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-Rep2-GSM1689021.35mers.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-Rep2-GSM1689021-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-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.849539995193 s Creating peak regions... Creating peak regions took 42.1288750172 s Estimating background... Estimating background took 0.30152797699 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.973752975464 s Creating peak regions... Creating peak regions took 39.8281910419 s Estimating background... Estimating background took 0.405128955841 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 1.07080292702 s Creating peak regions... Creating peak regions took 37.4139509201 s Estimating background... Estimating background took 0.42021894455 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.908763885498 s Creating peak regions... Creating peak regions took 37.5318098068 s Estimating background... Estimating background took 0.306817054749 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.985298156738 s Creating peak regions... Creating peak regions took 38.6657299995 s Estimating background... Estimating background took 0.290609836578 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.857686042786 s Creating peak regions... Creating peak regions took 31.1366651058 s Estimating background... Estimating background took 0.358566999435 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.821235895157 s Creating peak regions... Creating peak regions took 30.4157450199 s Estimating background... Estimating background took 0.294981002808 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.770576000214 s Creating peak regions... Creating peak regions took 29.3532850742 s Estimating background... Estimating background took 0.28545999527 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.787601947784 s Creating peak regions... Creating peak regions took 28.0376899242 s Estimating background... Estimating background took 0.311452150345 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.546793937683 s Creating peak regions... Creating peak regions took 19.0851597786 s Estimating background... Estimating background took 0.323194980621 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 1.92572689056 s Creating peak regions... Creating peak regions took 61.3604869843 s Estimating background... Estimating background took 0.455116033554 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0529329776764 s Creating peak regions... Creating peak regions took 0.133466959 s Estimating background... Estimating background took 0.229411125183 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0303068161011 s Creating peak regions... Creating peak regions took 0.300431966782 s Estimating background... Estimating background took 0.238914966583 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0330030918121 s Creating peak regions... Creating peak regions took 0.191854953766 s Estimating background... Estimating background took 0.221481084824 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0241658687592 s Creating peak regions... Creating peak regions took 0.213315010071 s Estimating background... Estimating background took 0.217043876648 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 1.83553004265 s Creating peak regions... Creating peak regions took 56.5115640163 s Estimating background... Estimating background took 0.45090508461 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 1.198595047 s Creating peak regions... Creating peak regions took 49.8377859592 s Estimating background... Estimating background took 0.332658052444 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 1.21959590912 s Creating peak regions... Creating peak regions took 49.0943870544 s Estimating background... Estimating background took 0.339435100555 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0458960533142 s Creating peak regions... Creating peak regions took 0.083419084549 s Estimating background... Estimating background took 0.23394203186 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 1.23424816132 s Creating peak regions... Creating peak regions took 45.4126861095 s Estimating background... Estimating background took 0.332515954971 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0233588218689 s Creating peak regions... Creating peak regions took 0.601744890213 s Estimating background... Estimating background took 0.241291046143 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 1.21571087837 s Creating peak regions... Creating peak regions took 45.0207901001 s Estimating background... Estimating background took 0.33918595314 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 1.14603590965 s Creating peak regions... Creating peak regions took 45.3679289818 s Estimating background... Estimating background took 0.332247018814 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 1.07955598831 s Creating peak regions... Creating peak regions took 40.0304009914 s Estimating background... Estimating background took 0.468749046326 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 1.12508201599 s Creating peak regions... Creating peak regions took 39.0216469765 s Estimating background... Estimating background took 4.57497000694 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0281751155853 s Creating peak regions... Creating peak regions took 0.0242111682892 s Estimating background... Estimating background took 0.28352689743 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0314259529114 s Creating peak regions... Creating peak regions took 0.0453009605408 s Estimating background... Estimating background took 0.284435033798 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0259640216827 s Creating peak regions... Creating peak regions took 0.0406279563904 s Estimating background... Estimating background took 0.285224914551 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0345680713654 s Creating peak regions... Creating peak regions took 0.0277729034424 s Estimating background... Estimating background took 0.264849901199 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.033175945282 s Creating peak regions... Creating peak regions took 0.0469460487366 s Estimating background... Estimating background took 0.286911010742 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0276319980621 s Creating peak regions... Creating peak regions took 0.037474155426 s Estimating background... Estimating background took 0.27564406395 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0282859802246 s Creating peak regions... Creating peak regions took 0.0304360389709 s Estimating background... Estimating background took 0.266422986984 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0335590839386 s Creating peak regions... Creating peak regions took 0.0536351203918 s Estimating background... Estimating background took 0.282292127609 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.027960062027 s Creating peak regions... Creating peak regions took 0.0294990539551 s Estimating background... Estimating background took 0.282495975494 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0777499675751 s Creating peak regions... Creating peak regions took 0.0356431007385 s Estimating background... Estimating background took 0.315896987915 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.035961151123 s Creating peak regions... Creating peak regions took 0.0391340255737 s Estimating background... Estimating background took 0.292083024979 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0486500263214 s Creating peak regions... Creating peak regions took 0.0657391548157 s Estimating background... Estimating background took 0.329658985138 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0360970497131 s Creating peak regions... Creating peak regions took 0.0532240867615 s Estimating background... Estimating background took 0.2898209095 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0340688228607 s Creating peak regions... Creating peak regions took 0.0278329849243 s Estimating background... Estimating background took 0.28080201149 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0353698730469 s Creating peak regions... Creating peak regions took 0.0331950187683 s Estimating background... Estimating background took 0.2849650383 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0519931316376 s Creating peak regions... Creating peak regions took 0.131329059601 s Estimating background... Estimating background took 0.298238992691 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.49985408783 s Creating peak regions... Creating peak regions took 53.0835549831 s Estimating background... Estimating background took 0.284847021103 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0388581752777 s Creating peak regions... Creating peak regions took 0.157614946365 s Estimating background... Estimating background took 0.277004957199 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Reading data took 0.0299417972565 s Creating peak regions... Creating peak regions took 25.7540149689 s Estimating background... Estimating background took 0.294664859772 s Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data... Processing TAL1-G1E-Rep2-GSM1689021.35mers.unique.bam Reading in data...