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='control_villi_E2f3-GSM1606990/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='control_villi_E2f3-GSM1606990/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='control_villi_E2f3-GSM1606990/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='control_villi_E2f3-GSM1606990/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 control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 13.9236140251 s Creating peak regions... Creating peak regions took 52.557238102 s Estimating background... Estimating background took 212.010761976 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 15.3745779991 s Creating peak regions... Creating peak regions took 56.3225519657 s Estimating background... Estimating background took 161.101886988 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 15.7244851589 s Creating peak regions... Creating peak regions took 56.8949711323 s Estimating background... Estimating background took 170.971143961 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 15.4888989925 s Creating peak regions... Creating peak regions took 56.5342550278 s Estimating background... Estimating background took 176.436566114 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 16.8808150291 s Creating peak regions... Creating peak regions took 63.6405901909 s Estimating background... Estimating background took 166.542899132 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 14.8552649021 s Creating peak regions... Creating peak regions took 55.5241618156 s Estimating background... Estimating background took 159.420467854 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 12.9443039894 s Creating peak regions... Creating peak regions took 50.8408210278 s Estimating background... Estimating background took 157.193214178 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 11.5635659695 s Creating peak regions... Creating peak regions took 46.3580219746 s Estimating background... Estimating background took 133.607920885 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 12.0987069607 s Creating peak regions... Creating peak regions took 43.5129160881 s Estimating background... Estimating background took 140.349994898 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 7.69521403313 s Creating peak regions... Creating peak regions took 30.5565769672 s Estimating background... Estimating background took 90.7119300365 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 24.6544370651 s Creating peak regions... Creating peak regions took 97.3002979755 s Estimating background... Estimating background took 304.293956995 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.620774030685 s Creating peak regions... Creating peak regions took 1.38474416733 s Estimating background... Estimating background took 0.428164958954 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0942149162292 s Creating peak regions... Creating peak regions took 0.366591930389 s Estimating background... Estimating background took 0.524947166443 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0575950145721 s Creating peak regions... Creating peak regions took 0.246897935867 s Estimating background... Estimating background took 0.447103977203 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0537221431732 s Creating peak regions... Creating peak regions took 0.305139064789 s Estimating background... Estimating background took 0.412676095963 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 31.1099221706 s Creating peak regions... Creating peak regions took 94.0213749409 s Estimating background... Estimating background took 273.896056175 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 30.9201958179 s Creating peak regions... Creating peak regions took 82.7876410484 s Estimating background... Estimating background took 256.629763126 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 26.5301470757 s Creating peak regions... Creating peak regions took 84.8960170746 s Estimating background... Estimating background took 229.006186008 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 1.01831912994 s Creating peak regions... Creating peak regions took 0.36691904068 s Estimating background... Estimating background took 0.517596960068 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0653867721558 s Creating peak regions... Creating peak regions took 0.0570349693298 s Estimating background... Estimating background took 0.446260929108 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0580871105194 s Creating peak regions... Creating peak regions took 0.00336885452271 s Estimating background... Estimating background took 0.419897079468 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 19.0898358822 s Creating peak regions... Creating peak regions took 77.8434569836 s Estimating background... Estimating background took 214.895500898 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.906191825867 s Creating peak regions... Creating peak regions took 0.458874940872 s Estimating background... Estimating background took 0.42227602005 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0423789024353 s Creating peak regions... Creating peak regions took 0.243834018707 s Estimating background... Estimating background took 0.439743995667 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0657389163971 s Creating peak regions... Creating peak regions took 1.35438799858 s Estimating background... Estimating background took 0.417331933975 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 20.286547184 s Creating peak regions... Creating peak regions took 70.0474140644 s Estimating background... Estimating background took 234.469136 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 24.3614890575 s Creating peak regions... Creating peak regions took 69.3765947819 s Estimating background... Estimating background took 179.3140769 