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='GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/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='GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/', 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 GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 5.03466415405 s
Creating peak regions... Creating peak regions took 60.1967229843 s
Estimating background... Estimating background took 17.1119451523 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 4.9025759697 s
Creating peak regions... Creating peak regions took 60.3498969078 s
Estimating background... Estimating background took 16.3082039356 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 4.52364706993 s
Creating peak regions... Creating peak regions took 61.9841680527 s
Estimating background... Estimating background took 13.7882699966 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 3.94340705872 s
Creating peak regions... Creating peak regions took 47.035615921 s
Estimating background... Estimating background took 11.6875960827 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 4.41554188728 s
Creating peak regions... Creating peak regions took 45.3616089821 s
Estimating background... Estimating background took 11.7209091187 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 4.02847218513 s
Creating peak regions... Creating peak regions took 46.2906649113 s
Estimating background... Estimating background took 12.4868228436 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 3.55242800713 s
Creating peak regions... Creating peak regions took 40.2989068031 s
Estimating background... Estimating background took 9.99625897408 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 2.97988200188 s
Creating peak regions... Creating peak regions took 38.8310987949 s
Estimating background... Estimating background took 9.48728108406 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 3.18822193146 s
Creating peak regions... Creating peak regions took 37.3170909882 s
Estimating background... Estimating background took 8.52984905243 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 2.77599096298 s
Creating peak regions... Creating peak regions took 34.2586190701 s
Estimating background... Estimating background took 9.00239896774 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 3.23412418365 s
Creating peak regions... Creating peak regions took 39.4459710121 s
Estimating background... Estimating background took 9.59285902977 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 2.58641791344 s
Creating peak regions... Creating peak regions took 35.3044230938 s
Estimating background... Estimating background took 10.0822367668 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 1.84391593933 s
Creating peak regions... Creating peak regions took 30.5132431984 s
Estimating background... Estimating background took 6.2427740097 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 2.0159330368 s
Creating peak regions... Creating peak regions took 28.6797308922 s
Estimating background... Estimating background took 7.11143994331 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 1.73004889488 s
Creating peak regions... Creating peak regions took 27.2918980122 s
Estimating background... Estimating background took 6.35082316399 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 2.13666582108 s
Creating peak regions... Creating peak regions took 25.7396519184 s
Estimating background... Estimating background took 6.03561306 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 1.78257703781 s
Creating peak regions... Creating peak regions took 20.9819850922 s
Estimating background... Estimating background took 6.5281689167 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 1.92196202278 s
Creating peak regions... Creating peak regions took 20.6258268356 s
Estimating background... Estimating background took 5.07173895836 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 1.67144393921 s
Creating peak regions... Creating peak regions took 17.7999258041 s
Estimating background... Estimating background took 5.39823317528 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 1.62008094788 s
Creating peak regions... Creating peak regions took 18.4353249073 s
Estimating background... Estimating background took 4.6786339283 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 1.1718351841 s
Creating peak regions... Creating peak regions took 12.8511691093 s
Estimating background... Estimating background took 3.09740805626 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 0.853374004364 s
Creating peak regions... Creating peak regions took 12.9207968712 s
Estimating background... Estimating background took 3.3579890728 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 2.04685688019 s
Creating peak regions... Creating peak regions took 36.3980071545 s
Estimating background... Estimating background took 5.38020300865 s


Processing GM12872_VDR_ChIP-exo_VD_stimulated-GSM1889569/aligned.36mers.unique.bam
Reading in data... Reading data took 0.545471906662 s
Creating peak regions... Creating peak regions took 0.185228824615 s
Estimating background... Estimating background took 1.27776813507 s