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='GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/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='GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/', 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 GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 4.83242511749 s
Creating peak regions... Creating peak regions took 61.033479929 s
Estimating background... Estimating background took 13.3090898991 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 4.6390068531 s
Creating peak regions... Creating peak regions took 67.1944041252 s
Estimating background... Estimating background took 13.3664400578 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 3.80907607079 s
Creating peak regions... Creating peak regions took 60.6179130077 s
Estimating background... Estimating background took 10.4744720459 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 3.55065703392 s
Creating peak regions... Creating peak regions took 54.2174720764 s
Estimating background... Estimating background took 9.55804395676 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 3.07669115067 s
Creating peak regions... Creating peak regions took 45.9664130211 s
Estimating background... Estimating background took 9.49911808968 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 3.38898086548 s
Creating peak regions... Creating peak regions took 43.8821220398 s
Estimating background... Estimating background took 9.72172904015 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 2.84221386909 s
Creating peak regions... Creating peak regions took 41.0034000874 s
Estimating background... Estimating background took 8.9186527729 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 2.86356902122 s
Creating peak regions... Creating peak regions took 35.729970932 s
Estimating background... Estimating background took 7.67662811279 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 2.03093504906 s
Creating peak regions... Creating peak regions took 33.4493448734 s
Estimating background... Estimating background took 6.89724993706 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 2.47651410103 s
Creating peak regions... Creating peak regions took 34.1042428017 s
Estimating background... Estimating background took 7.18385791779 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 2.49106812477 s
Creating peak regions... Creating peak regions took 33.3794050217 s
Estimating background... Estimating background took 7.08960604668 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 3.40641999245 s
Creating peak regions... Creating peak regions took 35.2384941578 s
Estimating background... Estimating background took 7.59657096863 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 1.6726269722 s
Creating peak regions... Creating peak regions took 27.8704710007 s
Estimating background... Estimating background took 5.68868303299 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 1.62560296059 s
Creating peak regions... Creating peak regions took 27.4131281376 s
Estimating background... Estimating background took 5.60287904739 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 1.92012786865 s
Creating peak regions... Creating peak regions took 28.2122411728 s
Estimating background... Estimating background took 4.962859869 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 1.36682486534 s
Creating peak regions... Creating peak regions took 22.818253994 s
Estimating background... Estimating background took 4.73802495003 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 1.66512799263 s
Creating peak regions... Creating peak regions took 20.1875400543 s
Estimating background... Estimating background took 5.11590313911 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 1.7152659893 s
Creating peak regions... Creating peak regions took 24.9192810059 s
Estimating background... Estimating background took 4.59173488617 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 1.16801404953 s
Creating peak regions... Creating peak regions took 15.3972020149 s
Estimating background... Estimating background took 3.65522313118 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 1.18234610558 s
Creating peak regions... Creating peak regions took 20.6000759602 s
Estimating background... Estimating background took 3.76876497269 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 0.767095088959 s
Creating peak regions... Creating peak regions took 12.4967420101 s
Estimating background... Estimating background took 1.61062192917 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 1.01831912994 s
Creating peak regions... Creating peak regions took 15.5034849644 s
Estimating background... Estimating background took 1.31628584862 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 2.88126182556 s
Creating peak regions... Creating peak regions took 41.7964818478 s
Estimating background... Estimating background took 6.42736005783 s


Processing GM11918_VDR_ChIP-exo_VD_stimulated-GSM1889562/aligned.36mers.unique.bam
Reading in data... Reading data took 0.222793102264 s
Creating peak regions... Creating peak regions took 0.195040941238 s
Estimating background... Estimating background took 1.19754886627 s