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='RbKO_crypts_E2f3-GSM1606984/alignments.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='RbKO_crypts_E2f3-GSM1606984/peakXus/', 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='RbKO_crypts_E2f3-GSM1606984/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='RbKO_crypts_E2f3-GSM1606984/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 RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 15.7622470856 s Creating peak regions... Creating peak regions took 54.8634178638 s Estimating background... Estimating background took 228.27286911 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 16.188421011 s Creating peak regions... Creating peak regions took 51.800342083 s Estimating background... Estimating background took 194.395249128 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 14.6750378609 s Creating peak regions... Creating peak regions took 53.9757139683 s Estimating background... Estimating background took 190.970817804 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 15.1619260311 s Creating peak regions... Creating peak regions took 57.5780079365 s Estimating background... Estimating background took 198.191051006 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 18.1049778461 s Creating peak regions... Creating peak regions took 67.433604002 s Estimating background... Estimating background took 191.409609795 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 15.4272360802 s Creating peak regions... Creating peak regions took 55.5221400261 s Estimating background... Estimating background took 168.29289794 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 14.8251450062 s Creating peak regions... Creating peak regions took 52.971529007 s Estimating background... Estimating background took 167.777951002 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 13.9427189827 s Creating peak regions... Creating peak regions took 47.7045938969 s Estimating background... Estimating background took 139.339688063 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 12.428221941 s Creating peak regions... Creating peak regions took 47.2721920013 s Estimating background... Estimating background took 156.294538021 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 8.35393691063 s Creating peak regions... Creating peak regions took 34.4412970543 s Estimating background... Estimating background took 101.635684967 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 25.7819900513 s Creating peak regions... Creating peak regions took 98.0552351475 s Estimating background... Estimating background took 345.326570988 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.604547023773 s Creating peak regions... Creating peak regions took 0.978253126144 s Estimating background... Estimating background took 0.48313498497 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0801129341125 s Creating peak regions... Creating peak regions took 0.347033977509 s Estimating background... Estimating background took 0.523521900177 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0914199352264 s Creating peak regions... Creating peak regions took 0.242284059525 s Estimating background... Estimating background took 0.406322956085 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0618951320648 s Creating peak regions... Creating peak regions took 0.302607059479 s Estimating background... Estimating background took 0.40749502182 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 31.584651947 s Creating peak regions... Creating peak regions took 91.1675779819 s Estimating background... Estimating background took 285.721035957 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 24.7418630123 s Creating peak regions... Creating peak regions took 87.2291679382 s Estimating background... Estimating background took 280.972129822 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 21.2692871094 s Creating peak regions... Creating peak regions took 84.1737720966 s Estimating background... Estimating background took 251.367609024 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.957481861115 s Creating peak regions... Creating peak regions took 0.406669139862 s Estimating background... Estimating background took 0.612462043762 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0591840744019 s Creating peak regions... Creating peak regions took 0.047080039978 s Estimating background... Estimating background took 0.418818950653 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0546510219574 s Creating peak regions... Creating peak regions took 0.00445294380188 s Estimating background... Estimating background took 0.436949014664 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 24.8288619518 s Creating peak regions... Creating peak regions took 78.1584248543 s Estimating background... Estimating background took 239.459642887 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 1.08517503738 s Creating peak regions... Creating peak regions took 0.345824956894 s Estimating background... Estimating background took 0.434979915619 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0608329772949 s Creating peak regions... Creating peak regions took 0.298191785812 s Estimating background... Estimating background took 0.458369016647 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0565819740295 s Creating peak regions... Creating peak regions took 0.302963972092 s Estimating background... Estimating background took 0.447748184204 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0822861194611 s Creating peak regions... Creating peak regions took 1.34963011742 s Estimating background... Estimating background took 0.460362195969 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 27.8957951069 s Creating peak regions... Creating peak regions took 75.2130560875 s Estimating background... Estimating background took 250.490231037 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 18.7247300148 s Creating peak regions... Creating