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_IRF4_rep2-GSM2259189/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_IRF4_rep2-GSM2259189/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_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 3.62295198441 s Creating peak regions... Creating peak regions took 32.9822969437 s Estimating background... Estimating background took 8.6475250721 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 3.75331306458 s Creating peak regions... Creating peak regions took 38.1308019161 s Estimating background... Estimating background took 7.76586484909 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 2.9575510025 s Creating peak regions... Creating peak regions took 34.523553133 s Estimating background... Estimating background took 6.45115303993 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 3.1152369976 s Creating peak regions... Creating peak regions took 38.086233139 s Estimating background... Estimating background took 7.03475308418 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 2.97546291351 s Creating peak regions... Creating peak regions took 33.7791860104 s Estimating background... Estimating background took 5.76344203949 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 3.03791904449 s Creating peak regions... Creating peak regions took 29.8928480148 s Estimating background... Estimating background took 5.94125699997 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 2.69419503212 s Creating peak regions... Creating peak regions took 31.8690550327 s Estimating background... Estimating background took 5.46920919418 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 2.80877709389 s Creating peak regions... Creating peak regions took 24.7532150745 s Estimating background... Estimating background took 5.18596100807 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 2.49786782265 s Creating peak regions... Creating peak regions took 26.2958939075 s Estimating background... Estimating background took 4.47629714012 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 1.61762690544 s Creating peak regions... Creating peak regions took 16.6228890419 s Estimating background... Estimating background took 3.70192408562 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 4.69262385368 s Creating peak regions... Creating peak regions took 51.955439806 s Estimating background... Estimating background took 9.98574018478 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.096489906311 s Creating peak regions... Creating peak regions took 0.370820045471 s Estimating background... Estimating background took 0.265520095825 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0540828704834 s Creating peak regions... Creating peak regions took 0.226222991943 s Estimating background... Estimating background took 0.262686014175 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0591418743134 s Creating peak regions... Creating peak regions took 0.200830936432 s Estimating background... Estimating background took 0.290515899658 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0472390651703 s Creating peak regions... Creating peak regions took 0.188899040222 s Estimating background... Estimating background took 0.260495901108 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 6.39971518517 s Creating peak regions... Creating peak regions took 46.5983150005 s Estimating background... Estimating background took 10.0216858387 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 4.15796899796 s Creating peak regions... Creating peak regions took 42.7511160374 s Estimating background... Estimating background took 8.13831996918 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 4.06138586998 s Creating peak regions... Creating peak regions took 45.0585970879 s Estimating background... Estimating background took 7.92483592033 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0727510452271 s Creating peak regions... Creating peak regions took 0.188770771027 s Estimating background... Estimating background took 0.33665394783 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0474579334259 s Creating peak regions... Creating peak regions took 0.0234110355377 s Estimating background... Estimating background took 0.345618963242 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0596859455109 s Creating peak regions... Creating peak regions took 0.00321698188782 s Estimating background... Estimating background took 0.312653064728 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 3.95439505577 s Creating peak regions... Creating peak regions took 40.0050132275 s Estimating background... Estimating background took 7.29241800308 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0643649101257 s Creating peak regions... Creating peak regions took 0.246261119843 s Estimating background... Estimating background took 0.362203121185 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0394539833069 s Creating peak regions... Creating peak regions took 0.537574052811 s Estimating background... Estimating background took 0.316097974777 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 3.52889204025 s Creating peak regions... Creating peak regions took 37.6576349735 s Estimating background... Estimating background took 7.34026789665 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 3.9695379734 s Creating peak regions... Creating peak regions took 34.4220561981 s Estimating background... Estimating background took 7.10718202591 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 2.65287208557 s Creating peak regions... Creating peak regions took 34.5395870209 s Estimating background... Estimating background took 6.30756616592 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 4.00981020927 s Creating peak regions... Creating peak regions took 35.8819088936 s Estimating background... Estimating background took 7.33326005936 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.162956953049 s Creating peak regions... Creating peak regions took 0.153928995132 s Estimating background... Estimating background took 0.320978164673 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0755958557129 s Creating peak regions... Creating peak regions took 0.0809881687164 s Estimating background... Estimating background took 0.344809055328 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0658981800079 s Creating peak regions... Creating peak regions took 0.0335371494293 s Estimating background... Estimating background took 0.343798160553 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0495550632477 s Creating peak regions... Creating peak regions took 0.043004989624 s Estimating background... Estimating background took 0.329079151154 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0541210174561 s Creating peak regions... Creating peak regions took 0.0825850963593 s Estimating background... Estimating background took 0.34531712532 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.077467918396 s Creating peak regions... Creating peak regions took 0.0844101905823 s Estimating background... Estimating background took 0.345756053925 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0543520450592 s Creating peak regions... Creating peak regions took 0.035120010376 s Estimating background... Estimating background took 0.353045225143 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.054190158844 s Creating peak regions... Creating peak regions took 0.0484628677368 s Estimating background... Estimating background took 0.344685792923 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0519740581512 s Creating peak regions... Creating peak regions took 0.0471489429474 s Estimating background... Estimating background took 0.342126846313 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0553538799286 s Creating peak regions... Creating peak regions took 0.0429818630219 s Estimating background... Estimating background took 0.320554971695 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0532999038696 s Creating peak regions... Creating peak regions took 0.115722894669 s Estimating background... Estimating background took 0.347029924393 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0494830608368 s Creating peak regions... Creating peak regions took 0.0328891277313 s Estimating background... Estimating background took 0.325953006744 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0651490688324 s Creating peak regions... Creating peak regions took 0.0348300933838 s Estimating background... Estimating background took 0.351012945175 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0777349472046 s Creating peak regions... Creating peak regions took 0.0751810073853 s Estimating background... Estimating background took 0.331254005432 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0762510299683 s Creating peak regions... Creating peak regions took 0.061203956604 s Estimating background... Estimating background took 0.327758073807 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0666999816895 s Creating peak regions... Creating peak regions took 0.0480599403381 s Estimating background... Estimating background took 0.310738801956 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.427717924118 s Creating peak regions... Creating peak regions took 0.0454671382904 s Estimating background... Estimating background took 0.53450012207 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0648970603943 s Creating peak regions... Creating peak regions took 0.091048002243 s Estimating background... Estimating background took 0.292407989502 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.142803907394 s Creating peak regions... Creating peak regions took 0.064915895462 s Estimating background... Estimating background took 0.298114061356 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0570631027222 s Creating peak regions... Creating peak regions took 0.106687068939 s Estimating background... Estimating background took 0.302538156509 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0485649108887 s Creating peak regions... Creating peak regions took 0.0318670272827 s Estimating background... Estimating background took 0.299120903015 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0839622020721 s Creating peak regions... Creating peak regions took 0.0639688968658 s Estimating background... Estimating background took 0.279299020767 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.127462863922 s Creating peak regions... Creating peak regions took 0.193755149841 s Estimating background... Estimating background took 1.31936597824 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 3.09189200401 s Creating peak regions... Creating peak regions took 42.4528369904 s Estimating background... Estimating background took 6.48353099823 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0674939155579 s Creating peak regions... Creating peak regions took 0.292652845383 s Estimating background... Estimating background took 0.292687892914 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Reading data took 0.0726292133331 s Creating peak regions... Creating peak regions took 19.3782548904 s Estimating background... Estimating background took 0.325083971024 s Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data... Processing exo_IRF4_rep2-GSM2259189/aligned.36mers.unique.bam Reading in data...