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='Sox2-GSM1308179/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='Sox2-GSM1308179/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='Sox2-GSM1308179/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='Sox2-GSM1308179/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 Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 9.03133893013 s Creating peak regions... Creating peak regions took 36.7411730289 s Estimating background... Estimating background took 32.8588871956 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 10.452986002 s Creating peak regions... Creating peak regions took 36.9301970005 s Estimating background... Estimating background took 41.8995211124 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 7.90271401405 s Creating peak regions... Creating peak regions took 35.0352101326 s Estimating background... Estimating background took 27.4752318859 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 8.3097910881 s Creating peak regions... Creating peak regions took 35.1721231937 s Estimating background... Estimating background took 32.5392830372 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 9.67799186707 s Creating peak regions... Creating peak regions took 41.0344121456 s Estimating background... Estimating background took 36.6519389153 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 8.13112092018 s Creating peak regions... Creating peak regions took 33.9108769894 s Estimating background... Estimating background took 25.5768129826 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 6.45338106155 s Creating peak regions... Creating peak regions took 26.7847971916 s Estimating background... Estimating background took 24.3253729343 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 7.19524788857 s Creating peak regions... Creating peak regions took 29.3589398861 s Estimating background... Estimating background took 26.7094202042 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 5.79354691505 s Creating peak regions... Creating peak regions took 25.2584578991 s Estimating background... Estimating background took 21.4748277664 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 4.82763981819 s Creating peak regions... Creating peak regions took 17.4417622089 s Estimating background... Estimating background took 16.9455771446 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 11.7912480831 s Creating peak regions... Creating peak regions took 56.421749115 s Estimating background... Estimating background took 48.8529970646 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.278682947159 s Creating peak regions... Creating peak regions took 0.544646978378 s Estimating background... Estimating background took 0.277171134949 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.088299036026 s Creating peak regions... Creating peak regions took 0.3781208992 s Estimating background... Estimating background took 0.279719114304 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0548601150513 s Creating peak regions... Creating peak regions took 0.205405950546 s Estimating background... Estimating background took 0.273787975311 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.046443939209 s Creating peak regions... Creating peak regions took 0.246002912521 s Estimating background... Estimating background took 0.275880098343 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 15.9471561909 s Creating peak regions... Creating peak regions took 55.3438382149 s Estimating background... Estimating background took 54.6519691944 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 11.5264439583 s Creating peak regions... Creating peak regions took 49.6589438915 s Estimating background... Estimating background took 39.8945088387 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 11.8608801365 s Creating peak regions... Creating peak regions took 50.7594540119 s Estimating background... Estimating background took 44.5166311264 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.369570016861 s Creating peak regions... Creating peak regions took 0.284204959869 s Estimating background... Estimating background took 0.315652132034 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0542809963226 s Creating peak regions... Creating peak regions took 0.021008014679 s Estimating background... Estimating background took 0.317850828171 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0487630367279 s Creating peak regions... Creating peak regions took 0.0025589466095 s Estimating background... Estimating background took 0.312559127808 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 11.941986084 s Creating peak regions... Creating peak regions took 42.9173591137 s Estimating background... Estimating background took 41.8672389984 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 1.98958396912 s Creating peak regions... Creating peak regions took 0.779078006744 s Estimating background... Estimating background took 0.370697021484 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0437920093536 s Creating peak regions... Creating peak regions took 1.06687784195 s Estimating background... Estimating background took 0.34819316864 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 11.5357530117 s Creating peak regions... Creating peak regions took 46.5355739594 s Estimating background... Estimating background took 39.9085969925 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 10.197701931 s Creating peak regions... Creating peak regions took 45.0280871391 s Estimating background... Estimating background took 38.8850409985 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 9.21730208397 s Creating peak regions... Creating peak regions took 39.6849339008 s Estimating background... Estimating background took 34.7429189682 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 10.9044971466 s Creating peak regions... Creating peak regions took 40.6295151711 s Estimating background... Estimating background took 38.8684940338 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.591021060944 s Creating peak regions... Creating peak regions took 0.33535194397 s Estimating background... Estimating background took 0.459621906281 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0806210041046 s Creating peak regions... Creating peak regions took 0.0957951545715 s Estimating background... Estimating background took 0.321909189224 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0540628433228 s Creating peak regions... Creating peak regions took 0.032665014267 s Estimating background... Estimating background took 0.364845991135 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0837159156799 s Creating peak regions... Creating peak regions took 0.0655381679535 s Estimating background... Estimating background took 0.369743824005 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0872228145599 s Creating peak regions... Creating peak regions took 0.12287902832 s Estimating background... Estimating background took 0.372980117798 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0806539058685 s Creating peak regions... Creating peak regions took 0.07648396492 s Estimating background... Estimating background took 0.370950937271 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0816910266876 s Creating peak regions... Creating peak regions took 0.0611369609833 s Estimating background... Estimating background took 0.353856086731 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0597591400146 s Creating peak regions... Creating peak regions took 0.0397081375122 s Estimating background... Estimating background took 0.323032140732 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0546569824219 s Creating peak regions... Creating peak regions took 0.0412559509277 s Estimating background... Estimating background took 0.356836080551 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0619540214539 s Creating peak regions... Creating peak regions took 0.0696489810944 s Estimating background... Estimating background took 0.371114969254 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0612199306488 s Creating peak regions... Creating peak regions took 0.129328966141 s Estimating background... Estimating background took 0.369666099548 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0845670700073 s Creating peak regions... Creating peak regions took 0.0425908565521 s Estimating background... Estimating background took 0.382277965546 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0598020553589 s Creating peak regions... Creating peak regions took 0.0347809791565 s Estimating background... Estimating background took 0.368352174759 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.116483926773 s Creating peak regions... Creating peak regions took 0.0946671962738 s Estimating background... Estimating background took 0.369528055191 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0643219947815 s Creating peak regions... Creating peak regions took 0.0605890750885 s Estimating background... Estimating background took 0.371042966843 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0820899009705 s Creating peak regions... Creating peak regions took 0.0458719730377 s Estimating background... Estimating background took 0.370009899139 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.211683034897 s Creating peak regions... Creating peak regions took 0.0524418354034 s Estimating background... Estimating background took 0.376207113266 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0705559253693 s Creating peak regions... Creating peak regions took 0.0670750141144 s Estimating background... Estimating background took 0.372453927994 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.142510890961 s Creating peak regions... Creating peak regions took 0.0497570037842 s Estimating background... Estimating background took 0.358734130859 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.094535112381 s Creating peak regions... Creating peak regions took 0.110072851181 s Estimating background... Estimating background took 0.346379041672 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0790159702301 s Creating peak regions... Creating peak regions took 0.0417091846466 s Estimating background... Estimating background took 0.325417041779 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.0894508361816 s Creating peak regions... Creating peak regions took 0.0588488578796 s Estimating background... Estimating background took 0.324552059174 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.22005200386 s Creating peak regions... Creating peak regions took 0.18141913414 s Estimating background... Estimating background took 0.747772932053 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 6.12141013145 s Creating peak regions... Creating peak regions took 49.8148031235 s Estimating background... Estimating background took 14.1529359818 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.137969970703 s Creating peak regions... Creating peak regions took 0.466329097748 s Estimating background... Estimating background took 0.357089996338 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Reading data took 0.238259077072 s Creating peak regions... Creating peak regions took 27.0905280113 s Estimating background... Estimating background took 0.561888933182 s Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data... Processing Sox2-GSM1308179/aligned.36mers.unique.bam Reading in data...