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='Brachyury-GSM1327309/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='Brachyury-GSM1327309/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='Brachyury-GSM1327309/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='Brachyury-GSM1327309/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 Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 19.0448410511 s Creating peak regions... Creating peak regions took 59.7704770565 s Estimating background... Estimating background took 196.796185017 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 22.2784159184 s Creating peak regions... Creating peak regions took 67.7938129902 s Estimating background... Estimating background took 273.33615303 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 17.673197031 s Creating peak regions... Creating peak regions took 55.0421409607 s Estimating background... Estimating background took 164.444535971 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 18.2905070782 s Creating peak regions... Creating peak regions took 59.7144510746 s Estimating background... Estimating background took 179.603515148 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 20.8596241474 s Creating peak regions... Creating peak regions took 54.2583060265 s Estimating background... Estimating background took 168.764253139 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 22.0833439827 s Creating peak regions... Creating peak regions took 61.7712020874 s Estimating background... Estimating background took 252.021197796 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 17.439576149 s Creating peak regions... Creating peak regions took 48.8426060677 s Estimating background... Estimating background took 135.634377003 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 17.345282793 s Creating peak regions... Creating peak regions took 47.6882741451 s Estimating background... Estimating background took 148.283939838 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 16.2303230762 s Creating peak regions... Creating peak regions took 46.2110381126 s Estimating background... Estimating background took 130.883602858 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 12.5812840462 s Creating peak regions... Creating peak regions took 33.8682928085 s Estimating background... Estimating background took 105.446630001 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 29.8684949875 s Creating peak regions... Creating peak regions took 89.1123101711 s Estimating background... Estimating background took 292.222863913 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.981342077255 s Creating peak regions... Creating peak regions took 1.26626110077 s Estimating background... Estimating background took 0.384112119675 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0646169185638 s Creating peak regions... Creating peak regions took 0.360331058502 s Estimating background... Estimating background took 0.378311872482 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0593571662903 s Creating peak regions... Creating peak regions took 0.238132953644 s Estimating background... Estimating background took 0.379467964172 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0556690692902 s Creating peak regions... Creating peak regions took 0.315513849258 s Estimating background... Estimating background took 0.377550125122 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 37.6475930214 s Creating peak regions... Creating peak regions took 89.0437068939 s Estimating background... Estimating background took 288.026508093 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 31.3690390587 s Creating peak regions... Creating peak regions took 80.6988611221 s Estimating background... Estimating background took 226.949685812 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 27.0385761261 s Creating peak regions... Creating peak regions took 78.8821351528 s Estimating background... Estimating background took 254.707452059 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 1.47635006905 s Creating peak regions... Creating peak regions took 0.506353855133 s Estimating background... Estimating background took 0.728698968887 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0530269145966 s Creating peak regions... Creating peak regions took 0.0338389873505 s Estimating background... Estimating background took 0.413709878922 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0444030761719 s Creating peak regions... Creating peak regions took 0.00452184677124 s Estimating background... Estimating background took 0.377526044846 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 27.0209441185 s Creating peak regions... Creating peak regions took 73.0433189869 s Estimating background... Estimating background took 245.618612051 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 2.09797501564 s Creating peak regions... Creating peak regions took 0.994274139404 s Estimating background... Estimating background took 0.431952953339 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0572249889374 s Creating peak regions... Creating peak regions took 1.35258507729 s Estimating background... Estimating background took 0.414994001389 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 28.3652000427 s Creating peak regions... Creating peak regions took 72.2973680496 s Estimating background... Estimating background took 223.988731861 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 24.5466399193 s Creating peak regions... Creating peak regions took 70.2191429138 s Estimating background... Estimating background took 229.13728714 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 28.2922179699 s Creating peak regions... Creating peak regions took 76.5024490356 s Estimating background... Estimating background took 349.669360876 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 23.292098999 s Creating peak regions... Creating peak regions took 63.8918812275 s Estimating background... Estimating background took 205.635043859 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 1.21114706993 s Creating peak regions... Creating peak regions took 0.310001134872 s Estimating background... Estimating background took 0.810426950455 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0668549537659 s Creating peak regions... Creating peak regions took 0.0671129226685 s Estimating background... Estimating background took 0.387241840363 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0543160438538 s Creating peak regions... Creating peak regions took 0.0630040168762 s Estimating background... Estimating background took 0.388644933701 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0559530258179 s Creating peak regions... Creating peak regions took 0.0694420337677 s Estimating background... Estimating background took 0.42143702507 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0634760856628 s Creating peak regions... Creating peak regions took 0.0995180606842 s Estimating background... Estimating background took 0.450241088867 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0593709945679 s Creating peak regions... Creating peak regions took 0.0966711044312 s Estimating background... Estimating background took 0.425740003586 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0569009780884 s Creating peak regions... Creating peak regions took 0.0535171031952 s Estimating background... Estimating background took 0.42404294014 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0615231990814 s Creating peak regions... Creating peak regions took 0.0841579437256 s Estimating background... Estimating background took 0.424535989761 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0522880554199 s Creating peak regions... Creating peak regions took 0.066535949707 s Estimating background... Estimating background took 0.388273954391 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0565371513367 s Creating peak regions... Creating peak regions took 0.0693099498749 s Estimating background... Estimating background took 0.389116048813 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.054888010025 s Creating peak regions... Creating peak regions took 0.132349967957 s Estimating background... Estimating background took 0.388354063034 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0539309978485 s Creating peak regions... Creating peak regions took 0.0674319267273 s Estimating background... Estimating background took 0.388003826141 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0522229671478 s Creating peak regions... Creating peak regions took 0.0418429374695 s Estimating background... Estimating background took 0.45828795433 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.108528852463 s Creating peak regions... Creating peak regions took 0.0744528770447 s Estimating background... Estimating background took 0.492583036423 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0571458339691 s Creating peak regions... Creating peak regions took 0.083377122879 s Estimating background... Estimating background took 0.386250019073 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0560190677643 s Creating peak regions... Creating peak regions took 0.0579988956451 s Estimating background... Estimating background took 0.420927047729 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.899343013763 s Creating peak regions... Creating peak regions took 0.0311570167542 s Estimating background... Estimating background took 0.737231016159 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.091637134552 s Creating peak regions... Creating peak regions took 0.0497739315033 s Estimating background... Estimating background took 0.38960313797 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.276541948318 s Creating peak regions... Creating peak regions took 0.0302679538727 s Estimating background... Estimating background took 0.495633840561 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0876748561859 s Creating peak regions... Creating peak regions took 0.101554870605 s Estimating background... Estimating background took 0.490427017212 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0549910068512 s Creating peak regions... Creating peak regions took 0.0648100376129 s Estimating background... Estimating background took 0.388508796692 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.0798888206482 s Creating peak regions... Creating peak regions took 0.0470960140228 s Estimating background... Estimating background took 0.389846086502 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.376446008682 s Creating peak regions... Creating peak regions took 0.214339971542 s Estimating background... Estimating background took 1.2210650444 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 12.231703043 s Creating peak regions... Creating peak regions took 58.938587904 s Estimating background... Estimating background took 62.7480459213 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 1.03991293907 s Creating peak regions... Creating peak regions took 0.71112704277 s Estimating background... Estimating background took 0.462202072144 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Reading data took 0.467209100723 s Creating peak regions... Creating peak regions took 31.727686882 s Estimating background... Estimating background took 1.22937297821 s Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data... Processing Brachyury-GSM1327309/aligned.36mers.unique.bam Reading in data...