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-ER4_3h_Rep1-GSM1689029/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-ER4_3h_Rep1-GSM1689029/', 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-ER4_3h_Rep1-GSM1689029/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-ER4_3h_Rep1-GSM1689029/', 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_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 1.14230394363 s Creating peak regions... Creating peak regions took 29.4889531136 s Estimating background... Estimating background took 2.88105106354 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 1.33804512024 s Creating peak regions... Creating peak regions took 27.5079171658 s Estimating background... Estimating background took 0.340879917145 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 1.24039006233 s Creating peak regions... Creating peak regions took 25.7613859177 s Estimating background... Estimating background took 0.326455831528 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 1.121062994 s Creating peak regions... Creating peak regions took 25.2611591816 s Estimating background... Estimating background took 0.331144094467 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 1.32235908508 s Creating peak regions... Creating peak regions took 26.2640221119 s Estimating background... Estimating background took 0.348557949066 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 1.00406813622 s Creating peak regions... Creating peak regions took 22.1736998558 s Estimating background... Estimating background took 0.330412864685 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 1.03377485275 s Creating peak regions... Creating peak regions took 21.1621599197 s Estimating background... Estimating background took 0.330856084824 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 1.11774301529 s Creating peak regions... Creating peak regions took 20.1759819984 s Estimating background... Estimating background took 0.326948881149 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.995631933212 s Creating peak regions... Creating peak regions took 19.494300127 s Estimating background... Estimating background took 0.231205940247 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.637465000153 s Creating peak regions... Creating peak regions took 13.2452158928 s Estimating background... Estimating background took 0.34117603302 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 1.93274116516 s Creating peak regions... Creating peak regions took 42.4173369408 s Estimating background... Estimating background took 0.472315073013 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.094507932663 s Creating peak regions... Creating peak regions took 0.22833609581 s Estimating background... Estimating background took 0.265794992447 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.037801027298 s Creating peak regions... Creating peak regions took 0.277412176132 s Estimating background... Estimating background took 0.270405054092 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0319077968597 s Creating peak regions... Creating peak regions took 0.166883945465 s Estimating background... Estimating background took 0.267723083496 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0369729995728 s Creating peak regions... Creating peak regions took 0.210597038269 s Estimating background... Estimating background took 0.282624006271 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 2.59557008743 s Creating peak regions... Creating peak regions took 46.0789568424 s Estimating background... Estimating background took 3.98972511292 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 1.25433397293 s Creating peak regions... Creating peak regions took 34.7246420383 s Estimating background... Estimating background took 0.359283924103 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 1.62879896164 s Creating peak regions... Creating peak regions took 33.7583909035 s Estimating background... Estimating background took 0.38375711441 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0645730495453 s Creating peak regions... Creating peak regions took 0.0825860500336 s Estimating background... Estimating background took 0.289061784744 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 1.83198690414 s Creating peak regions... Creating peak regions took 36.321352005 s Estimating background... Estimating background took 0.391587972641 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0228400230408 s Creating peak regions... Creating peak regions took 0.383323907852 s Estimating background... Estimating background took 0.302436113358 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 1.23397779465 s Creating peak regions... Creating peak regions took 32.6850011349 s Estimating background... Estimating background took 0.409294128418 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 1.46598505974 s Creating peak regions... Creating peak regions took 30.5741341114 s Estimating background... Estimating background took 0.515316963196 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 1.6215159893 s Creating peak regions... Creating peak regions took 27.6563282013 s Estimating background... Estimating background took 0.3903028965 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 1.46224498749 s Creating peak regions... Creating peak regions took 26.7538590431 s Estimating background... Estimating background took 0.53505396843 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0981550216675 s Creating peak regions... Creating peak regions took 0.039733171463 s Estimating background... Estimating background took 0.32198381424 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0312922000885 s Creating peak regions... Creating peak regions took 0.050076007843 s Estimating background... Estimating background took 0.297825098038 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0558309555054 s Creating peak regions... Creating peak regions took 0.068598985672 s Estimating background... Estimating background took 0.315647125244 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0281040668488 s Creating peak regions... Creating peak regions took 0.0189139842987 s Estimating background... Estimating background took 0.297617912292 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0366070270538 s Creating peak regions... Creating peak regions took 0.0183928012848 s Estimating background... Estimating background took 0.308215856552 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0493972301483 s Creating peak regions... Creating peak regions took 0.0366549491882 s Estimating background... Estimating background took 0.326215028763 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0571489334106 s Creating peak regions... Creating peak regions took 0.0716319084167 s Estimating background... Estimating background took 0.31648516655 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.102738142014 s Creating peak regions... Creating peak regions took 0.0309569835663 s Estimating background... Estimating background took 0.306421995163 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0371489524841 s Creating peak regions... Creating peak regions took 0.0329129695892 s Estimating background... Estimating background took 0.289260149002 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.05193400383 s Creating peak regions... Creating peak regions took 0.07941198349 s Estimating background... Estimating background took 0.284889936447 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0403518676758 s Creating peak regions... Creating peak regions took 0.0738489627838 s Estimating background... Estimating background took 0.300215959549 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0334620475769 s Creating peak regions... Creating peak regions took 0.0357220172882 s Estimating background... Estimating background took 0.321265935898 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0367119312286 s Creating peak regions... Creating peak regions took 0.0318720340729 s Estimating background... Estimating background took 0.317228078842 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0589361190796 s Creating peak regions... Creating peak regions took 0.216804981232 s Estimating background... Estimating background took 0.30122089386 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.782425880432 s Creating peak regions... Creating peak regions took 35.5567750931 s Estimating background... Estimating background took 0.309400081635 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0777869224548 s Creating peak regions... Creating peak regions took 0.36420917511 s Estimating background... Estimating background took 0.320579051971 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Reading data took 0.0554039478302 s Creating peak regions... Creating peak regions took 18.1921498775 s Estimating background... Estimating background took 0.297755002975 s Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data... Processing TAL1_G1E-ER4_3h_Rep1-GSM1689029/aligned.36mers.unique.bam Reading in data...