peak regions took 67.2778141499 s Estimating background... Estimating background took 204.71559 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 16.8412559032 s Creating peak regions... Creating peak regions took 66.4322180748 s Estimating background... Estimating background took 220.079160213 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 22.4378249645 s Creating peak regions... Creating peak regions took 63.9087870121 s Estimating background... Estimating background took 191.196696043 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 4.34967517853 s Creating peak regions... Creating peak regions took 0.657571792603 s Estimating background... Estimating background took 0.982351064682 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0832810401917 s Creating peak regions... Creating peak regions took 0.0760681629181 s Estimating background... Estimating background took 0.646250009537 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0800950527191 s Creating peak regions... Creating peak regions took 0.0699751377106 s Estimating background... Estimating background took 0.434504985809 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.100783109665 s Creating peak regions... Creating peak regions took 0.0841770172119 s Estimating background... Estimating background took 0.454949140549 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0660197734833 s Creating peak regions... Creating peak regions took 0.0864839553833 s Estimating background... Estimating background took 0.446600914001 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0704221725464 s Creating peak regions... Creating peak regions took 0.0738561153412 s Estimating background... Estimating background took 0.553827047348 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0722641944885 s Creating peak regions... Creating peak regions took 0.0826959609985 s Estimating background... Estimating background took 0.460349082947 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.120143890381 s Creating peak regions... Creating peak regions took 0.0706779956818 s Estimating background... Estimating background took 0.572663068771 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.08669090271 s Creating peak regions... Creating peak regions took 0.0503261089325 s Estimating background... Estimating background took 0.449470043182 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0685079097748 s Creating peak regions... Creating peak regions took 0.0689289569855 s Estimating background... Estimating background took 0.465529918671 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0964078903198 s Creating peak regions... Creating peak regions took 0.131617069244 s Estimating background... Estimating background took 0.441747903824 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0879650115967 s Creating peak regions... Creating peak regions took 0.0723011493683 s Estimating background... Estimating background took 0.450885057449 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0616788864136 s Creating peak regions... Creating peak regions took 0.0597860813141 s Estimating background... Estimating background took 0.453325986862 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.189384937286 s Creating peak regions... Creating peak regions took 0.080118894577 s Estimating background... Estimating background took 0.770559072495 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0895211696625 s Creating peak regions... Creating peak regions took 0.0920441150665 s Estimating background... Estimating background took 0.442770957947 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.065171957016 s Creating peak regions... Creating peak regions took 0.0688610076904 s Estimating background... Estimating background took 0.449959993362 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 1.15078496933 s Creating peak regions... Creating peak regions took 0.0315370559692 s Estimating background... Estimating background took 0.88521695137 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.121763944626 s Creating peak regions... Creating peak regions took 0.0476899147034 s Estimating background... Estimating background took 0.656430959702 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.383629083633 s Creating peak regions... Creating peak regions took 0.0357780456543 s Estimating background... Estimating background took 0.652359008789 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.140902042389 s Creating peak regions... Creating peak regions took 0.103933095932 s Estimating background... Estimating background took 0.525882959366 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.0660531520844 s Creating peak regions... Creating peak regions took 0.057060956955 s Estimating background... Estimating background took 0.438053846359 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.110597848892 s Creating peak regions... Creating peak regions took 0.0408048629761 s Estimating background... Estimating background took 0.529156923294 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.494713783264 s Creating peak regions... Creating peak regions took 0.201382875443 s Estimating background... Estimating background took 1.36763000488 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 19.9403700829 s Creating peak regions... Creating peak regions took 73.6608819962 s Estimating background... Estimating background took 169.440714121 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 1.63345217705 s Creating peak regions... Creating peak regions took 0.69255399704 s Estimating background... Estimating background took 0.754968881607 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Reading data took 0.354007005692 s Creating peak regions... Creating peak regions took 34.4761390686 s Estimating background... Estimating background took 1.24634385109 s Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data... Processing RbKO_crypts_E2f3-GSM1606984/aligned.36mers.unique.bam Reading in data...