INPUT PARAMETERS: Namespace(B2=None, N4=1000, N6=1000, S4=1, UMIs=None, adapters1=None, b3=0.05, blacklist='/home/users/marinovg/genomes/blacklists/mm10/mm10.blacklist.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes', e4='PeakXus', fastq='TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.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-ER4-3h-Rep2-GSM1689030-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 TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.773271083832 s Creating peak regions... Creating peak regions took 41.6218290329 s Estimating background... Estimating background took 0.310761928558 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.801172971725 s Creating peak regions... Creating peak regions took 38.551213026 s Estimating background... Estimating background took 0.403064012527 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.715397834778 s Creating peak regions... Creating peak regions took 36.9822630882 s Estimating background... Estimating background took 0.303491830826 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.678982973099 s Creating peak regions... Creating peak regions took 37.3383281231 s Estimating background... Estimating background took 0.294872045517 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.699752807617 s Creating peak regions... Creating peak regions took 38.4067380428 s Estimating background... Estimating background took 0.321547985077 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.647315979004 s Creating peak regions... Creating peak regions took 32.1756398678 s Estimating background... Estimating background took 0.357111215591 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.599032878876 s Creating peak regions... Creating peak regions took 30.3890769482 s Estimating background... Estimating background took 0.292866945267 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.706789016724 s Creating peak regions... Creating peak regions took 29.2510619164 s Estimating background... Estimating background took 0.321171998978 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.543365955353 s Creating peak regions... Creating peak regions took 27.9303069115 s Estimating background... Estimating background took 0.305326938629 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.445608854294 s Creating peak regions... Creating peak regions took 19.0041899681 s Estimating background... Estimating background took 0.313458919525 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 1.41062808037 s Creating peak regions... Creating peak regions took 61.051181078 s Estimating background... Estimating background took 0.47881102562 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0472228527069 s Creating peak regions... Creating peak regions took 0.2275390625 s Estimating background... Estimating background took 0.244860887527 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0316088199615 s Creating peak regions... Creating peak regions took 0.256020069122 s Estimating background... Estimating background took 0.242943048477 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0304970741272 s Creating peak regions... Creating peak regions took 0.172402858734 s Estimating background... Estimating background took 0.243206977844 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 1.37502408028 s Creating peak regions... Creating peak regions took 56.9026038647 s Estimating background... Estimating background took 0.443284988403 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.869624853134 s Creating peak regions... Creating peak regions took 49.7418041229 s Estimating background... Estimating background took 0.352618932724 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.885134935379 s Creating peak regions... Creating peak regions took 48.6377820969 s Estimating background... Estimating background took 0.371427059174 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0459749698639 s Creating peak regions... Creating peak regions took 0.0773639678955 s Estimating background... Estimating background took 0.244795799255 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.910446882248 s Creating peak regions... Creating peak regions took 45.6600379944 s Estimating background... Estimating background took 0.346076965332 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.02281498909 s Creating peak regions... Creating peak regions took 0.514516115189 s Estimating background... Estimating background took 0.232234954834 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.899945020676 s Creating peak regions... Creating peak regions took 46.2565920353 s Estimating background... Estimating background took 0.354471921921 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 1.08733797073 s Creating peak regions... Creating peak regions took 45.1344637871 s Estimating background... Estimating background took 4.33905982971 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.722492933273 s Creating peak regions... Creating peak regions took 39.4245588779 s Estimating background... Estimating background took 0.388379096985 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.812371015549 s Creating peak regions... Creating peak regions took 38.5918931961 s Estimating background... Estimating background took 0.532837152481 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0469739437103 s Creating peak regions... Creating peak regions took 0.0259430408478 s Estimating background... Estimating background took 0.285901069641 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0295810699463 s Creating peak regions... Creating peak regions took 0.0521650314331 s Estimating background... Estimating background took 0.288022041321 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0253450870514 s Creating peak regions... Creating peak regions took 0.0415811538696 s Estimating background... Estimating background took 0.278197050095 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0284481048584 s Creating peak regions... Creating peak regions took 0.00363183021545 s Estimating background... Estimating background took 0.285480976105 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0246300697327 s Creating peak regions... Creating peak regions took 0.0305349826813 s Estimating background... Estimating background took 0.28605389595 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0244598388672 s Creating peak regions... Creating peak regions took 0.0214598178864 s Estimating background... Estimating background took 0.290535926819 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0250310897827 s Creating peak regions... Creating peak regions took 0.0295870304108 s Estimating background... Estimating background took 0.275742053986 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0270819664001 s Creating peak regions... Creating peak regions took 0.061644077301 s Estimating background... Estimating background took 0.289132118225 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0534038543701 s Creating peak regions... Creating peak regions took 0.0371649265289 s Estimating background... Estimating background took 0.290037155151 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0309150218964 s Creating peak regions... Creating peak regions took 0.0392420291901 s Estimating background... Estimating background took 0.293515920639 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.038006067276 s Creating peak regions... Creating peak regions took 0.0597190856934 s Estimating background... Estimating background took 0.303998947144 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0297141075134 s Creating peak regions... Creating peak regions took 0.0813488960266 s Estimating background... Estimating background took 0.282301902771 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0265481472015 s Creating peak regions... Creating peak regions took 0.0342390537262 s Estimating background... Estimating background took 0.283820867538 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0401570796967 s Creating peak regions... Creating peak regions took 0.21448802948 s Estimating background... Estimating background took 0.287640094757 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.410114049911 s Creating peak regions... Creating peak regions took 51.1740198135 s Estimating background... Estimating background took 0.355094909668 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0386579036713 s Creating peak regions... Creating peak regions took 0.200632095337 s Estimating background... Estimating background took 0.284151077271 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Reading data took 0.0298421382904 s Creating peak regions... Creating peak regions took 26.0211219788 s Estimating background... Estimating background took 0.296386003494 s Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data... Processing TAL1-G1E-ER4-3h-Rep2-GSM1689030.35mers.unique.bam Reading in data...