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_Myc-GSM1606991/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_Myc-GSM1606991/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_Myc-GSM1606991/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_Myc-GSM1606991/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_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 14.4205751419 s Creating peak regions... Creating peak regions took 53.1618289948 s Estimating background... Estimating background took 232.144610882 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 15.4505488873 s Creating peak regions... Creating peak regions took 53.8276319504 s Estimating background... Estimating background took 185.677599907 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 16.0618789196 s Creating peak regions... Creating peak regions took 59.3512330055 s Estimating background... Estimating background took 192.888809919 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 17.8045520782 s Creating peak regions... Creating peak regions took 60.7209310532 s Estimating background... Estimating background took 205.41752696 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 16.9736318588 s Creating peak regions... Creating peak regions took 57.7542898655 s Estimating background... Estimating background took 203.290302038 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 15.5348300934 s Creating peak regions... Creating peak regions took 57.5838191509 s Estimating background... Estimating background took 172.860176086 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 15.3709640503 s Creating peak regions... Creating peak regions took 56.9671320915 s Estimating background... Estimating background took 173.992645979 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 13.6852300167 s Creating peak regions... Creating peak regions took 48.1052179337 s Estimating background... Estimating background took 137.297211885 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 13.8513169289 s Creating peak regions... Creating peak regions took 50.6689670086 s Estimating background... Estimating background took 158.363803864 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 8.06947493553 s Creating peak regions... Creating peak regions took 30.59907794 s Estimating background... Estimating background took 97.3968131542 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 26.8767669201 s Creating peak regions... Creating peak regions took 104.5415411 s Estimating background... Estimating background took 358.817238808 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.709426879883 s Creating peak regions... Creating peak regions took 1.22120189667 s Estimating background... Estimating background took 0.436481952667 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.067314863205 s Creating peak regions... Creating peak regions took 0.333208084106 s Estimating background... Estimating background took 0.50489115715 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0880630016327 s Creating peak regions... Creating peak regions took 0.242877960205 s Estimating background... Estimating background took 0.421785116196 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.063423871994 s Creating peak regions... Creating peak regions took 0.299755096436 s Estimating background... Estimating background took 0.407340049744 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 33.2874689102 s Creating peak regions... Creating peak regions took 93.4547250271 s Estimating background... Estimating background took 309.006044149 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 33.2352931499 s Creating peak regions... Creating peak regions took 86.5483410358 s Estimating background... Estimating background took 295.203161955 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 26.3861420155 s Creating peak regions... Creating peak regions took 82.9084010124 s Estimating background... Estimating background took 243.362866879 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.884337902069 s Creating peak regions... Creating peak regions took 0.380606174469 s Estimating background... Estimating background took 0.599787950516 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0550241470337 s Creating peak regions... Creating peak regions took 0.0438220500946 s Estimating background... Estimating background took 0.403033971786 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0537710189819 s Creating peak regions... Creating peak regions took 0.00242280960083 s Estimating background... Estimating background took 0.426117181778 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 20.3132970333 s Creating peak regions... Creating peak regions took 83.8765239716 s Estimating background... Estimating background took 228.650894165 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 1.04939699173 s Creating peak regions... Creating peak regions took 0.465245962143 s Estimating background... Estimating background took 0.406013011932 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0672090053558 s Creating peak regions... Creating peak regions took 0.282511949539 s Estimating background... Estimating background took 0.408829927444 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0789530277252 s Creating peak regions... Creating peak regions took 0.300737857819 s Estimating background... Estimating background took 0.407284975052 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0635221004486 s Creating peak regions... Creating peak regions took 1.31758999825 s Estimating background... Estimating background took 0.411699056625 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 20.6325900555 s Creating peak regions... Creating peak regions took 78.8771808147 s Estimating background... Estimating background took 250.598160982 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 23.9659149647 s Creating peak regions... Creating peak regions took 74.5047428608 