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 17.6315481663 s Creating peak regions... Creating peak regions took 65.1145210266 s Estimating background... Estimating background took 188.295284033 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 19.8262329102 s Creating peak regions... Creating peak regions took 63.1744968891 s Estimating background... Estimating background took 170.099906206 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 1.04854798317 s Creating peak regions... Creating peak regions took 0.303766012192 s Estimating background... Estimating background took 0.587936878204 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0683269500732 s Creating peak regions... Creating peak regions took 0.0860879421234 s Estimating background... Estimating background took 0.600782155991 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0649800300598 s Creating peak regions... Creating peak regions took 0.061094045639 s Estimating background... Estimating background took 0.396363973618 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0949690341949 s Creating peak regions... Creating peak regions took 0.0810029506683 s Estimating background... Estimating background took 0.411660909653 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0637619495392 s Creating peak regions... Creating peak regions took 0.0891709327698 s Estimating background... Estimating background took 0.443627119064 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0974879264832 s Creating peak regions... Creating peak regions took 0.0845580101013 s Estimating background... Estimating background took 0.434442043304 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0659201145172 s Creating peak regions... Creating peak regions took 0.0660150051117 s Estimating background... Estimating background took 0.426387071609 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0689899921417 s Creating peak regions... Creating peak regions took 0.0652298927307 s Estimating background... Estimating background took 0.502051115036 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0840268135071 s Creating peak regions... Creating peak regions took 0.0539381504059 s Estimating background... Estimating background took 0.399391174316 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0668730735779 s Creating peak regions... Creating peak regions took 0.0743889808655 s Estimating background... Estimating background took 0.407118082047 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0879778862 s Creating peak regions... Creating peak regions took 0.131480932236 s Estimating background... Estimating background took 0.402822971344 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.10115981102 s Creating peak regions... Creating peak regions took 0.081974029541 s Estimating background... Estimating background took 0.404881000519 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0843780040741 s Creating peak regions... Creating peak regions took 0.0573160648346 s Estimating background... Estimating background took 0.408193826675 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.222491025925 s Creating peak regions... Creating peak regions took 0.0743517875671 s Estimating background... Estimating background took 0.7334420681 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0953121185303 s Creating peak regions... Creating peak regions took 0.0784919261932 s Estimating background... Estimating background took 0.449244022369 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.063560962677 s Creating peak regions... Creating peak regions took 0.069305896759 s Estimating background... Estimating background took 0.447381019592 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 1.38121700287 s Creating peak regions... Creating peak regions took 0.040894985199 s Estimating background... Estimating background took 1.09627795219 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.139819860458 s Creating peak regions... Creating peak regions took 0.0549008846283 s Estimating background... Estimating background took 0.493498086929 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.381123065948 s Creating peak regions... Creating peak regions took 0.0371088981628 s Estimating background... Estimating background took 0.585257053375 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.113732814789 s Creating peak regions... Creating peak regions took 0.112089157104 s Estimating background... Estimating background took 0.515422105789 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.0918169021606 s Creating peak regions... Creating peak regions took 0.0710790157318 s Estimating background... Estimating background took 0.448166131973 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.150886058807 s Creating peak regions... Creating peak regions took 0.0550789833069 s Estimating background... Estimating background took 0.551480054855 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.534728050232 s Creating peak regions... Creating peak regions took 0.227024078369 s Estimating background... Estimating background took 1.46456384659 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 17.1579420567 s Creating peak regions... Creating peak regions took 74.696352005 s Estimating background... Estimating background took 159.219220161 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 1.33305215836 s Creating peak regions... Creating peak regions took 0.912311077118 s Estimating background... Estimating background took 0.771901845932 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Reading data took 0.37114906311 s Creating peak regions... Creating peak regions took 38.9825868607 s Estimating background... Estimating background took 1.53982996941 s Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data... Processing control_villi_E2f3-GSM1606990/aligned.36mers.unique.bam Reading in data...