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='GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/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='GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/', 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 GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 2.88880085945 s
Creating peak regions... Creating peak regions took 61.4167649746 s
Estimating background... Estimating background took 8.6700720787 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 2.61030912399 s
Creating peak regions... Creating peak regions took 58.15863204 s
Estimating background... Estimating background took 9.0169198513 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 2.71639990807 s
Creating peak regions... Creating peak regions took 64.2768311501 s
Estimating background... Estimating background took 7.85559391975 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 2.18424677849 s
Creating peak regions... Creating peak regions took 50.7513349056 s
Estimating background... Estimating background took 7.1721508503 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 2.31018209457 s
Creating peak regions... Creating peak regions took 47.4947729111 s
Estimating background... Estimating background took 7.07940006256 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 2.0420050621 s
Creating peak regions... Creating peak regions took 44.9970290661 s
Estimating background... Estimating background took 6.94304013252 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 1.78861498833 s
Creating peak regions... Creating peak regions took 41.7189249992 s
Estimating background... Estimating background took 6.32755303383 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 1.77813696861 s
Creating peak regions... Creating peak regions took 42.9912650585 s
Estimating background... Estimating background took 6.23017907143 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 1.69523692131 s
Creating peak regions... Creating peak regions took 36.0652358532 s
Estimating background... Estimating background took 4.98162698746 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 2.0099439621 s
Creating peak regions... Creating peak regions took 34.3899259567 s
Estimating background... Estimating background took 5.21102499962 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 1.88835501671 s
Creating peak regions... Creating peak regions took 34.7117037773 s
Estimating background... Estimating background took 5.36861801147 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 1.71258807182 s
Creating peak regions... Creating peak regions took 32.9947440624 s
Estimating background... Estimating background took 5.28647708893 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 1.49407196045 s
Creating peak regions... Creating peak regions took 35.4141769409 s
Estimating background... Estimating background took 4.27091813087 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 1.15462803841 s
Creating peak regions... Creating peak regions took 28.6616339684 s
Estimating background... Estimating background took 4.26947999001 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 0.863157987595 s
Creating peak regions... Creating peak regions took 27.6548700333 s
Estimating background... Estimating background took 4.03224420547 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 1.13291788101 s
Creating peak regions... Creating peak regions took 27.495360136 s
Estimating background... Estimating background took 3.96488714218 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 1.16747498512 s
Creating peak regions... Creating peak regions took 21.0480749607 s
Estimating background... Estimating background took 3.35669112206 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 1.30246901512 s
Creating peak regions... Creating peak regions took 22.9525449276 s
Estimating background... Estimating background took 3.42644906044 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 0.723262786865 s
Creating peak regions... Creating peak regions took 15.6581990719 s
Estimating background... Estimating background took 1.38863110542 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 1.14327812195 s
Creating peak regions... Creating peak regions took 16.7000479698 s
Estimating background... Estimating background took 2.91548490524 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 0.57704782486 s
Creating peak regions... Creating peak regions took 11.7031970024 s
Estimating background... Estimating background took 2.49812197685 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 0.549619913101 s
Creating peak regions... Creating peak regions took 13.2917568684 s
Estimating background... Estimating background took 1.0298538208 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 1.32091808319 s
Creating peak regions... Creating peak regions took 43.5039591789 s
Estimating background... Estimating background took 4.57400608063 s


Processing GM19236_VDR_ChIP-exo_VD_stimulated-GSM1889577/aligned.36mers.unique.bam
Reading in data... Reading data took 0.426847934723 s
Creating peak regions... Creating peak regions took 0.173823833466 s
Estimating background... Estimating background took 1.53753185272 s