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='GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/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='GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/', 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 GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 2.4076731205 s
Creating peak regions... Creating peak regions took 59.5490751266 s
Estimating background... Estimating background took 6.74923801422 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 2.27200889587 s
Creating peak regions... Creating peak regions took 57.6351099014 s
Estimating background... Estimating background took 6.87902283669 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 1.6890630722 s
Creating peak regions... Creating peak regions took 49.1785130501 s
Estimating background... Estimating background took 5.68858480453 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 1.60750794411 s
Creating peak regions... Creating peak regions took 54.8227319717 s
Estimating background... Estimating background took 5.76298809052 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 1.67409396172 s
Creating peak regions... Creating peak regions took 44.6292278767 s
Estimating background... Estimating background took 5.16821408272 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 1.7046020031 s
Creating peak regions... Creating peak regions took 47.751458168 s
Estimating background... Estimating background took 5.81586909294 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 1.36373806 s
Creating peak regions... Creating peak regions took 37.7371170521 s
Estimating background... Estimating background took 4.54822897911 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 1.23062515259 s
Creating peak regions... Creating peak regions took 33.9834930897 s
Estimating background... Estimating background took 4.33875894547 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 1.04314017296 s
Creating peak regions... Creating peak regions took 34.9035599232 s
Estimating background... Estimating background took 1.10092902184 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 1.40723204613 s
Creating peak regions... Creating peak regions took 33.6355750561 s
Estimating background... Estimating background took 4.24300098419 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 1.47731995583 s
Creating peak regions... Creating peak regions took 31.5170960426 s
Estimating background... Estimating background took 4.13698601723 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 1.39992189407 s
Creating peak regions... Creating peak regions took 29.1520440578 s
Estimating background... Estimating background took 4.20654296875 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 0.953235149384 s
Creating peak regions... Creating peak regions took 26.638092041 s
Estimating background... Estimating background took 3.32699298859 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 0.93719291687 s
Creating peak regions... Creating peak regions took 24.3585460186 s
Estimating background... Estimating background took 0.880405902863 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 0.679268836975 s
Creating peak regions... Creating peak regions took 22.1041111946 s
Estimating background... Estimating background took 3.30432987213 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 0.896291971207 s
Creating peak regions... Creating peak regions took 20.5607509613 s
Estimating background... Estimating background took 2.8221309185 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 0.638844966888 s
Creating peak regions... Creating peak regions took 18.6644060612 s
Estimating background... Estimating background took 0.988619089127 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 0.786098957062 s
Creating peak regions... Creating peak regions took 18.693600893 s
Estimating background... Estimating background took 2.64121389389 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 0.626853942871 s
Creating peak regions... Creating peak regions took 15.2802379131 s
Estimating background... Estimating background took 0.909111022949 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 0.811959981918 s
Creating peak regions... Creating peak regions took 16.5884821415 s
Estimating background... Estimating background took 0.698513031006 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 0.480985879898 s
Creating peak regions... Creating peak regions took 12.8871939182 s
Estimating background... Estimating background took 0.641584873199 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 0.407385110855 s
Creating peak regions... Creating peak regions took 11.7497470379 s
Estimating background... Estimating background took 0.570156097412 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 1.52553892136 s
Creating peak regions... Creating peak regions took 36.4578819275 s
Estimating background... Estimating background took 0.89996099472 s


Processing GM06989_VDR_ChIP-exo_VD_stimulated-GSM1889553/aligned.36mers.unique.bam
Reading in data... Reading data took 0.235020875931 s
Creating peak regions... Creating peak regions took 0.140063047409 s
Estimating background... Estimating background took 3.99233412743 s