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='GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/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='GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/', 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 GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 4.74071311951 s
Creating peak regions... Creating peak regions took 61.7578840256 s
Estimating background... Estimating background took 14.8278710842 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 4.80199694633 s
Creating peak regions... Creating peak regions took 61.4783320427 s
Estimating background... Estimating background took 14.9845249653 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 3.983522892 s
Creating peak regions... Creating peak regions took 51.4007890224 s
Estimating background... Estimating background took 11.9670519829 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 3.73262500763 s
Creating peak regions... Creating peak regions took 47.8060941696 s
Estimating background... Estimating background took 10.8151130676 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 3.7671558857 s
Creating peak regions... Creating peak regions took 54.8920750618 s
Estimating background... Estimating background took 10.7802820206 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 4.48855018616 s
Creating peak regions... Creating peak regions took 47.9673550129 s
Estimating background... Estimating background took 11.2566790581 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 3.22152209282 s
Creating peak regions... Creating peak regions took 39.3336610794 s
Estimating background... Estimating background took 9.98909902573 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 3.39922714233 s
Creating peak regions... Creating peak regions took 37.0131080151 s
Estimating background... Estimating background took 9.03662014008 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 2.54487991333 s
Creating peak regions... Creating peak regions took 35.5116758347 s
Estimating background... Estimating background took 7.75707983971 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 2.65944600105 s
Creating peak regions... Creating peak regions took 36.7830560207 s
Estimating background... Estimating background took 8.64294099808 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 3.02158808708 s
Creating peak regions... Creating peak regions took 39.9744939804 s
Estimating background... Estimating background took 8.60522985458 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 3.29028201103 s
Creating peak regions... Creating peak regions took 33.5132858753 s
Estimating background... Estimating background took 8.41691803932 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 2.1941640377 s
Creating peak regions... Creating peak regions took 37.5797870159 s
Estimating background... Estimating background took 6.51365804672 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 2.12275290489 s
Creating peak regions... Creating peak regions took 28.5572860241 s
Estimating background... Estimating background took 6.27437901497 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 1.72382116318 s
Creating peak regions... Creating peak regions took 26.9022011757 s
Estimating background... Estimating background took 5.78965401649 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 1.66709804535 s
Creating peak regions... Creating peak regions took 23.6022250652 s
Estimating background... Estimating background took 5.3487071991 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 1.77412009239 s
Creating peak regions... Creating peak regions took 21.6817750931 s
Estimating background... Estimating background took 5.43310809135 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 2.07494807243 s
Creating peak regions... Creating peak regions took 21.0639710426 s
Estimating background... Estimating background took 5.00354790688 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 1.55076098442 s
Creating peak regions... Creating peak regions took 16.9003369808 s
Estimating background... Estimating background took 4.32481098175 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 1.54085302353 s
Creating peak regions... Creating peak regions took 16.962225914 s
Estimating background... Estimating background took 4.19992113113 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 0.847576141357 s
Creating peak regions... Creating peak regions took 12.3862850666 s
Estimating background... Estimating background took 3.05079889297 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 0.953747034073 s
Creating peak regions... Creating peak regions took 12.6993319988 s
Estimating background... Estimating background took 1.7080218792 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 2.12942790985 s
Creating peak regions... Creating peak regions took 38.997633934 s
Estimating background... Estimating background took 5.04500007629 s


Processing GM11829_VDR_ChIP-exo_VD_stimulated-GSM1889560/aligned.36mers.unique.bam
Reading in data... Reading data took 0.289162158966 s
Creating peak regions... Creating peak regions took 0.18078994751 s
Estimating background... Estimating background took 1.41030597687 s