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='GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/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='GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/', 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 GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 9.51166391373 s
Creating peak regions... Creating peak regions took 79.6628661156 s
Estimating background... Estimating background took 39.1564040184 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 10.3210790157 s
Creating peak regions... Creating peak regions took 78.4045920372 s
Estimating background... Estimating background took 39.8614990711 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 8.46535181999 s
Creating peak regions... Creating peak regions took 65.4639818668 s
Estimating background... Estimating background took 33.2026820183 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 9.48313498497 s
Creating peak regions... Creating peak regions took 70.6248571873 s
Estimating background... Estimating background took 31.3142659664 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 7.39822101593 s
Creating peak regions... Creating peak regions took 60.4433920383 s
Estimating background... Estimating background took 31.4655320644 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 7.77486801147 s
Creating peak regions... Creating peak regions took 62.0320601463 s
Estimating background... Estimating background took 29.4586069584 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 6.84330606461 s
Creating peak regions... Creating peak regions took 59.0905201435 s
Estimating background... Estimating background took 24.9032440186 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 6.55070114136 s
Creating peak regions... Creating peak regions took 53.736123085 s
Estimating background... Estimating background took 24.1397469044 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 4.96206307411 s
Creating peak regions... Creating peak regions took 45.3004200459 s
Estimating background... Estimating background took 19.3190419674 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 5.78176403046 s
Creating peak regions... Creating peak regions took 49.5969419479 s
Estimating background... Estimating background took 22.7688031197 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 5.88285183907 s
Creating peak regions... Creating peak regions took 42.4228329659 s
Estimating background... Estimating background took 21.6488528252 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 5.84202408791 s
Creating peak regions... Creating peak regions took 40.6663100719 s
Estimating background... Estimating background took 21.4398560524 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 4.60992312431 s
Creating peak regions... Creating peak regions took 41.4288849831 s
Estimating background... Estimating background took 15.4762761593 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 4.04043698311 s
Creating peak regions... Creating peak regions took 34.0904898643 s
Estimating background... Estimating background took 14.5179669857 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 3.86731100082 s
Creating peak regions... Creating peak regions took 34.0028560162 s
Estimating background... Estimating background took 14.0078570843 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 3.38854885101 s
Creating peak regions... Creating peak regions took 27.2247800827 s
Estimating background... Estimating background took 13.014647007 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 3.39359092712 s
Creating peak regions... Creating peak regions took 26.0644869804 s
Estimating background... Estimating background took 13.295830965 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 3.43846297264 s
Creating peak regions... Creating peak regions took 27.2466731071 s
Estimating background... Estimating background took 12.8573639393 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 2.29007601738 s
Creating peak regions... Creating peak regions took 16.908080101 s
Estimating background... Estimating background took 8.72355794907 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 2.51883602142 s
Creating peak regions... Creating peak regions took 22.9824669361 s
Estimating background... Estimating background took 10.1208798885 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 1.79110693932 s
Creating peak regions... Creating peak regions took 14.727132082 s
Estimating background... Estimating background took 6.52824091911 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 1.35062813759 s
Creating peak regions... Creating peak regions took 18.7032630444 s
Estimating background... Estimating background took 5.77164793015 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 4.01463603973 s
Creating peak regions... Creating peak regions took 50.6654441357 s
Estimating background... Estimating background took 8.69074702263 s


Processing GM19189_VDR_ChIP-exo_VD_stimulated-GSM1889570/aligned.36mers.unique.bam
Reading in data... Reading data took 0.835994958878 s
Creating peak regions... Creating peak regions took 0.21232008934 s
Estimating background... Estimating background took 1.84383010864 s