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_Rep4-GSM1689023/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_Rep4-GSM1689023/', 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_Rep4-GSM1689023/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_Rep4-GSM1689023/', 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_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 1.0905380249 s Creating peak regions... Creating peak regions took 29.729227066 s Estimating background... Estimating background took 0.551713943481 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 1.16526412964 s Creating peak regions... Creating peak regions took 29.546257019 s Estimating background... Estimating background took 0.65708398819 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 1.32754397392 s Creating peak regions... Creating peak regions took 27.6438570023 s Estimating background... Estimating background took 2.63274717331 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.859515190125 s Creating peak regions... Creating peak regions took 25.1695108414 s Estimating background... Estimating background took 0.542418003082 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 1.24283695221 s Creating peak regions... Creating peak regions took 27.481926918 s Estimating background... Estimating background took 0.535807132721 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 1.01916003227 s Creating peak regions... Creating peak regions took 22.8457062244 s Estimating background... Estimating background took 0.535042047501 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.8268430233 s Creating peak regions... Creating peak regions took 22.1562409401 s Estimating background... Estimating background took 0.454662084579 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.837159156799 s Creating peak regions... Creating peak regions took 22.321669817 s Estimating background... Estimating background took 0.65697312355 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.889186143875 s Creating peak regions... Creating peak regions took 21.1871180534 s Estimating background... Estimating background took 0.439311027527 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.663911819458 s Creating peak regions... Creating peak regions took 14.3570859432 s Estimating background... Estimating background took 0.558216094971 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 3.22382998466 s Creating peak regions... Creating peak regions took 47.2601749897 s Estimating background... Estimating background took 4.25756287575 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0502588748932 s Creating peak regions... Creating peak regions took 0.123185157776 s Estimating background... Estimating background took 0.28040599823 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0587270259857 s Creating peak regions... Creating peak regions took 0.216094017029 s Estimating background... Estimating background took 0.311789989471 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0691480636597 s Creating peak regions... Creating peak regions took 0.180774211884 s Estimating background... Estimating background took 0.256196022034 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0451581478119 s Creating peak regions... Creating peak regions took 0.199572086334 s Estimating background... Estimating background took 0.258057117462 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 2.00312900543 s Creating peak regions... Creating peak regions took 40.5786058903 s Estimating background... Estimating background took 0.794999837875 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 1.3887090683 s Creating peak regions... Creating peak regions took 33.3230919838 s Estimating background... Estimating background took 0.720315933228 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 1.43843507767 s Creating peak regions... Creating peak regions took 34.0865571499 s Estimating background... Estimating background took 3.51594090462 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0508151054382 s Creating peak regions... Creating peak regions took 0.0623488426208 s Estimating background... Estimating background took 0.270226955414 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0389728546143 s Creating peak regions... Creating peak regions took 0.0150480270386 s Estimating background... Estimating background took 0.293081998825 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 1.24628901482 s Creating peak regions... Creating peak regions took 37.1274111271 s Estimating background... Estimating background took 0.719231128693 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0266170501709 s Creating peak regions... Creating peak regions took 0.367800951004 s Estimating background... Estimating background took 0.301660060883 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 1.48972201347 s Creating peak regions... Creating peak regions took 34.1388728619 s Estimating background... Estimating background took 0.609710931778 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 1.52897191048 s Creating peak regions... Creating peak regions took 32.2034258842 s Estimating background... Estimating background took 3.34481406212 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 1.03488898277 s Creating peak regions... Creating peak regions took 27.9083440304 s Estimating background... Estimating background took 0.599513053894 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 1.24147987366 s Creating peak regions... Creating peak regions took 26.2418038845 s Estimating background... Estimating background took 0.709115028381 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.106779098511 s Creating peak regions... Creating peak regions took 0.0442590713501 s Estimating background... Estimating background took 0.269562005997 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0560660362244 s Creating peak regions... Creating peak regions took 0.0588591098785 s Estimating background... Estimating background took 0.297487020493 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0343749523163 s Creating peak regions... Creating peak regions took 0.0245118141174 s Estimating background... Estimating background took 0.302860021591 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0563209056854 s Creating peak regions... Creating peak regions took 0.0486631393433 s Estimating background... Estimating background took 0.297212123871 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0349369049072 s Creating peak regions... Creating peak regions took 0.0560569763184 s Estimating background... Estimating background took 0.303308010101 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0354640483856 s Creating peak regions... Creating peak regions took 0.0322530269623 s Estimating background... Estimating background took 0.295412063599 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.057816028595 s Creating peak regions... Creating peak regions took 0.0359470844269 s Estimating background... Estimating background took 0.30966591835 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0394320487976 s Creating peak regions... Creating peak regions took 0.0361340045929 s Estimating background... Estimating background took 0.307193994522 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0579349994659 s Creating peak regions... Creating peak regions took 0.0442221164703 s Estimating background... Estimating background took 0.310802936554 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0486099720001 s Creating peak regions... Creating peak regions took 0.0953798294067 s Estimating background... Estimating background took 0.303573131561 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.05637383461 s Creating peak regions... Creating peak regions took 0.0356540679932 s Estimating background... Estimating background took 0.303350925446 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.059103012085 s Creating peak regions... Creating peak regions took 0.0996499061584 s Estimating background... Estimating background took 0.301692008972 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.041454076767 s Creating peak regions... Creating peak regions took 0.0409398078918 s Estimating background... Estimating background took 0.308985948563 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0566620826721 s Creating peak regions... Creating peak regions took 0.0382771492004 s Estimating background... Estimating background took 0.307049036026 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.142737865448 s Creating peak regions... Creating peak regions took 0.0511219501495 s Estimating background... Estimating background took 0.306900978088 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0632739067078 s Creating peak regions... Creating peak regions took 0.0594310760498 s Estimating background... Estimating background took 0.301390886307 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0777180194855 s Creating peak regions... Creating peak regions took 0.0826859474182 s Estimating background... Estimating background took 0.309638023376 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0599610805511 s Creating peak regions... Creating peak regions took 0.0918509960175 s Estimating background... Estimating background took 0.302192926407 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0401430130005 s Creating peak regions... Creating peak regions took 0.0380609035492 s Estimating background... Estimating background took 0.28329706192 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0494959354401 s Creating peak regions... Creating peak regions took 0.196359157562 s Estimating background... Estimating background took 0.31822514534 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.863373994827 s Creating peak regions... Creating peak regions took 40.3700039387 s Estimating background... Estimating background took 0.389909982681 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.102173089981 s Creating peak regions... Creating peak regions took 0.330523014069 s Estimating background... Estimating background took 0.281278848648 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Reading data took 0.0592470169067 s Creating peak regions... Creating peak regions took 17.5398240089 s Estimating background... Estimating background took 0.266312122345 s Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E_Rep4-GSM1689023/aligned.36mers.unique.bam Reading in data...