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/female.mm10.chrom.sizes', e4='PeakXus', fastq='TAL1_G1E_Rep3-GSM1689022/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='TAL1_G1E_Rep3-GSM1689022/', 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='TAL1_G1E_Rep3-GSM1689022/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='TAL1_G1E_Rep3-GSM1689022/', 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 TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 1.06416916847 s Creating peak regions... Creating peak regions took 30.4912500381 s Estimating background... Estimating background took 0.467375040054 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 1.39573001862 s Creating peak regions... Creating peak regions took 24.7989451885 s Estimating background... Estimating background took 0.53350019455 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 1.13568496704 s Creating peak regions... Creating peak regions took 24.5022640228 s Estimating background... Estimating background took 0.421853065491 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.961313962936 s Creating peak regions... Creating peak regions took 25.4927098751 s Estimating background... Estimating background took 0.416474819183 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 1.01415681839 s Creating peak regions... Creating peak regions took 24.1528069973 s Estimating background... Estimating background took 0.446244001389 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.93617105484 s Creating peak regions... Creating peak regions took 21.0064370632 s Estimating background... Estimating background took 2.45859885216 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.73011803627 s Creating peak regions... Creating peak regions took 19.6345200539 s Estimating background... Estimating background took 0.435130119324 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.724636077881 s Creating peak regions... Creating peak regions took 20.1177489758 s Estimating background... Estimating background took 0.429934978485 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.646951913834 s Creating peak regions... Creating peak regions took 19.2177860737 s Estimating background... Estimating background took 0.336530923843 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.689116001129 s Creating peak regions... Creating peak regions took 12.997756958 s Estimating background... Estimating background took 0.298142910004 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 1.89265298843 s Creating peak regions... Creating peak regions took 41.2889330387 s Estimating background... Estimating background took 3.8783159256 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0396828651428 s Creating peak regions... Creating peak regions took 0.0697348117828 s Estimating background... Estimating background took 0.265914201736 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0582361221313 s Creating peak regions... Creating peak regions took 0.109218120575 s Estimating background... Estimating background took 0.274261951447 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0515420436859 s Creating peak regions... Creating peak regions took 0.085070848465 s Estimating background... Estimating background took 0.273494005203 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0244998931885 s Creating peak regions... Creating peak regions took 0.115910053253 s Estimating background... Estimating background took 0.269603013992 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 1.64989519119 s Creating peak regions... Creating peak regions took 37.359541893 s Estimating background... Estimating background took 0.601171016693 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 1.39639997482 s Creating peak regions... Creating peak regions took 32.6768159866 s Estimating background... Estimating background took 0.425308227539 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 1.23214483261 s Creating peak regions... Creating peak regions took 34.765004158 s Estimating background... Estimating background took 0.501708030701 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0781800746918 s Creating peak regions... Creating peak regions took 0.063022851944 s Estimating background... Estimating background took 0.31963801384 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 1.67132091522 s Creating peak regions... Creating peak regions took 36.7517478466 s Estimating background... Estimating background took 0.541424036026 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 1.64850378036 s Creating peak regions... Creating peak regions took 31.758054018 s Estimating background... Estimating background took 4.08374619484 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 1.07353591919 s Creating peak regions... Creating peak regions took 29.2762129307 s Estimating background... Estimating background took 0.468142986298 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 1.04210615158 s Creating peak regions... Creating peak regions took 27.8733849525 s Estimating background... Estimating background took 0.466253042221 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 1.60535597801 s Creating peak regions... Creating peak regions took 30.7404050827 s Estimating background... Estimating background took 0.524662971497 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.086051940918 s Creating peak regions... Creating peak regions took 0.036661863327 s Estimating background... Estimating background took 0.310975074768 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.027095079422 s Creating peak regions... Creating peak regions took 0.0422837734222 s Estimating background... Estimating background took 0.191201925278 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0407547950745 s Creating peak regions... Creating peak regions took 0.0653340816498 s Estimating background... Estimating background took 0.310606002808 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0294108390808 s Creating peak regions... Creating peak regions took 0.0333850383759 s Estimating background... Estimating background took 0.302901983261 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0514581203461 s Creating peak regions... Creating peak regions took 0.0622458457947 s Estimating background... Estimating background took 0.331466197968 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0358917713165 s Creating peak regions... Creating peak regions took 0.0255839824677 s Estimating background... Estimating background took 0.310127019882 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0316920280457 s Creating peak regions... Creating peak regions took 0.0203628540039 s Estimating background... Estimating background took 0.301476955414 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0503680706024 s Creating peak regions... Creating peak regions took 0.042149066925 s Estimating background... Estimating background took 0.31903886795 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0318810939789 s Creating peak regions... Creating peak regions took 0.0292129516602 s Estimating background... Estimating background took 0.303763866425 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.048388004303 s Creating peak regions... Creating peak regions took 0.0952060222626 s Estimating background... Estimating background took 0.33314204216 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0229980945587 s Creating peak regions... Creating peak regions took 0.0168159008026 s Estimating background... Estimating background took 0.308631896973 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0355081558228 s Creating peak regions... Creating peak regions took 0.0442190170288 s Estimating background... Estimating background took 0.275452136993 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0782110691071 s Creating peak regions... Creating peak regions took 0.0265169143677 s Estimating background... Estimating background took 0.278696060181 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0353300571442 s Creating peak regions... Creating peak regions took 0.0257749557495 s Estimating background... Estimating background took 0.278712034225 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0519289970398 s Creating peak regions... Creating peak regions took 0.0610880851746 s Estimating background... Estimating background took 0.300565958023 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0556688308716 s Creating peak regions... Creating peak regions took 0.0826971530914 s Estimating background... Estimating background took 0.296669960022 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0511491298676 s Creating peak regions... Creating peak regions took 0.0379920005798 s Estimating background... Estimating background took 0.30929017067 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0528240203857 s Creating peak regions... Creating peak regions took 0.0346460342407 s Estimating background... Estimating background took 0.307592868805 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.0799069404602 s Creating peak regions... Creating peak regions took 0.248861789703 s Estimating background... Estimating background took 0.302968978882 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.572504043579 s Creating peak regions... Creating peak regions took 40.2217609882 s Estimating background... Estimating background took 0.304308891296 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.038666009903 s Creating peak regions... Creating peak regions took 0.284905195236 s Estimating background... Estimating background took 0.334143161774 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Reading data took 0.029876947403 s Creating peak regions... Creating peak regions took 18.2084760666 s Estimating background... Estimating background took 0.299753904343 s Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep3-GSM1689022/aligned.36mers.unique.bam Reading in data...