s Estimating background... Estimating background took 189.22942996 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 18.4816310406 s Creating peak regions... Creating peak regions took 72.8083291054 s Estimating background... Estimating background took 211.801164865 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 17.8405559063 s Creating peak regions... Creating peak regions took 63.6612360477 s Estimating background... Estimating background took 190.329485893 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 1.10110116005 s Creating peak regions... Creating peak regions took 0.292555093765 s Estimating background... Estimating background took 0.487242937088 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0980708599091 s Creating peak regions... Creating peak regions took 0.0794019699097 s Estimating background... Estimating background took 0.598093032837 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0888350009918 s Creating peak regions... Creating peak regions took 0.0679440498352 s Estimating background... Estimating background took 0.398916959763 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0622889995575 s Creating peak regions... Creating peak regions took 0.066712141037 s Estimating background... Estimating background took 0.381237983704 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0868539810181 s Creating peak regions... Creating peak regions took 0.0874338150024 s Estimating background... Estimating background took 0.408148050308 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0665500164032 s Creating peak regions... Creating peak regions took 0.0751421451569 s Estimating background... Estimating background took 0.381597995758 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0601780414581 s Creating peak regions... Creating peak regions took 0.0519540309906 s Estimating background... Estimating background took 0.389912843704 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0656270980835 s Creating peak regions... Creating peak regions took 0.0532410144806 s Estimating background... Estimating background took 0.500672101974 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0795431137085 s Creating peak regions... Creating peak regions took 0.0508828163147 s Estimating background... Estimating background took 0.399152994156 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0639319419861 s Creating peak regions... Creating peak regions took 0.0625069141388 s Estimating background... Estimating background took 0.401191949844 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0631198883057 s Creating peak regions... Creating peak regions took 0.113733053207 s Estimating background... Estimating background took 0.42175078392 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0644090175629 s Creating peak regions... Creating peak regions took 0.0791039466858 s Estimating background... Estimating background took 0.446928977966 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0648190975189 s Creating peak regions... Creating peak regions took 0.0614950656891 s Estimating background... Estimating background took 0.444103002548 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.203996181488 s Creating peak regions... Creating peak regions took 0.0788731575012 s Estimating background... Estimating background took 0.76621389389 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0897018909454 s Creating peak regions... Creating peak regions took 0.078644990921 s Estimating background... Estimating background took 0.449844121933 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0898070335388 s Creating peak regions... Creating peak regions took 0.0699899196625 s Estimating background... Estimating background took 0.451711893082 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 1.51942396164 s Creating peak regions... Creating peak regions took 0.0330410003662 s Estimating background... Estimating background took 1.07308793068 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.174216985703 s Creating peak regions... Creating peak regions took 0.0531561374664 s Estimating background... Estimating background took 0.655740022659 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.471160888672 s Creating peak regions... Creating peak regions took 0.0372080802917 s Estimating background... Estimating background took 0.671372890472 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.143579006195 s Creating peak regions... Creating peak regions took 0.111628055573 s Estimating background... Estimating background took 0.52038192749 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.0881469249725 s Creating peak regions... Creating peak regions took 0.0635061264038 s Estimating background... Estimating background took 0.426198005676 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.161697149277 s Creating peak regions... Creating peak regions took 0.0481200218201 s Estimating background... Estimating background took 0.552703857422 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.531100034714 s Creating peak regions... Creating peak regions took 0.241327047348 s Estimating background... Estimating background took 1.59623193741 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 20.5231859684 s Creating peak regions... Creating peak regions took 72.0922050476 s Estimating background... Estimating background took 169.328426123 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 1.06718993187 s Creating peak regions... Creating peak regions took 0.602434158325 s Estimating background... Estimating background took 0.791927099228 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Reading data took 0.470211029053 s Creating peak regions... Creating peak regions took 28.5429029465 s Estimating background... Estimating background took 1.7161989212 s Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data... Processing control_villi_Myc-GSM1606991/aligned.36mers.unique.bam Reading in data...