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_Rep3-GSM1689034/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_Rep3-GSM1689034/', 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_Rep3-GSM1689034/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_Rep3-GSM1689034/', 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_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.846098899841 s Creating peak regions... Creating peak regions took 29.6790840626 s Estimating background... Estimating background took 0.333250999451 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 1.14933609962 s Creating peak regions... Creating peak regions took 27.7946050167 s Estimating background... Estimating background took 0.431463956833 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.91348195076 s Creating peak regions... Creating peak regions took 29.4934420586 s Estimating background... Estimating background took 0.451691150665 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.767132997513 s Creating peak regions... Creating peak regions took 26.6341810226 s Estimating background... Estimating background took 0.521409034729 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.89538693428 s Creating peak regions... Creating peak regions took 29.2919521332 s Estimating background... Estimating background took 0.334764957428 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.782058000565 s Creating peak regions... Creating peak regions took 25.581651926 s Estimating background... Estimating background took 0.328602075577 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.723875045776 s Creating peak regions... Creating peak regions took 23.6361248493 s Estimating background... Estimating background took 0.34250497818 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.640189886093 s Creating peak regions... Creating peak regions took 22.3584029675 s Estimating background... Estimating background took 0.46932387352 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.70237493515 s Creating peak regions... Creating peak regions took 21.6285059452 s Estimating background... Estimating background took 0.342616081238 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.489617109299 s Creating peak regions... Creating peak regions took 14.5583431721 s Estimating background... Estimating background took 0.320869922638 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 2.14730596542 s Creating peak regions... Creating peak regions took 46.611038208 s Estimating background... Estimating background took 0.58965086937 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0826900005341 s Creating peak regions... Creating peak regions took 0.153034925461 s Estimating background... Estimating background took 0.296884059906 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0397198200226 s Creating peak regions... Creating peak regions took 0.319400072098 s Estimating background... Estimating background took 0.295938014984 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0547449588776 s Creating peak regions... Creating peak regions took 0.183042049408 s Estimating background... Estimating background took 0.291517972946 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0384290218353 s Creating peak regions... Creating peak regions took 0.34205698967 s Estimating background... Estimating background took 0.296509027481 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 1.65717697144 s Creating peak regions... Creating peak regions took 43.0332770348 s Estimating background... Estimating background took 4.4256401062 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 1.02170610428 s Creating peak regions... Creating peak regions took 37.8877007961 s Estimating background... Estimating background took 0.418228149414 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 1.41736388206 s Creating peak regions... Creating peak regions took 39.3093309402 s Estimating background... Estimating background took 0.515451908112 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0890231132507 s Creating peak regions... Creating peak regions took 0.0860819816589 s Estimating background... Estimating background took 0.307729005814 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 1.35356283188 s Creating peak regions... Creating peak regions took 37.9095249176 s Estimating background... Estimating background took 0.6363260746 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0305390357971 s Creating peak regions... Creating peak regions took 0.551936864853 s Estimating background... Estimating background took 0.313003063202 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 1.21329307556 s Creating peak regions... Creating peak regions took 34.572095871 s Estimating background... Estimating background took 0.712167978287 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 1.59193086624 s Creating peak regions... Creating peak regions took 34.652504921 s Estimating background... Estimating background took 0.718322038651 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.970234870911 s Creating peak regions... Creating peak regions took 30.7821571827 s Estimating background... Estimating background took 3.82064914703 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 1.03912210464 s Creating peak regions... Creating peak regions took 33.0385870934 s Estimating background... Estimating background took 0.642562866211 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0823888778687 s Creating peak regions... Creating peak regions took 0.044872045517 s Estimating background... Estimating background took 0.296519994736 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0349769592285 s Creating peak regions... Creating peak regions took 0.0589849948883 s Estimating background... Estimating background took 0.299062013626 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0466010570526 s Creating peak regions... Creating peak regions took 0.0308561325073 s Estimating background... Estimating background took 0.304920911789 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0515961647034 s Creating peak regions... Creating peak regions took 0.0486369132996 s Estimating background... Estimating background took 0.30251288414 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0543520450592 s Creating peak regions... Creating peak regions took 0.0683970451355 s Estimating background... Estimating background took 0.303068876266 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0537550449371 s Creating peak regions... Creating peak regions took 0.0561890602112 s Estimating background... Estimating background took 0.30018901825 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0542559623718 s Creating peak regions... Creating peak regions took 0.032644033432 s Estimating background... Estimating background took 0.304062128067 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0545558929443 s Creating peak regions... Creating peak regions took 0.0523917675018 s Estimating background... Estimating background took 0.304835796356 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0384750366211 s Creating peak regions... Creating peak regions took 0.0360779762268 s Estimating background... Estimating background took 0.305751085281 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0513560771942 s Creating peak regions... Creating peak regions took 0.110431909561 s Estimating background... Estimating background took 0.303766965866 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0545239448547 s Creating peak regions... Creating peak regions took 0.0379478931427 s Estimating background... Estimating background took 0.294762849808 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0412428379059 s Creating peak regions... Creating peak regions took 0.071849822998 s Estimating background... Estimating background took 0.293529987335 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0393369197845 s Creating peak regions... Creating peak regions took 0.0386929512024 s Estimating background... Estimating background took 0.310539007187 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.109388113022 s Creating peak regions... Creating peak regions took 0.0422821044922 s Estimating background... Estimating background took 0.296897888184 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0426790714264 s Creating peak regions... Creating peak regions took 0.0395288467407 s Estimating background... Estimating background took 0.297799110413 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0696561336517 s Creating peak regions... Creating peak regions took 0.0890009403229 s Estimating background... Estimating background took 0.296723127365 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.051411151886 s Creating peak regions... Creating peak regions took 0.0871911048889 s Estimating background... Estimating background took 0.293724060059 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0332279205322 s Creating peak regions... Creating peak regions took 0.0318830013275 s Estimating background... Estimating background took 0.294145107269 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0493280887604 s Creating peak regions... Creating peak regions took 0.192837953568 s Estimating background... Estimating background took 0.293869972229 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.53226184845 s Creating peak regions... Creating peak regions took 42.3777410984 s Estimating background... Estimating background took 0.323770046234 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0604720115662 s Creating peak regions... Creating peak regions took 0.251946926117 s Estimating background... Estimating background took 0.291375160217 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Reading data took 0.0541999340057 s Creating peak regions... Creating peak regions took 20.7547969818 s Estimating background... Estimating background took 0.295337915421 s Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_24h_Rep3-GSM1689034/aligned.36mers.unique.bam Reading in data...