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_villi_E2f3-GSM1606986/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_villi_E2f3-GSM1606986/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_villi_E2f3-GSM1606986/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_villi_E2f3-GSM1606986/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_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 9.38714122772 s Creating peak regions... Creating peak regions took 42.6072580814 s Estimating background... Estimating background took 100.035878897 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 8.60853910446 s Creating peak regions... Creating peak regions took 41.3147530556 s Estimating background... Estimating background took 80.47103405 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 9.04870700836 s Creating peak regions... Creating peak regions took 44.9583170414 s Estimating background... Estimating background took 88.4091100693 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 9.47976613045 s Creating peak regions... Creating peak regions took 45.4658339024 s Estimating background... Estimating background took 91.1296601295 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 10.6863319874 s Creating peak regions... Creating peak regions took 48.7257630825 s Estimating background... Estimating background took 93.6677110195 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 7.68620109558 s Creating peak regions... Creating peak regions took 40.0835340023 s Estimating background... Estimating background took 76.3933291435 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 8.48468899727 s Creating peak regions... Creating peak regions took 41.0616719723 s Estimating background... Estimating background took 81.4896478653 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 7.23053598404 s Creating peak regions... Creating peak regions took 33.3618888855 s Estimating background... Estimating background took 64.6850819588 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 7.9603729248 s Creating peak regions... Creating peak regions took 38.396517992 s Estimating background... Estimating background took 67.0826711655 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 4.72047400475 s Creating peak regions... Creating peak regions took 24.3456070423 s Estimating background... Estimating background took 43.4757969379 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 15.431240797 s Creating peak regions... Creating peak regions took 72.4277639389 s Estimating background... Estimating background took 153.560409069 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.395342111588 s Creating peak regions... Creating peak regions took 0.812319993973 s Estimating background... Estimating background took 0.343256950378 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0807909965515 s Creating peak regions... Creating peak regions took 0.300882101059 s Estimating background... Estimating background took 0.338267087936 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0486071109772 s Creating peak regions... Creating peak regions took 0.181163787842 s Estimating background... Estimating background took 0.328686952591 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0578370094299 s Creating peak regions... Creating peak regions took 0.282157182693 s Estimating background... Estimating background took 0.34241604805 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 19.1399719715 s Creating peak regions... Creating peak regions took 81.5065989494 s Estimating background... Estimating background took 134.13780117 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 14.8534228802 s Creating peak regions... Creating peak regions took 61.0383980274 s Estimating background... Estimating background took 145.356934071 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 16.0053350925 s Creating peak regions... Creating peak regions took 76.907845974 s Estimating background... Estimating background took 119.263253927 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.77748799324 s Creating peak regions... Creating peak regions took 0.468541145325 s Estimating background... Estimating background took 0.494828939438 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0550889968872 s Creating peak regions... Creating peak regions took 0.0357058048248 s Estimating background... Estimating background took 0.404398918152 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0542070865631 s Creating peak regions... Creating peak regions took 0.00281286239624 s Estimating background... Estimating background took 0.404505968094 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 14.9106149673 s Creating peak regions... Creating peak regions took 62.7275519371 s Estimating background... Estimating background took 113.196967125 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.973464012146 s Creating peak regions... Creating peak regions took 0.480517148972 s Estimating background... Estimating background took 0.391335964203 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.052768945694 s Creating peak regions... Creating peak regions took 0.249500989914 s Estimating background... Estimating background took 0.39610004425 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0820579528809 s Creating peak regions... Creating peak regions took 0.264315843582 s Estimating background... Estimating background took 0.415355920792 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0584111213684 s Creating peak regions... Creating peak regions took 1.10184788704 s Estimating background... Estimating background took 0.362276077271 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 12.2903518677 s Creating peak regions... Creating peak regions took 59.2961139679 s Estimating background... Estimating background took 122.880697966 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 15.0039410591 s Creating peak regions... Creating peak