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/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed', center6=0, chromnames='/oak/stanford/groups/akundaje/marinovg/genomes/hg19/female.hg19.chrom.sizes', e4='PeakXus', fastq='GM12878_Smc3_nexus-GSM1872891/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='GM12878_Smc3_nexus-GSM1872891/', 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 GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 9.53367590904 s
Creating peak regions... Creating peak regions took 67.1312429905 s
Estimating background... Estimating background took 78.278938055 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 11.0160119534 s
Creating peak regions... Creating peak regions took 70.0161349773 s
Estimating background... Estimating background took 68.6164522171 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 9.61386609077 s
Creating peak regions... Creating peak regions took 59.9740278721 s
Estimating background... Estimating background took 57.2801270485 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 8.53058791161 s
Creating peak regions... Creating peak regions took 56.9009299278 s
Estimating background... Estimating background took 47.6999490261 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 8.16881394386 s
Creating peak regions... Creating peak regions took 52.5335888863 s
Estimating background... Estimating background took 50.5928461552 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 8.61938881874 s
Creating peak regions... Creating peak regions took 60.9216561317 s
Estimating background... Estimating background took 56.3602528572 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 6.62589788437 s
Creating peak regions... Creating peak regions took 48.5298461914 s
Estimating background... Estimating background took 44.9239327908 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 6.94382500648 s
Creating peak regions... Creating peak regions took 50.4630250931 s
Estimating background... Estimating background took 40.6652870178 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 4.70724010468 s
Creating peak regions... Creating peak regions took 44.2250649929 s
Estimating background... Estimating background took 34.2798779011 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 5.95406413078 s
Creating peak regions... Creating peak regions took 39.3029069901 s
Estimating background... Estimating background took 45.1732831001 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 6.52038407326 s
Creating peak regions... Creating peak regions took 46.8436470032 s
Estimating background... Estimating background took 43.93506217 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 6.52534604073 s
Creating peak regions... Creating peak regions took 43.776736021 s
Estimating background... Estimating background took 47.7274770737 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 4.06350779533 s
Creating peak regions... Creating peak regions took 36.1643788815 s
Estimating background... Estimating background took 24.5518510342 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 5.1392519474 s
Creating peak regions... Creating peak regions took 38.1893370152 s
Estimating background... Estimating background took 30.5265109539 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 4.16270399094 s
Creating peak regions... Creating peak regions took 30.0565781593 s
Estimating background... Estimating background took 27.6137189865 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 4.00651502609 s
Creating peak regions... Creating peak regions took 28.7201230526 s
Estimating background... Estimating background took 25.5611979961 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 4.39958882332 s
Creating peak regions... Creating peak regions took 24.8482329845 s
Estimating background... Estimating background took 31.4613139629 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 3.35371112823 s
Creating peak regions... Creating peak regions took 24.1549289227 s
Estimating background... Estimating background took 20.6340219975 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 3.17392396927 s
Creating peak regions... Creating peak regions took 18.2896969318 s
Estimating background... Estimating background took 25.5375130177 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 2.94491195679 s
Creating peak regions... Creating peak regions took 17.8907251358 s
Estimating background... Estimating background took 19.918254137 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 1.64274120331 s
Creating peak regions... Creating peak regions took 13.2677490711 s
Estimating background... Estimating background took 11.4842119217 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 1.87469100952 s
Creating peak regions... Creating peak regions took 14.166369915 s
Estimating background... Estimating background took 13.6518330574 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 4.81903886795 s
Creating peak regions... Creating peak regions took 44.3213739395 s
Estimating background... Estimating background took 28.9566130638 s


Processing GM12878_Smc3_nexus-GSM1872891/aligned.36mers.unique.bam
Reading in data... Reading data took 0.410195112228 s
Creating peak regions... Creating peak regions took 0.445429086685 s
Estimating background... Estimating background took 1.21149897575 s