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='GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/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='GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/', 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 GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 1.15732502937 s
Creating peak regions... Creating peak regions took 56.4824120998 s
Estimating background... Estimating background took 0.624907970428 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.844559907913 s
Creating peak regions... Creating peak regions took 57.9054160118 s
Estimating background... Estimating background took 5.11204099655 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 1.00096297264 s
Creating peak regions... Creating peak regions took 45.5237650871 s
Estimating background... Estimating background took 0.650290966034 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.912383079529 s
Creating peak regions... Creating peak regions took 43.0043988228 s
Estimating background... Estimating background took 0.494391918182 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.944642066956 s
Creating peak regions... Creating peak regions took 41.0627100468 s
Estimating background... Estimating background took 0.490880012512 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.919002056122 s
Creating peak regions... Creating peak regions took 38.4657039642 s
Estimating background... Estimating background took 0.65703701973 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.73490190506 s
Creating peak regions... Creating peak regions took 36.5371510983 s
Estimating background... Estimating background took 4.26736998558 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.674833059311 s
Creating peak regions... Creating peak regions took 33.2960548401 s
Estimating background... Estimating background took 0.559165000916 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.533399105072 s
Creating peak regions... Creating peak regions took 31.9506289959 s
Estimating background... Estimating background took 1.44793105125 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.746714830399 s
Creating peak regions... Creating peak regions took 35.2560560703 s
Estimating background... Estimating background took 0.568019151688 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.824575185776 s
Creating peak regions... Creating peak regions took 34.100564003 s
Estimating background... Estimating background took 0.541191101074 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.670104980469 s
Creating peak regions... Creating peak regions took 30.2041740417 s
Estimating background... Estimating background took 0.568517923355 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.492032051086 s
Creating peak regions... Creating peak regions took 26.9505069256 s
Estimating background... Estimating background took 0.461002826691 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.47297000885 s
Creating peak regions... Creating peak regions took 23.2351660728 s
Estimating background... Estimating background took 0.439041852951 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.411279916763 s
Creating peak regions... Creating peak regions took 22.6572861671 s
Estimating background... Estimating background took 0.435730934143 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.332015037537 s
Creating peak regions... Creating peak regions took 20.8931131363 s
Estimating background... Estimating background took 0.437084913254 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.389939069748 s
Creating peak regions... Creating peak regions took 19.1890649796 s
Estimating background... Estimating background took 0.441168069839 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.430796146393 s
Creating peak regions... Creating peak regions took 16.7584741116 s
Estimating background... Estimating background took 0.425781011581 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.289235830307 s
Creating peak regions... Creating peak regions took 13.2163648605 s
Estimating background... Estimating background took 0.409921884537 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.37505698204 s
Creating peak regions... Creating peak regions took 15.2314169407 s
Estimating background... Estimating background took 0.435600042343 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.208060979843 s
Creating peak regions... Creating peak regions took 11.114428997 s
Estimating background... Estimating background took 0.41876578331 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.160991191864 s
Creating peak regions... Creating peak regions took 11.2556970119 s
Estimating background... Estimating background took 0.295965909958 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.384514093399 s
Creating peak regions... Creating peak regions took 35.6718518734 s
Estimating background... Estimating background took 0.45831990242 s


Processing GM11919_VDR_ChIP-exo_VD_stimulated-GSM1889563/aligned.36mers.unique.bam
Reading in data... Reading data took 0.137377023697 s
Creating peak regions... Creating peak regions took 0.0909259319305 s
Estimating background... Estimating background took 3.98340296745 s