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_Myc-GSM1606987/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_Myc-GSM1606987/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_Myc-GSM1606987/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_Myc-GSM1606987/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_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 9.0440158844 s Creating peak regions... Creating peak regions took 42.7475249767 s Estimating background... Estimating background took 103.9042449 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 8.74213480949 s Creating peak regions... Creating peak regions took 45.5866820812 s Estimating background... Estimating background took 85.4585487843 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 9.12529683113 s Creating peak regions... Creating peak regions took 47.0285110474 s Estimating background... Estimating background took 88.5512089729 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 8.11109685898 s Creating peak regions... Creating peak regions took 43.1768629551 s Estimating background... Estimating background took 90.5183849335 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 9.28584194183 s Creating peak regions... Creating peak regions took 48.6520690918 s Estimating background... Estimating background took 91.8490490913 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 8.4031150341 s Creating peak regions... Creating peak regions took 37.8612008095 s Estimating background... Estimating background took 76.6805410385 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 8.42490005493 s Creating peak regions... Creating peak regions took 41.3824090958 s Estimating background... Estimating background took 81.1522591114 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 7.19360494614 s Creating peak regions... Creating peak regions took 40.8126289845 s Estimating background... Estimating background took 67.2159171104 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 6.96553301811 s Creating peak regions... Creating peak regions took 32.7224061489 s Estimating background... Estimating background took 69.0113730431 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 5.26402115822 s Creating peak regions... Creating peak regions took 25.8048560619 s Estimating background... Estimating background took 44.8021240234 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 14.1250369549 s Creating peak regions... Creating peak regions took 70.3356969357 s Estimating background... Estimating background took 153.857872963 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.363649845123 s Creating peak regions... Creating peak regions took 0.788352012634 s Estimating background... Estimating background took 0.347222089767 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0843169689178 s Creating peak regions... Creating peak regions took 0.370447874069 s Estimating background... Estimating background took 0.365708112717 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0602838993073 s Creating peak regions... Creating peak regions took 0.233818054199 s Estimating background... Estimating background took 0.348999977112 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0590009689331 s Creating peak regions... Creating peak regions took 0.29868388176 s Estimating background... Estimating background took 0.358423948288 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 18.4593629837 s Creating peak regions... Creating peak regions took 72.4500601292 s Estimating background... Estimating background took 141.802464962 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 13.1286730766 s Creating peak regions... Creating peak regions took 61.6365339756 s Estimating background... Estimating background took 141.839385986 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 14.3250670433 s Creating peak regions... Creating peak regions took 62.2678070068 s Estimating background... Estimating background took 120.283901215 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.795187950134 s Creating peak regions... Creating peak regions took 0.441091060638 s Estimating background... Estimating background took 0.457966804504 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0435900688171 s Creating peak regions... Creating peak regions took 0.0300371646881 s Estimating background... Estimating background took 0.356861114502 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0466711521149 s Creating peak regions... Creating peak regions took 0.00241899490356 s Estimating background... Estimating background took 0.352835893631 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 12.2815492153 s Creating peak regions... Creating peak regions took 56.4044978619 s Estimating background... Estimating background took 126.214179039 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.818151950836 s Creating peak regions... Creating peak regions took 0.403967142105 s Estimating background... Estimating background took 0.400848865509 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0820288658142 s Creating peak regions... Creating peak regions took 0.342032909393 s Estimating background... Estimating background took 0.400227069855 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0541081428528 s Creating peak regions... Creating peak regions took 0.283327102661 s Estimating background... Estimating background took 0.376960992813 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0673270225525 s Creating peak regions... Creating peak regions took 1.08670496941 s Estimating background... Estimating background took 0.367926120758 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 11.9290709496 s Creating peak regions... Creating peak regions took 56.643928051 s Estimating background... Estimating background took 132.508822203 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 14.7188558578 s Creating peak regions... Creating peak regions took 54.9371979237 