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='ChIP_exo_Lhx3_iNIL-GSM2098379/alignments.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='ChIP_exo_Lhx3_iNIL-GSM2098379/peakXus/', 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='ChIP_exo_Lhx3_iNIL-GSM2098379/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='ChIP_exo_Lhx3_iNIL-GSM2098379/peakXus/', 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='ChIP_exo_Lhx3_iNIL-GSM2098379/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='ChIP_exo_Lhx3_iNIL-GSM2098379/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 ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 3.78319597244 s Creating peak regions... Creating peak regions took 30.2488059998 s Estimating background... Estimating background took 0.56157207489 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 3.23744082451 s Creating peak regions... Creating peak regions took 27.2906489372 s Estimating background... Estimating background took 0.550488948822 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 3.40187096596 s Creating peak regions... Creating peak regions took 26.9555139542 s Estimating background... Estimating background took 0.556762933731 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 2.98405313492 s Creating peak regions... Creating peak regions took 28.8962860107 s Estimating background... Estimating background took 0.55743098259 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 3.35400605202 s Creating peak regions... Creating peak regions took 27.690857172 s Estimating background... Estimating background took 0.652064085007 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 2.85882306099 s Creating peak regions... Creating peak regions took 23.0331680775 s Estimating background... Estimating background took 3.22994494438 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 3.11487603188 s Creating peak regions... Creating peak regions took 21.724036932 s Estimating background... Estimating background took 0.550102949142 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 2.189453125 s Creating peak regions... Creating peak regions took 21.1762440205 s Estimating background... Estimating background took 0.466163873672 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 3.08405995369 s Creating peak regions... Creating peak regions took 20.5907659531 s Estimating background... Estimating background took 0.583977937698 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 2.01906108856 s Creating peak regions... Creating peak regions took 14.7394518852 s Estimating background... Estimating background took 0.364968061447 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 5.72395396233 s Creating peak regions... Creating peak regions took 48.3407361507 s Estimating background... Estimating background took 0.84561085701 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0836341381073 s Creating peak regions... Creating peak regions took 0.192702054977 s Estimating background... Estimating background took 0.30280995369 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0632832050323 s Creating peak regions... Creating peak regions took 0.341615915298 s Estimating background... Estimating background took 0.312066078186 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0551209449768 s Creating peak regions... Creating peak regions took 0.198875188828 s Estimating background... Estimating background took 0.313847064972 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0388519763947 s Creating peak regions... Creating peak regions took 0.11564207077 s Estimating background... Estimating background took 0.292820930481 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 6.03473687172 s Creating peak regions... Creating peak regions took 44.8086938858 s Estimating background... Estimating background took 0.975473880768 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 4.99515104294 s Creating peak regions... Creating peak regions took 38.9497060776 s Estimating background... Estimating background took 5.81137108803 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 4.51273798943 s Creating peak regions... Creating peak regions took 45.0952789783 s Estimating background... Estimating background took 0.750612974167 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.1009349823 s Creating peak regions... Creating peak regions took 0.0709490776062 s Estimating background... Estimating background took 0.302218914032 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 4.12868785858 s Creating peak regions... Creating peak regions took 36.3270640373 s Estimating background... Estimating background took 0.751145839691 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0311851501465 s Creating peak regions... Creating peak regions took 0.432124853134 s Estimating background... Estimating background took 0.322749853134 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 4.19552087784 s Creating peak regions... Creating peak regions took 37.1120560169 s Estimating background... Estimating background took 4.05814909935 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 3.16523098946 s Creating peak regions... Creating peak regions took 30.8017661572 s Estimating background... Estimating background took 0.497724056244 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 3.37287306786 s Creating peak regions... Creating peak regions took 27.7008559704 s Estimating background... Estimating background took 0.700502872467 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 3.2768509388 s Creating peak regions... Creating peak regions took 27.3246839046 s Estimating background... Estimating background took 0.716027021408 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.186367988586 s Creating peak regions... Creating peak regions took 0.0843360424042 s Estimating background... Estimating background took 0.386643886566 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0492730140686 s Creating peak regions... Creating peak regions took 0.0586960315704 s Estimating background... Estimating background took 0.296725988388 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0560071468353 s Creating peak regions... Creating peak regions took 0.0332021713257 s Estimating background... Estimating background took 0.299510955811 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0547142028809 s Creating peak regions... Creating peak regions took 0.0492951869965 s Estimating background... Estimating background took 0.293857097626 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0560619831085 s Creating peak regions... Creating peak regions took 0.0691428184509 s Estimating background... Estimating background took 0.288532018661 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0550580024719 s Creating peak regions... Creating peak regions took 0.0470499992371 s Estimating background... Estimating background took 0.298462152481 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0545489788055 s Creating peak regions... Creating peak regions took 0.0307960510254 s Estimating background... Estimating background took 0.301706075668 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0553820133209 s Creating peak regions... Creating peak regions took 0.0286948680878 s Estimating background... Estimating background took 0.290254116058 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0412430763245 s Creating peak regions... Creating peak regions took 0.0450050830841 s Estimating background... Estimating background took 0.30106306076 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0547499656677 s Creating peak regions... Creating peak regions took 0.0944490432739 s Estimating background... Estimating background took 0.296648979187 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0402760505676 s Creating peak regions... Creating peak regions took 0.0621440410614 s Estimating background... Estimating background took 0.289405107498 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0565919876099 s Creating peak regions... Creating peak regions took 0.0350909233093 s Estimating background... Estimating background took 0.291061878204 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.151736974716 s Creating peak regions... Creating peak regions took 0.0265130996704 s Estimating background... Estimating background took 0.2921230793 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0628900527954 s Creating peak regions... Creating peak regions took 0.04301404953 s Estimating background... Estimating background took 0.301601886749 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0648820400238 s Creating peak regions... Creating peak regions took 0.0637209415436 s Estimating background... Estimating background took 0.289426088333 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0391099452972 s Creating peak regions... Creating peak regions took 0.0712780952454 s Estimating background... Estimating background took 0.283195972443 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0343809127808 s Creating peak regions... Creating peak regions took 0.036504983902 s Estimating background... Estimating background took 0.296921014786 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0606718063354 s Creating peak regions... Creating peak regions took 0.0386559963226 s Estimating background... Estimating background took 0.292563915253 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0982010364532 s Creating peak regions... Creating peak regions took 0.168909072876 s Estimating background... Estimating background took 0.287205934525 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 2.19815397263 s Creating peak regions... Creating peak regions took 37.1919147968 s Estimating background... Estimating background took 0.390561103821 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.0884909629822 s Creating peak regions... Creating peak regions took 0.397053956985 s Estimating background... Estimating background took 0.307328939438 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Reading data took 0.112549066544 s Creating peak regions... Creating peak regions took 18.7028300762 s Estimating background... Estimating background took 0.338855981827 s Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data... Processing ChIP_exo_Lhx3_iNIL-GSM2098379/aligned.36mers.unique.bam Reading in data...