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='exo_BATF_rep3-GSM2259186/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='exo_BATF_rep3-GSM2259186/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 exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 4.92167115211 s Creating peak regions... Creating peak regions took 34.4566950798 s Estimating background... Estimating background took 15.6538000107 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 4.4217031002 s Creating peak regions... Creating peak regions took 32.0656487942 s Estimating background... Estimating background took 16.7226159573 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 4.64191603661 s Creating peak regions... Creating peak regions took 41.9904689789 s Estimating background... Estimating background took 12.6187810898 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 4.40973687172 s Creating peak regions... Creating peak regions took 34.4519691467 s Estimating background... Estimating background took 13.5885539055 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 3.9409160614 s Creating peak regions... Creating peak regions took 37.7257671356 s Estimating background... Estimating background took 12.1005110741 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 3.49548006058 s Creating peak regions... Creating peak regions took 27.8763680458 s Estimating background... Estimating background took 11.695704937 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 3.84247303009 s Creating peak regions... Creating peak regions took 26.4907059669 s Estimating background... Estimating background took 11.0751550198 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 3.03565001488 s Creating peak regions... Creating peak regions took 26.7690780163 s Estimating background... Estimating background took 10.7851829529 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 3.01611304283 s Creating peak regions... Creating peak regions took 25.4291141033 s Estimating background... Estimating background took 9.37851190567 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 2.23466396332 s Creating peak regions... Creating peak regions took 16.0803799629 s Estimating background... Estimating background took 7.83150291443 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 7.02829313278 s Creating peak regions... Creating peak regions took 53.8367419243 s Estimating background... Estimating background took 21.0703778267 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0684189796448 s Creating peak regions... Creating peak regions took 0.284622907639 s Estimating background... Estimating background took 0.270947933197 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0756349563599 s Creating peak regions... Creating peak regions took 0.297611951828 s Estimating background... Estimating background took 0.274677991867 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0504109859467 s Creating peak regions... Creating peak regions took 0.201597929001 s Estimating background... Estimating background took 0.281884908676 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0412721633911 s Creating peak regions... Creating peak regions took 0.247680902481 s Estimating background... Estimating background took 0.27650308609 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 7.73284697533 s Creating peak regions... Creating peak regions took 51.7298698425 s Estimating background... Estimating background took 22.0928270817 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 5.09753608704 s Creating peak regions... Creating peak regions took 41.1300339699 s Estimating background... Estimating background took 16.7462990284 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 5.38996005058 s Creating peak regions... Creating peak regions took 40.1908378601 s Estimating background... Estimating background took 15.367249012 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.151464939117 s Creating peak regions... Creating peak regions took 0.283239841461 s Estimating background... Estimating background took 0.340946912766 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0498850345612 s Creating peak regions... Creating peak regions took 0.0228290557861 s Estimating background... Estimating background took 0.35408616066 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0537061691284 s Creating peak regions... Creating peak regions took 0.00301694869995 s Estimating background... Estimating background took 0.357695817947 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 5.10594797134 s Creating peak regions... Creating peak regions took 44.947644949 s Estimating background... Estimating background took 15.6848227978 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.169229984283 s Creating peak regions... Creating peak regions took 0.339955806732 s Estimating background... Estimating background took 0.345328092575 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0481390953064 s Creating peak regions... Creating peak regions took 0.809710979462 s Estimating background... Estimating background took 0.328955888748 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 5.46459412575 s Creating peak regions... Creating peak regions took 41.3329520226 s Estimating background... Estimating background took 17.5602860451 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 4.41487908363 s Creating peak regions... Creating peak regions took 38.4694969654 s Estimating background... Estimating background took 15.534031868 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 4.18091607094 s Creating peak regions... Creating peak regions took 42.2379691601 s Estimating background... Estimating background took 12.0888860226 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 4.61531996727 s Creating peak regions... Creating peak regions took 37.2626650333 s Estimating background... Estimating background took 15.3754329681 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.338916063309 s Creating peak regions... Creating peak regions took 0.233673095703 s Estimating background... Estimating background took 0.862408161163 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0871598720551 s Creating peak regions... Creating peak regions took 0.0660049915314 s Estimating background... Estimating background took 0.347845077515 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0588619709015 s Creating peak regions... Creating peak regions took 0.0315520763397 s Estimating background... Estimating background took 0.33127117157 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0778210163116 s Creating peak regions... Creating peak regions took 0.0579309463501 s Estimating background... Estimating background took 0.329404115677 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0543768405914 s Creating peak regions... Creating peak regions took 0.0729157924652 s Estimating background... Estimating background took 0.321315050125 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0783538818359 s Creating peak regions... Creating peak regions took 0.0776710510254 s Estimating background... Estimating background took 0.324163913727 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0533668994904 s Creating peak regions... Creating peak regions took 0.0320661067963 s Estimating background... Estimating background took 0.321217060089 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0535161495209 s Creating peak regions... Creating peak regions took 0.0398049354553 s Estimating background... Estimating background took 0.322852134705 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0667328834534 s Creating peak regions... Creating peak regions took 0.0407340526581 s Estimating background... Estimating background took 0.32839512825 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0471200942993 s Creating peak regions... Creating peak regions took 0.0403339862823 s Estimating background... Estimating background took 0.326950073242 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0475940704346 s Creating peak regions... Creating peak regions took 0.0971450805664 s Estimating background... Estimating background took 0.320943117142 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0521230697632 s Creating peak regions... Creating peak regions took 0.0335850715637 s Estimating background... Estimating background took 0.324695825577 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0454788208008 s Creating peak regions... Creating peak regions took 0.0278232097626 s Estimating background... Estimating background took 0.319764137268 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0966382026672 s Creating peak regions... Creating peak regions took 0.0717499256134 s Estimating background... Estimating background took 0.325483083725 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0740768909454 s Creating peak regions... Creating peak regions took 0.0508608818054 s Estimating background... Estimating background took 0.32387304306 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0764338970184 s Creating peak regions... Creating peak regions took 0.0418429374695 s Estimating background... Estimating background took 0.320868968964 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.352823019028 s Creating peak regions... Creating peak regions took 0.0340240001678 s Estimating background... Estimating background took 0.42800784111 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0897350311279 s Creating peak regions... Creating peak regions took 0.0573120117188 s Estimating background... Estimating background took 0.321778059006 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.134036064148 s Creating peak regions... Creating peak regions took 0.0412931442261 s Estimating background... Estimating background took 0.325081110001 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0832929611206 s Creating peak regions... Creating peak regions took 0.101036787033 s Estimating background... Estimating background took 0.326559066772 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0542471408844 s Creating peak regions... Creating peak regions took 0.0430150032043 s Estimating background... Estimating background took 0.320127010345 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.0621020793915 s Creating peak regions... Creating peak regions took 0.0602869987488 s Estimating background... Estimating background took 0.318475961685 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.159302949905 s Creating peak regions... Creating peak regions took 0.202547073364 s Estimating background... Estimating background took 0.506768941879 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 5.70391392708 s Creating peak regions... Creating peak regions took 55.8632919788 s Estimating background... Estimating background took 10.6242911816 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.100867986679 s Creating peak regions... Creating peak regions took 0.416548013687 s Estimating background... Estimating background took 0.351562023163 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Reading data took 0.051600933075 s Creating peak regions... Creating peak regions took 20.6434998512 s Estimating background... Estimating background took 0.369025945663 s Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep3-GSM2259186/aligned.36mers.unique.bam Reading in data...