s Estimating background... Estimating background took 90.2445750237 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 9.07548117638 s Creating peak regions... Creating peak regions took 52.1234781742 s Estimating background... Estimating background took 102.906852007 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 14.9500501156 s Creating peak regions... Creating peak regions took 60.3737130165 s Estimating background... Estimating background took 95.4168009758 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 1.10243201256 s Creating peak regions... Creating peak regions took 0.262025117874 s Estimating background... Estimating background took 0.621373176575 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0902209281921 s Creating peak regions... Creating peak regions took 0.107146978378 s Estimating background... Estimating background took 0.521822929382 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0789458751678 s Creating peak regions... Creating peak regions took 0.0686831474304 s Estimating background... Estimating background took 0.420121908188 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0843381881714 s Creating peak regions... Creating peak regions took 0.0786240100861 s Estimating background... Estimating background took 0.420700073242 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0875179767609 s Creating peak regions... Creating peak regions took 0.0994019508362 s Estimating background... Estimating background took 0.421018123627 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0651018619537 s Creating peak regions... Creating peak regions took 0.0819048881531 s Estimating background... Estimating background took 0.421292066574 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0949740409851 s Creating peak regions... Creating peak regions took 0.0740649700165 s Estimating background... Estimating background took 0.430083036423 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0651051998138 s Creating peak regions... Creating peak regions took 0.0627450942993 s Estimating background... Estimating background took 0.518038988113 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0851731300354 s Creating peak regions... Creating peak regions took 0.0568070411682 s Estimating background... Estimating background took 0.424778938293 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0642828941345 s Creating peak regions... Creating peak regions took 0.0755908489227 s Estimating background... Estimating background took 0.411422014236 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0897891521454 s Creating peak regions... Creating peak regions took 0.169973134995 s Estimating background... Estimating background took 0.420510053635 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.060879945755 s Creating peak regions... Creating peak regions took 0.0666038990021 s Estimating background... Estimating background took 0.421713113785 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0601968765259 s Creating peak regions... Creating peak regions took 0.0451378822327 s Estimating background... Estimating background took 0.421530008316 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.105085134506 s Creating peak regions... Creating peak regions took 0.0636370182037 s Estimating background... Estimating background took 0.494916915894 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.084762096405 s Creating peak regions... Creating peak regions took 0.0814120769501 s Estimating background... Estimating background took 0.40992307663 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0851118564606 s Creating peak regions... Creating peak regions took 0.0843479633331 s Estimating background... Estimating background took 0.409424066544 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.955718040466 s Creating peak regions... Creating peak regions took 0.028774023056 s Estimating background... Estimating background took 0.717875003815 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.138890028 s Creating peak regions... Creating peak regions took 0.0508050918579 s Estimating background... Estimating background took 0.522572040558 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.327428102493 s Creating peak regions... Creating peak regions took 0.0342240333557 s Estimating background... Estimating background took 0.621356010437 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.122427940369 s Creating peak regions... Creating peak regions took 0.101091146469 s Estimating background... Estimating background took 0.508500099182 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0885539054871 s Creating peak regions... Creating peak regions took 0.0678470134735 s Estimating background... Estimating background took 0.4187541008 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.0993649959564 s Creating peak regions... Creating peak regions took 0.0478510856628 s Estimating background... Estimating background took 0.508358001709 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.284951925278 s Creating peak regions... Creating peak regions took 0.2034471035 s Estimating background... Estimating background took 1.23972010612 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 15.278578043 s Creating peak regions... Creating peak regions took 67.251791954 s Estimating background... Estimating background took 97.492898941 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 3.6373398304 s Creating peak regions... Creating peak regions took 0.99792098999 s Estimating background... Estimating background took 0.584542989731 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Reading data took 0.261244058609 s Creating peak regions... Creating peak regions took 31.4331870079 s Estimating background... Estimating background took 0.693559169769 s Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data... Processing RbKO_villi_Myc-GSM1606987/aligned.36mers.unique.bam Reading in data...