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_Rep2-GSM1689021/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_Rep2-GSM1689021/', 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_Rep2-GSM1689021/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_Rep2-GSM1689021/', 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_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.893872976303 s Creating peak regions... Creating peak regions took 27.2472310066 s Estimating background... Estimating background took 0.335089921951 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.853955984116 s Creating peak regions... Creating peak regions took 27.1652970314 s Estimating background... Estimating background took 0.317824840546 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.897223949432 s Creating peak regions... Creating peak regions took 24.8287079334 s Estimating background... Estimating background took 0.310329914093 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.779341936111 s Creating peak regions... Creating peak regions took 24.9886860847 s Estimating background... Estimating background took 0.324316978455 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.864782810211 s Creating peak regions... Creating peak regions took 24.7405920029 s Estimating background... Estimating background took 0.340749025345 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.667884111404 s Creating peak regions... Creating peak regions took 22.2681398392 s Estimating background... Estimating background took 0.35342001915 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.809977054596 s Creating peak regions... Creating peak regions took 23.1943678856 s Estimating background... Estimating background took 0.349804878235 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.70099401474 s Creating peak regions... Creating peak regions took 20.3035559654 s Estimating background... Estimating background took 0.342780828476 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.670382022858 s Creating peak regions... Creating peak regions took 20.5181839466 s Estimating background... Estimating background took 0.347851037979 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.518586158752 s Creating peak regions... Creating peak regions took 13.909268856 s Estimating background... Estimating background took 0.33656001091 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 1.656031847 s Creating peak regions... Creating peak regions took 44.7569320202 s Estimating background... Estimating background took 0.488570928574 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0726959705353 s Creating peak regions... Creating peak regions took 0.105532884598 s Estimating background... Estimating background took 0.277611017227 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0497388839722 s Creating peak regions... Creating peak regions took 0.310865879059 s Estimating background... Estimating background took 0.285797834396 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0484590530396 s Creating peak regions... Creating peak regions took 0.16813993454 s Estimating background... Estimating background took 0.277971982956 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0347979068756 s Creating peak regions... Creating peak regions took 0.210953950882 s Estimating background... Estimating background took 0.286329030991 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 1.56437492371 s Creating peak regions... Creating peak regions took 38.0598239899 s Estimating background... Estimating background took 0.353090047836 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.966370820999 s Creating peak regions... Creating peak regions took 33.2857151031 s Estimating background... Estimating background took 0.363862037659 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 1.02564382553 s Creating peak regions... Creating peak regions took 32.8929889202 s Estimating background... Estimating background took 0.380645990372 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0678448677063 s Creating peak regions... Creating peak regions took 0.0736849308014 s Estimating background... Estimating background took 0.278711080551 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 1.24384593964 s Creating peak regions... Creating peak regions took 35.2239949703 s Estimating background... Estimating background took 0.381388902664 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0208089351654 s Creating peak regions... Creating peak regions took 0.530169963837 s Estimating background... Estimating background took 0.29624915123 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 1.0678858757 s Creating peak regions... Creating peak regions took 34.4683461189 s Estimating background... Estimating background took 0.381418943405 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 1.13635778427 s Creating peak regions... Creating peak regions took 31.3008139133 s Estimating background... Estimating background took 0.383176803589 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 1.00709605217 s Creating peak regions... Creating peak regions took 27.8485620022 s Estimating background... Estimating background took 0.384819984436 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 1.07283401489 s Creating peak regions... Creating peak regions took 29.7549910545 s Estimating background... Estimating background took 0.40297293663 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0705740451813 s Creating peak regions... Creating peak regions took 0.0259990692139 s Estimating background... Estimating background took 0.306062936783 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0288860797882 s Creating peak regions... Creating peak regions took 0.0515539646149 s Estimating background... Estimating background took 0.310652971268 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0243110656738 s Creating peak regions... Creating peak regions took 0.0387580394745 s Estimating background... Estimating background took 0.309283018112 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0495150089264 s Creating peak regions... Creating peak regions took 0.0366518497467 s Estimating background... Estimating background took 0.316632986069 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0471880435944 s Creating peak regions... Creating peak regions took 0.0666570663452 s Estimating background... Estimating background took 0.308220863342 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.025719165802 s Creating peak regions... Creating peak regions took 0.0363659858704 s Estimating background... Estimating background took 0.310417890549 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0329930782318 s Creating peak regions... Creating peak regions took 0.0201630592346 s Estimating background... Estimating background took 0.331793069839 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0285680294037 s Creating peak regions... Creating peak regions took 0.0541059970856 s Estimating background... Estimating background took 0.303530931473 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0347700119019 s Creating peak regions... Creating peak regions took 0.0355651378632 s Estimating background... Estimating background took 0.313195943832 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.109477996826 s Creating peak regions... Creating peak regions took 0.0195560455322 s Estimating background... Estimating background took 0.303365945816 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0425610542297 s Creating peak regions... Creating peak regions took 0.0329649448395 s Estimating background... Estimating background took 0.301932811737 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0942509174347 s Creating peak regions... Creating peak regions took 0.0603950023651 s Estimating background... Estimating background took 0.299343109131 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0431740283966 s Creating peak regions... Creating peak regions took 0.0847699642181 s Estimating background... Estimating background took 0.301055908203 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0478219985962 s Creating peak regions... Creating peak regions took 0.0311589241028 s Estimating background... Estimating background took 0.318598985672 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0522398948669 s Creating peak regions... Creating peak regions took 0.0358889102936 s Estimating background... Estimating background took 0.305557012558 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0750029087067 s Creating peak regions... Creating peak regions took 0.183837890625 s Estimating background... Estimating background took 0.299638032913 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.501862049103 s Creating peak regions... Creating peak regions took 39.0760440826 s Estimating background... Estimating background took 0.316504001617 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0548098087311 s Creating peak regions... Creating peak regions took 0.405454158783 s Estimating background... Estimating background took 0.294335842133 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Reading data took 0.0502111911774 s Creating peak regions... Creating peak regions took 17.7200090885 s Estimating background... Estimating background took 0.303618907928 s Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep2-GSM1689021/aligned.36mers.unique.bam Reading in data...