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_RAD21_nexus-GSM1872890/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_RAD21_nexus-GSM1872890/', 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_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 7.1348991394 s
Creating peak regions... Creating peak regions took 62.473692894 s
Estimating background... Estimating background took 56.9201340675 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 8.3518269062 s
Creating peak regions... Creating peak regions took 68.8379170895 s
Estimating background... Estimating background took 48.7664690018 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 6.50882196426 s
Creating peak regions... Creating peak regions took 58.7985880375 s
Estimating background... Estimating background took 41.6425039768 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 5.8342730999 s
Creating peak regions... Creating peak regions took 54.8840389252 s
Estimating background... Estimating background took 33.7793209553 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 5.31003594398 s
Creating peak regions... Creating peak regions took 49.2226889133 s
Estimating background... Estimating background took 38.3032507896 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 6.40574216843 s
Creating peak regions... Creating peak regions took 47.960873127 s
Estimating background... Estimating background took 40.9888620377 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 5.54313898087 s
Creating peak regions... Creating peak regions took 46.3356540203 s
Estimating background... Estimating background took 32.4910161495 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 4.31485700607 s
Creating peak regions... Creating peak regions took 41.0561859608 s
Estimating background... Estimating background took 29.9098272324 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 4.18294000626 s
Creating peak regions... Creating peak regions took 35.3386490345 s
Estimating background... Estimating background took 25.522851944 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 4.50552296638 s
Creating peak regions... Creating peak regions took 37.2215261459 s
Estimating background... Estimating background took 29.2056419849 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 4.39340305328 s
Creating peak regions... Creating peak regions took 35.4069890976 s
Estimating background... Estimating background took 29.1842489243 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 5.53708910942 s
Creating peak regions... Creating peak regions took 42.0696260929 s
Estimating background... Estimating background took 32.0077829361 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 2.88055109978 s
Creating peak regions... Creating peak regions took 31.4253540039 s
Estimating background... Estimating background took 20.0345978737 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 3.50554895401 s
Creating peak regions... Creating peak regions took 31.5751750469 s
Estimating background... Estimating background took 20.5848851204 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 3.20645093918 s
Creating peak regions... Creating peak regions took 27.5985109806 s
Estimating background... Estimating background took 20.3227100372 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 3.11057901382 s
Creating peak regions... Creating peak regions took 24.4529099464 s
Estimating background... Estimating background took 17.9958510399 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 3.16479992867 s
Creating peak regions... Creating peak regions took 24.1539311409 s
Estimating background... Estimating background took 24.2369270325 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 3.05902910233 s
Creating peak regions... Creating peak regions took 22.0290088654 s
Estimating background... Estimating background took 14.7905218601 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 2.42182397842 s
Creating peak regions... Creating peak regions took 16.7108278275 s
Estimating background... Estimating background took 17.034952879 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 2.39586687088 s
Creating peak regions... Creating peak regions took 19.7125940323 s
Estimating background... Estimating background took 15.6467058659 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 1.55075192451 s
Creating peak regions... Creating peak regions took 15.2355730534 s
Estimating background... Estimating background took 8.01504898071 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 1.60822319984 s
Creating peak regions... Creating peak regions took 14.460668087 s
Estimating background... Estimating background took 9.57254505157 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 3.74311900139 s
Creating peak regions... Creating peak regions took 42.6060950756 s
Estimating background... Estimating background took 21.2522671223 s


Processing GM12878_RAD21_nexus-GSM1872890/aligned.36mers.unique.bam
Reading in data... Reading data took 0.111644029617 s
Creating peak regions... Creating peak regions took 0.277809143066 s
Estimating background... Estimating background took 0.659940004349 s