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='GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/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='GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/', 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 GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 1.89689779282 s
Creating peak regions... Creating peak regions took 58.9840080738 s
Estimating background... Estimating background took 5.74619698524 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 1.84335279465 s
Creating peak regions... Creating peak regions took 67.5301430225 s
Estimating background... Estimating background took 7.1243429184 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 1.27308511734 s
Creating peak regions... Creating peak regions took 43.6668269634 s
Estimating background... Estimating background took 5.38875794411 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 1.70871591568 s
Creating peak regions... Creating peak regions took 47.2889368534 s
Estimating background... Estimating background took 4.71526503563 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 1.32187199593 s
Creating peak regions... Creating peak regions took 43.6948149204 s
Estimating background... Estimating background took 5.53883600235 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 1.24270200729 s
Creating peak regions... Creating peak regions took 41.7675299644 s
Estimating background... Estimating background took 5.34867882729 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 1.14821696281 s
Creating peak regions... Creating peak regions took 37.067317009 s
Estimating background... Estimating background took 4.2084710598 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 1.32292795181 s
Creating peak regions... Creating peak regions took 33.3242189884 s
Estimating background... Estimating background took 0.898662805557 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 0.82213306427 s
Creating peak regions... Creating peak regions took 31.7158179283 s
Estimating background... Estimating background took 4.13715600967 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 0.856271028519 s
Creating peak regions... Creating peak regions took 29.9535238743 s
Estimating background... Estimating background took 1.09090805054 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 1.31739091873 s
Creating peak regions... Creating peak regions took 31.4449400902 s
Estimating background... Estimating background took 3.97571992874 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 0.899898052216 s
Creating peak regions... Creating peak regions took 31.9652500153 s
Estimating background... Estimating background took 3.87284111977 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 1.09809994698 s
Creating peak regions... Creating peak regions took 28.6563100815 s
Estimating background... Estimating background took 0.789878129959 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 0.80580496788 s
Creating peak regions... Creating peak regions took 24.767619133 s
Estimating background... Estimating background took 0.788526058197 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 0.784805059433 s
Creating peak regions... Creating peak regions took 24.6243159771 s
Estimating background... Estimating background took 0.795449972153 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 0.734127044678 s
Creating peak regions... Creating peak regions took 21.0751738548 s
Estimating background... Estimating background took 0.791579008102 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 0.903535842896 s
Creating peak regions... Creating peak regions took 18.287553072 s
Estimating background... Estimating background took 0.780370950699 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 0.640999078751 s
Creating peak regions... Creating peak regions took 18.4810020924 s
Estimating background... Estimating background took 3.39753913879 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 0.532439947128 s
Creating peak regions... Creating peak regions took 13.5834701061 s
Estimating background... Estimating background took 0.70521402359 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 0.743041992188 s
Creating peak regions... Creating peak regions took 15.3919539452 s
Estimating background... Estimating background took 0.704652070999 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 0.414621114731 s
Creating peak regions... Creating peak regions took 11.7099888325 s
Estimating background... Estimating background took 0.599811077118 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 0.342087984085 s
Creating peak regions... Creating peak regions took 12.4853849411 s
Estimating background... Estimating background took 0.500325202942 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 1.33616495132 s
Creating peak regions... Creating peak regions took 34.8717169762 s
Estimating background... Estimating background took 0.831017971039 s


Processing GM10831_VDR_ChIP-exo_VD_stimulated-GSM1889557/aligned.36mers.unique.bam
Reading in data... Reading data took 0.257625102997 s
Creating peak regions... Creating peak regions took 0.172885894775 s
Estimating background... Estimating background took 4.85511398315 s