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_rep1-GSM2259184/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_rep1-GSM2259184/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_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 4.38531780243 s Creating peak regions... Creating peak regions took 34.3998630047 s Estimating background... Estimating background took 21.7849440575 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 4.55789685249 s Creating peak regions... Creating peak regions took 37.3338930607 s Estimating background... Estimating background took 22.8205358982 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 3.78923106194 s Creating peak regions... Creating peak regions took 30.8521909714 s Estimating background... Estimating background took 17.5506980419 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 3.92642307281 s Creating peak regions... Creating peak regions took 31.649422884 s Estimating background... Estimating background took 19.7342500687 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 3.18658399582 s Creating peak regions... Creating peak regions took 33.4317080975 s Estimating background... Estimating background took 15.7850689888 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 3.22746801376 s Creating peak regions... Creating peak regions took 29.248707056 s Estimating background... Estimating background took 17.7032401562 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 3.42909312248 s Creating peak regions... Creating peak regions took 28.2557239532 s Estimating background... Estimating background took 16.6810708046 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 3.433989048 s Creating peak regions... Creating peak regions took 29.4563241005 s Estimating background... Estimating background took 15.6655888557 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 2.8551940918 s Creating peak regions... Creating peak regions took 26.5973610878 s Estimating background... Estimating background took 13.4745020866 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 2.35839986801 s Creating peak regions... Creating peak regions took 17.497606039 s Estimating background... Estimating background took 10.6418728828 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 6.18441510201 s Creating peak regions... Creating peak regions took 57.9468889236 s Estimating background... Estimating background took 30.6094651222 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.140814065933 s Creating peak regions... Creating peak regions took 0.512360095978 s Estimating background... Estimating background took 0.286543130875 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0845620632172 s Creating peak regions... Creating peak regions took 0.390398979187 s Estimating background... Estimating background took 0.279340028763 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0815949440002 s Creating peak regions... Creating peak regions took 0.25283908844 s Estimating background... Estimating background took 0.289521217346 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0533139705658 s Creating peak regions... Creating peak regions took 0.318181037903 s Estimating background... Estimating background took 0.278748989105 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 7.47441101074 s Creating peak regions... Creating peak regions took 48.4970569611 s Estimating background... Estimating background took 30.9259500504 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 6.06025600433 s Creating peak regions... Creating peak regions took 48.4906859398 s Estimating background... Estimating background took 24.7276830673 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 5.24644207954 s Creating peak regions... Creating peak regions took 43.3918118477 s Estimating background... Estimating background took 24.4479129314 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.460802078247 s Creating peak regions... Creating peak regions took 0.514404058456 s Estimating background... Estimating background took 0.34473490715 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0693440437317 s Creating peak regions... Creating peak regions took 0.0233850479126 s Estimating background... Estimating background took 0.318915128708 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0526988506317 s Creating peak regions... Creating peak regions took 0.00312495231628 s Estimating background... Estimating background took 0.321613073349 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 5.03490996361 s Creating peak regions... Creating peak regions took 44.4622280598 s Estimating background... Estimating background took 23.1465778351 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.285238027573 s Creating peak regions... Creating peak regions took 0.352072000504 s Estimating background... Estimating background took 0.340991020203 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0536839962006 s Creating peak regions... Creating peak regions took 1.14954900742 s Estimating background... Estimating background took 0.365232944489 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 5.1965739727 s Creating peak regions... Creating peak regions took 41.9289019108 s Estimating background... Estimating background took 25.66248703 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 4.78406596184 s Creating peak regions... Creating peak regions took 42.2993240356 s Estimating background... Estimating background took 22.6992781162 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 4.30658006668 s Creating peak regions... Creating peak regions took 37.6574280262 s Estimating background... Estimating background took 18.7934858799 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 4.53609704971 s Creating peak regions... Creating peak regions took 38.637871027 s Estimating background... Estimating background took 23.7606270313 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.502614974976 s Creating peak regions... Creating peak regions took 0.312518835068 s Estimating background... Estimating background took 0.950618982315 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0747470855713 s Creating peak regions... Creating peak regions took 0.0772800445557 s Estimating background... Estimating background took 0.335530996323 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.077730178833 s Creating peak regions... Creating peak regions took 0.0400049686432 s Estimating background... Estimating background took 0.330430984497 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.052442073822 s Creating peak regions... Creating peak regions took 0.0501260757446 s Estimating background... Estimating background took 0.329226970673 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0629870891571 s Creating peak regions... Creating peak regions took 0.0666830539703 s Estimating background... Estimating background took 0.327558994293 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0805070400238 s Creating peak regions... Creating peak regions took 0.0852990150452 s Estimating background... Estimating background took 0.34260392189 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0577790737152 s Creating peak regions... Creating peak regions took 0.0386509895325 s Estimating background... Estimating background took 0.344261169434 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0791010856628 s Creating peak regions... Creating peak regions took 0.0478930473328 s Estimating background... Estimating background took 0.321073055267 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0777490139008 s Creating peak regions... Creating peak regions took 0.0430548191071 s Estimating background... Estimating background took 0.337630033493 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0657289028168 s Creating peak regions... Creating peak regions took 0.0494999885559 s Estimating background... Estimating background took 0.342725038528 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0608220100403 s Creating peak regions... Creating peak regions took 0.124599933624 s Estimating background... Estimating background took 0.335739135742 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0771069526672 s Creating peak regions... Creating peak regions took 0.0446789264679 s Estimating background... Estimating background took 0.324309825897 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0765738487244 s Creating peak regions... Creating peak regions took 0.038722038269 s Estimating background... Estimating background took 0.32473897934 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0975439548492 s Creating peak regions... Creating peak regions took 0.0775530338287 s Estimating background... Estimating background took 0.324573040009 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0523731708527 s Creating peak regions... Creating peak regions took 0.0482800006866 s Estimating background... Estimating background took 0.328526973724 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0795431137085 s Creating peak regions... Creating peak regions took 0.049309015274 s Estimating background... Estimating background took 0.342381954193 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.378684043884 s Creating peak regions... Creating peak regions took 0.0323059558868 s Estimating background... Estimating background took 0.450536966324 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0939710140228 s Creating peak regions... Creating peak regions took 0.0794489383698 s Estimating background... Estimating background took 0.344549894333 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.117475032806 s Creating peak regions... Creating peak regions took 0.0506801605225 s Estimating background... Estimating background took 0.428529977798 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0812559127808 s Creating peak regions... Creating peak regions took 0.0990569591522 s Estimating background... Estimating background took 0.350195169449 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0778839588165 s Creating peak regions... Creating peak regions took 0.0425429344177 s Estimating background... Estimating background took 0.353314876556 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.0669710636139 s Creating peak regions... Creating peak regions took 0.0580930709839 s Estimating background... Estimating background took 0.345692873001 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.161635875702 s Creating peak regions... Creating peak regions took 0.18892288208 s Estimating background... Estimating background took 0.749310016632 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 4.70875096321 s Creating peak regions... Creating peak regions took 50.1924388409 s Estimating background... Estimating background took 16.1228289604 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.153618097305 s Creating peak regions... Creating peak regions took 0.431529998779 s Estimating background... Estimating background took 0.349365949631 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Reading data took 0.085578918457 s Creating peak regions... Creating peak regions took 21.1429948807 s Estimating background... Estimating background took 0.350898981094 s Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data... Processing exo_BATF_rep1-GSM2259184/aligned.36mers.unique.bam Reading in data...