.0374479293823 s Estimating background... Estimating background took 0.270392894745 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0464870929718 s Creating peak regions... Creating peak regions took 0.0940539836884 s Estimating background... Estimating background took 0.272659063339 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.040176153183 s Creating peak regions... Creating peak regions took 0.0321168899536 s Estimating background... Estimating background took 0.271234989166 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0515048503876 s Creating peak regions... Creating peak regions took 0.0331020355225 s Estimating background... Estimating background took 0.272323131561 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0426299571991 s Creating peak regions... Creating peak regions took 0.172842979431 s Estimating background... Estimating background took 0.265954017639 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.407335996628 s Creating peak regions... Creating peak regions took 38.6764371395 s Estimating background... Estimating background took 0.279761075974 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0392241477966 s Creating peak regions... Creating peak regions took 0.45269203186 s Estimating background... Estimating background took 0.280132055283 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Reading data took 0.0501899719238 s Creating peak regions... Creating peak regions took 19.6574759483 s Estimating background... Estimating background took 0.275292158127 s Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep1-GSM1689032/aligned.36mers.unique.bam Reading in data...