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='GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/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='GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/', 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 GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 4.32719993591 s
Creating peak regions... Creating peak regions took 58.8921399117 s
Estimating background... Estimating background took 12.9019467831 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 4.51069307327 s
Creating peak regions... Creating peak regions took 61.90508008 s
Estimating background... Estimating background took 13.5054268837 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 4.25861907005 s
Creating peak regions... Creating peak regions took 54.624694109 s
Estimating background... Estimating background took 11.3549251556 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 3.24061894417 s
Creating peak regions... Creating peak regions took 49.8344209194 s
Estimating background... Estimating background took 9.95700716972 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 3.28565001488 s
Creating peak regions... Creating peak regions took 48.022632122 s
Estimating background... Estimating background took 10.3479669094 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 3.35398888588 s
Creating peak regions... Creating peak regions took 43.8498389721 s
Estimating background... Estimating background took 10.245620966 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 2.93172192574 s
Creating peak regions... Creating peak regions took 42.033675909 s
Estimating background... Estimating background took 8.75026297569 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 2.84696483612 s
Creating peak regions... Creating peak regions took 34.7444310188 s
Estimating background... Estimating background took 8.42425990105 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 2.36898899078 s
Creating peak regions... Creating peak regions took 34.0377919674 s
Estimating background... Estimating background took 7.26392889023 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 2.88742613792 s
Creating peak regions... Creating peak regions took 33.0444309711 s
Estimating background... Estimating background took 7.73111104965 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 2.48859214783 s
Creating peak regions... Creating peak regions took 33.4584159851 s
Estimating background... Estimating background took 7.61946797371 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 3.11481595039 s
Creating peak regions... Creating peak regions took 41.4346108437 s
Estimating background... Estimating background took 8.03055095673 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 1.85441398621 s
Creating peak regions... Creating peak regions took 27.8861129284 s
Estimating background... Estimating background took 5.4966070652 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 1.91305184364 s
Creating peak regions... Creating peak regions took 27.4551138878 s
Estimating background... Estimating background took 5.61770486832 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 1.78379583359 s
Creating peak regions... Creating peak regions took 26.1712999344 s
Estimating background... Estimating background took 5.33688402176 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 1.42023515701 s
Creating peak regions... Creating peak regions took 23.2737572193 s
Estimating background... Estimating background took 5.14288401604 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 1.4942510128 s
Creating peak regions... Creating peak regions took 21.2406959534 s
Estimating background... Estimating background took 5.14387893677 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 1.51414608955 s
Creating peak regions... Creating peak regions took 19.6587688923 s
Estimating background... Estimating background took 4.56745100021 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 1.25147604942 s
Creating peak regions... Creating peak regions took 14.986825943 s
Estimating background... Estimating background took 3.64912509918 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 1.23110699654 s
Creating peak regions... Creating peak regions took 15.9222171307 s
Estimating background... Estimating background took 3.86084580421 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 0.649448871613 s
Creating peak regions... Creating peak regions took 11.7114799023 s
Estimating background... Estimating background took 2.76043391228 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 0.555280923843 s
Creating peak regions... Creating peak regions took 11.4033639431 s
Estimating background... Estimating background took 2.8682141304 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 1.43948411942 s
Creating peak regions... Creating peak regions took 35.0194859505 s
Estimating background... Estimating background took 4.66562414169 s


Processing GM07029_VDR_ChIP-exo_VD_stimulated-GSM1889555/aligned.36mers.unique.bam
Reading in data... Reading data took 0.291576862335 s
Creating peak regions... Creating peak regions took 0.161608934402 s
Estimating background... Estimating background took 1.06951189041 s