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='GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/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='GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/', 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 GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 3.18329000473 s
Creating peak regions... Creating peak regions took 56.7871959209 s
Estimating background... Estimating background took 10.1927690506 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 3.71925997734 s
Creating peak regions... Creating peak regions took 62.6925830841 s
Estimating background... Estimating background took 10.9787080288 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 3.05393195152 s
Creating peak regions... Creating peak regions took 55.7955567837 s
Estimating background... Estimating background took 10.2133219242 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 3.16631984711 s
Creating peak regions... Creating peak regions took 50.6673550606 s
Estimating background... Estimating background took 8.35109901428 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 2.58381891251 s
Creating peak regions... Creating peak regions took 42.5531840324 s
Estimating background... Estimating background took 8.12320780754 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 2.73980593681 s
Creating peak regions... Creating peak regions took 53.5994770527 s
Estimating background... Estimating background took 8.97101187706 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 2.71909117699 s
Creating peak regions... Creating peak regions took 51.4382090569 s
Estimating background... Estimating background took 8.40760803223 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 2.91929602623 s
Creating peak regions... Creating peak regions took 41.9257321358 s
Estimating background... Estimating background took 7.15311288834 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 1.9570479393 s
Creating peak regions... Creating peak regions took 42.3569288254 s
Estimating background... Estimating background took 6.63240599632 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 2.53883981705 s
Creating peak regions... Creating peak regions took 37.2660298347 s
Estimating background... Estimating background took 6.41054415703 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 2.0244281292 s
Creating peak regions... Creating peak regions took 42.2052111626 s
Estimating background... Estimating background took 6.90203499794 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 2.78505897522 s
Creating peak regions... Creating peak regions took 36.3641149998 s
Estimating background... Estimating background took 7.11787414551 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 1.56387805939 s
Creating peak regions... Creating peak regions took 34.8051121235 s
Estimating background... Estimating background took 5.241492033 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 1.91205501556 s
Creating peak regions... Creating peak regions took 29.3979539871 s
Estimating background... Estimating background took 4.8434779644 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 1.22024393082 s
Creating peak regions... Creating peak regions took 28.6848080158 s
Estimating background... Estimating background took 4.94367218018 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 1.42302393913 s
Creating peak regions... Creating peak regions took 25.136015892 s
Estimating background... Estimating background took 4.33643102646 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 1.47907996178 s
Creating peak regions... Creating peak regions took 21.1947689056 s
Estimating background... Estimating background took 4.22406983376 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 1.57840108871 s
Creating peak regions... Creating peak regions took 22.8887009621 s
Estimating background... Estimating background took 3.82078003883 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 1.08948397636 s
Creating peak regions... Creating peak regions took 16.4127509594 s
Estimating background... Estimating background took 3.37381887436 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 1.07921600342 s
Creating peak regions... Creating peak regions took 16.5290999413 s
Estimating background... Estimating background took 3.56165504456 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 0.696989059448 s
Creating peak regions... Creating peak regions took 14.8732788563 s
Estimating background... Estimating background took 1.42442893982 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 0.810357809067 s
Creating peak regions... Creating peak regions took 15.450594902 s
Estimating background... Estimating background took 1.31630301476 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 2.10508513451 s
Creating peak regions... Creating peak regions took 43.8288910389 s
Estimating background... Estimating background took 6.05785083771 s


Processing GM19247_VDR_ChIP-exo_VD_stimulated-GSM1889579/aligned.36mers.unique.bam
Reading in data... Reading data took 0.422361850739 s
Creating peak regions... Creating peak regions took 0.256441831589 s
Estimating background... Estimating background took 1.43205595016 s