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='GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/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='GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/', 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 GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 2.36171293259 s
Creating peak regions... Creating peak regions took 57.1796729565 s
Estimating background... Estimating background took 6.65471196175 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 2.01692199707 s
Creating peak regions... Creating peak regions took 60.0244188309 s
Estimating background... Estimating background took 6.69026899338 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 1.8707690239 s
Creating peak regions... Creating peak regions took 62.2318019867 s
Estimating background... Estimating background took 6.03715705872 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 1.32812595367 s
Creating peak regions... Creating peak regions took 48.1367120743 s
Estimating background... Estimating background took 5.52850008011 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 2.86628198624 s
Creating peak regions... Creating peak regions took 48.4481720924 s
Estimating background... Estimating background took 5.20411705971 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 1.5847928524 s
Creating peak regions... Creating peak regions took 39.0823178291 s
Estimating background... Estimating background took 5.46414113045 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 1.71647310257 s
Creating peak regions... Creating peak regions took 39.3672881126 s
Estimating background... Estimating background took 4.70832800865 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 1.51615905762 s
Creating peak regions... Creating peak regions took 32.7202761173 s
Estimating background... Estimating background took 4.36788678169 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 1.18105697632 s
Creating peak regions... Creating peak regions took 31.9842069149 s
Estimating background... Estimating background took 4.07689118385 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 0.898609876633 s
Creating peak regions... Creating peak regions took 30.7579550743 s
Estimating background... Estimating background took 4.11700415611 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 1.42927789688 s
Creating peak regions... Creating peak regions took 32.8608129025 s
Estimating background... Estimating background took 4.13541603088 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 1.53241300583 s
Creating peak regions... Creating peak regions took 32.2954390049 s
Estimating background... Estimating background took 4.1224489212 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 0.778563976288 s
Creating peak regions... Creating peak regions took 27.177325964 s
Estimating background... Estimating background took 0.93571305275 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 1.31918501854 s
Creating peak regions... Creating peak regions took 29.4997749329 s
Estimating background... Estimating background took 1.14993691444 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 1.11031413078 s
Creating peak regions... Creating peak regions took 29.3407449722 s
Estimating background... Estimating background took 3.34038591385 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 0.797007083893 s
Creating peak regions... Creating peak regions took 24.7145648003 s
Estimating background... Estimating background took 3.20774698257 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 1.09637188911 s
Creating peak regions... Creating peak regions took 19.9028160572 s
Estimating background... Estimating background took 2.93248295784 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 0.762611150742 s
Creating peak regions... Creating peak regions took 18.3494839668 s
Estimating background... Estimating background took 0.869551181793 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 0.829391002655 s
Creating peak regions... Creating peak regions took 14.0645031929 s
Estimating background... Estimating background took 2.63157081604 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 0.741929769516 s
Creating peak regions... Creating peak regions took 16.4522979259 s
Estimating background... Estimating background took 2.36797499657 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 0.464677095413 s
Creating peak regions... Creating peak regions took 11.4925909042 s
Estimating background... Estimating background took 0.654013872147 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 0.343151092529 s
Creating peak regions... Creating peak regions took 12.8300349712 s
Estimating background... Estimating background took 0.561748981476 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 1.08416485786 s
Creating peak regions... Creating peak regions took 37.2606608868 s
Estimating background... Estimating background took 0.698230981827 s


Processing GM06986_VDR_ChIP-exo_VD_stimulated-GSM1889552/aligned.36mers.unique.bam
Reading in data... Reading data took 0.253826141357 s
Creating peak regions... Creating peak regions took 0.134677886963 s
Estimating background... Estimating background took 4.40903282166 s