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='GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/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='GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/', 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 GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 3.19429206848 s
Creating peak regions... Creating peak regions took 57.1160008907 s
Estimating background... Estimating background took 9.25829315186 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 2.99380898476 s
Creating peak regions... Creating peak regions took 55.2566490173 s
Estimating background... Estimating background took 9.01610207558 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 2.48591995239 s
Creating peak regions... Creating peak regions took 47.3430261612 s
Estimating background... Estimating background took 7.51456689835 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 2.02810907364 s
Creating peak regions... Creating peak regions took 53.104460001 s
Estimating background... Estimating background took 7.61638498306 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 2.17176198959 s
Creating peak regions... Creating peak regions took 44.2316761017 s
Estimating background... Estimating background took 6.75247311592 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 1.91327500343 s
Creating peak regions... Creating peak regions took 41.7377138138 s
Estimating background... Estimating background took 6.53075194359 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 2.2107629776 s
Creating peak regions... Creating peak regions took 38.7251729965 s
Estimating background... Estimating background took 5.83473610878 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 1.85820603371 s
Creating peak regions... Creating peak regions took 36.1524341106 s
Estimating background... Estimating background took 5.56201004982 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 1.54481983185 s
Creating peak regions... Creating peak regions took 32.3600430489 s
Estimating background... Estimating background took 5.31175994873 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 1.51672196388 s
Creating peak regions... Creating peak regions took 36.778249979 s
Estimating background... Estimating background took 5.39100193977 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 1.69651913643 s
Creating peak regions... Creating peak regions took 32.863530159 s
Estimating background... Estimating background took 5.66043806076 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 1.68925094604 s
Creating peak regions... Creating peak regions took 32.2627699375 s
Estimating background... Estimating background took 5.30556988716 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 1.42017698288 s
Creating peak regions... Creating peak regions took 27.5243430138 s
Estimating background... Estimating background took 3.9833650589 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 1.46148204803 s
Creating peak regions... Creating peak regions took 26.2230210304 s
Estimating background... Estimating background took 4.02526688576 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 0.983736038208 s
Creating peak regions... Creating peak regions took 24.8954119682 s
Estimating background... Estimating background took 4.07175278664 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 0.899861097336 s
Creating peak regions... Creating peak regions took 22.2672390938 s
Estimating background... Estimating background took 3.82133197784 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 1.16986322403 s
Creating peak regions... Creating peak regions took 19.7304291725 s
Estimating background... Estimating background took 3.68060112 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 1.10682487488 s
Creating peak regions... Creating peak regions took 19.9193408489 s
Estimating background... Estimating background took 3.50405716896 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 0.801536083221 s
Creating peak regions... Creating peak regions took 16.1397109032 s
Estimating background... Estimating background took 1.41629695892 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 1.17682600021 s
Creating peak regions... Creating peak regions took 16.7738618851 s
Estimating background... Estimating background took 3.21677803993 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 0.562788963318 s
Creating peak regions... Creating peak regions took 12.1600577831 s
Estimating background... Estimating background took 2.21958804131 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 0.737906932831 s
Creating peak regions... Creating peak regions took 12.7495291233 s
Estimating background... Estimating background took 2.18024897575 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 1.26794099808 s
Creating peak regions... Creating peak regions took 37.5204849243 s
Estimating background... Estimating background took 4.80468511581 s


Processing GM19237_VDR_ChIP-exo_VD_stimulated-GSM1889578/aligned.36mers.unique.bam
Reading in data... Reading data took 0.433567047119 s
Creating peak regions... Creating peak regions took 0.179811954498 s
Estimating background... Estimating background took 1.48321008682 s