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='GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/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='GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/', 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 GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 4.56965303421 s
Creating peak regions... Creating peak regions took 62.3309218884 s
Estimating background... Estimating background took 16.3928010464 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 4.24547505379 s
Creating peak regions... Creating peak regions took 66.1145660877 s
Estimating background... Estimating background took 15.9637870789 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 5.09148406982 s
Creating peak regions... Creating peak regions took 65.351503849 s
Estimating background... Estimating background took 13.3623480797 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 3.46333312988 s
Creating peak regions... Creating peak regions took 60.3268089294 s
Estimating background... Estimating background took 13.4645810127 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 3.38292312622 s
Creating peak regions... Creating peak regions took 47.3442008495 s
Estimating background... Estimating background took 12.0908229351 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 3.23431301117 s
Creating peak regions... Creating peak regions took 47.8869419098 s
Estimating background... Estimating background took 13.0381259918 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 2.76922893524 s
Creating peak regions... Creating peak regions took 38.3391191959 s
Estimating background... Estimating background took 10.6390829086 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 3.02020907402 s
Creating peak regions... Creating peak regions took 41.8604118824 s
Estimating background... Estimating background took 10.2117879391 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 2.10642385483 s
Creating peak regions... Creating peak regions took 37.2487242222 s
Estimating background... Estimating background took 8.38378286362 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 2.63432788849 s
Creating peak regions... Creating peak regions took 41.3166239262 s
Estimating background... Estimating background took 9.04706406593 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 2.85931587219 s
Creating peak regions... Creating peak regions took 36.1183187962 s
Estimating background... Estimating background took 9.5764131546 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 3.00781583786 s
Creating peak regions... Creating peak regions took 37.3479878902 s
Estimating background... Estimating background took 9.38579010963 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 2.76094198227 s
Creating peak regions... Creating peak regions took 32.1113569736 s
Estimating background... Estimating background took 6.84989905357 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 1.96849703789 s
Creating peak regions... Creating peak regions took 30.6988201141 s
Estimating background... Estimating background took 7.1564719677 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 1.58182406425 s
Creating peak regions... Creating peak regions took 30.197876215 s
Estimating background... Estimating background took 6.82211089134 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 1.66632294655 s
Creating peak regions... Creating peak regions took 21.4091079235 s
Estimating background... Estimating background took 5.88704991341 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 1.94109416008 s
Creating peak regions... Creating peak regions took 20.9522469044 s
Estimating background... Estimating background took 6.55936193466 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 1.55472707748 s
Creating peak regions... Creating peak regions took 20.2698040009 s
Estimating background... Estimating background took 5.36248612404 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 1.34781813622 s
Creating peak regions... Creating peak regions took 20.8292679787 s
Estimating background... Estimating background took 5.40020799637 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 1.96036911011 s
Creating peak regions... Creating peak regions took 18.5022392273 s
Estimating background... Estimating background took 4.6006500721 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 0.834811925888 s
Creating peak regions... Creating peak regions took 13.0486011505 s
Estimating background... Estimating background took 3.62409496307 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 0.805656909943 s
Creating peak regions... Creating peak regions took 12.9633178711 s
Estimating background... Estimating background took 3.25221610069 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 1.57862901688 s
Creating peak regions... Creating peak regions took 38.0587530136 s
Estimating background... Estimating background took 5.60228610039 s


Processing GM19248_VDR_ChIP-exo_VD_stimulated-GSM1889580/aligned.36mers.unique.bam
Reading in data... Reading data took 0.621683835983 s
Creating peak regions... Creating peak regions took 0.201201915741 s
Estimating background... Estimating background took 1.5598180294 s