regions took 58.1193668842 s Estimating background... Estimating background took 90.5725529194 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 10.4786789417 s Creating peak regions... Creating peak regions took 54.2564051151 s Estimating background... Estimating background took 103.558533192 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 12.3008580208 s Creating peak regions... Creating peak regions took 54.0837440491 s Estimating background... Estimating background took 97.2486898899 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 1.35124993324 s Creating peak regions... Creating peak regions took 0.371502876282 s Estimating background... Estimating background took 0.590359210968 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0844979286194 s Creating peak regions... Creating peak regions took 0.0760600566864 s Estimating background... Estimating background took 0.483824014664 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0856699943542 s Creating peak regions... Creating peak regions took 0.0782198905945 s Estimating background... Estimating background took 0.380735874176 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0831379890442 s Creating peak regions... Creating peak regions took 0.0795478820801 s Estimating background... Estimating background took 0.381575107574 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0852370262146 s Creating peak regions... Creating peak regions took 0.0963299274445 s Estimating background... Estimating background took 0.390141963959 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0640330314636 s Creating peak regions... Creating peak regions took 0.078469991684 s Estimating background... Estimating background took 0.365802049637 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0829181671143 s Creating peak regions... Creating peak regions took 0.0682089328766 s Estimating background... Estimating background took 0.393845081329 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0913968086243 s Creating peak regions... Creating peak regions took 0.0622181892395 s Estimating background... Estimating background took 0.498159885406 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0838499069214 s Creating peak regions... Creating peak regions took 0.0474109649658 s Estimating background... Estimating background took 0.387725114822 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0605659484863 s Creating peak regions... Creating peak regions took 0.0706610679626 s Estimating background... Estimating background took 0.378543138504 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.087630033493 s Creating peak regions... Creating peak regions took 0.160531997681 s Estimating background... Estimating background took 0.374215126038 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0900850296021 s Creating peak regions... Creating peak regions took 0.0643770694733 s Estimating background... Estimating background took 0.374499082565 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0584080219269 s Creating peak regions... Creating peak regions took 0.0384430885315 s Estimating background... Estimating background took 0.374366998672 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.161335945129 s Creating peak regions... Creating peak regions took 0.0764648914337 s Estimating background... Estimating background took 0.591099023819 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0816490650177 s Creating peak regions... Creating peak regions took 0.0863149166107 s Estimating background... Estimating background took 0.372529029846 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0840628147125 s Creating peak regions... Creating peak regions took 0.0919489860535 s Estimating background... Estimating background took 0.38744020462 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.962392807007 s Creating peak regions... Creating peak regions took 0.0298631191254 s Estimating background... Estimating background took 0.729058027267 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.11559009552 s Creating peak regions... Creating peak regions took 0.0495698451996 s Estimating background... Estimating background took 0.517857074738 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.319759130478 s Creating peak regions... Creating peak regions took 0.0350689888 s Estimating background... Estimating background took 0.627236843109 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.117260932922 s Creating peak regions... Creating peak regions took 0.104475021362 s Estimating background... Estimating background took 0.514127969742 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.0838680267334 s Creating peak regions... Creating peak regions took 0.063493013382 s Estimating background... Estimating background took 0.407674074173 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.128259897232 s Creating peak regions... Creating peak regions took 0.0487279891968 s Estimating background... Estimating background took 0.494255065918 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.37645983696 s Creating peak regions... Creating peak regions took 0.223930835724 s Estimating background... Estimating background took 1.21834993362 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 15.4643669128 s Creating peak regions... Creating peak regions took 67.2697072029 s Estimating background... Estimating background took 93.5298690796 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.883428096771 s Creating peak regions... Creating peak regions took 0.608985900879 s Estimating background... Estimating background took 0.583887815475 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Reading data took 0.214054107666 s Creating peak regions... Creating peak regions took 29.2955110073 s Estimating background... Estimating background took 0.720427036285 s Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_E2f3-GSM1606986/aligned.36mers.unique.bam Reading in data...