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='GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/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='GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/', 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 GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 1.13934183121 s
Creating peak regions... Creating peak regions took 55.645277977 s
Estimating background... Estimating background took 4.81262683868 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 1.16992402077 s
Creating peak regions... Creating peak regions took 59.0857591629 s
Estimating background... Estimating background took 0.811172008514 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.986171960831 s
Creating peak regions... Creating peak regions took 45.5819709301 s
Estimating background... Estimating background took 0.597191095352 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 1.02151298523 s
Creating peak regions... Creating peak regions took 41.4005749226 s
Estimating background... Estimating background took 0.63649892807 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.983999013901 s
Creating peak regions... Creating peak regions took 39.7088038921 s
Estimating background... Estimating background took 0.614992141724 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.921290159225 s
Creating peak regions... Creating peak regions took 37.6913528442 s
Estimating background... Estimating background took 0.825419902802 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.882488965988 s
Creating peak regions... Creating peak regions took 35.428579092 s
Estimating background... Estimating background took 3.79887509346 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.639808893204 s
Creating peak regions... Creating peak regions took 31.8242051601 s
Estimating background... Estimating background took 0.491650104523 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.636169910431 s
Creating peak regions... Creating peak regions took 31.0771899223 s
Estimating background... Estimating background took 0.52125787735 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.69237279892 s
Creating peak regions... Creating peak regions took 29.0337688923 s
Estimating background... Estimating background took 0.628901958466 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.803185939789 s
Creating peak regions... Creating peak regions took 29.6936869621 s
Estimating background... Estimating background took 0.518829107285 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.564389944077 s
Creating peak regions... Creating peak regions took 29.4911010265 s
Estimating background... Estimating background took 0.641781806946 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.56716299057 s
Creating peak regions... Creating peak regions took 24.9460160732 s
Estimating background... Estimating background took 0.519637823105 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.44672703743 s
Creating peak regions... Creating peak regions took 24.0370049477 s
Estimating background... Estimating background took 0.518414020538 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.536792039871 s
Creating peak regions... Creating peak regions took 22.8911778927 s
Estimating background... Estimating background took 0.52149105072 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.442784070969 s
Creating peak regions... Creating peak regions took 20.3702340126 s
Estimating background... Estimating background took 0.538848161697 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.574043989182 s
Creating peak regions... Creating peak regions took 20.2271299362 s
Estimating background... Estimating background took 0.546216964722 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.560361146927 s
Creating peak regions... Creating peak regions took 19.3517549038 s
Estimating background... Estimating background took 0.552712917328 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.317774057388 s
Creating peak regions... Creating peak regions took 13.915915966 s
Estimating background... Estimating background took 0.550384998322 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.267803907394 s
Creating peak regions... Creating peak regions took 15.6191289425 s
Estimating background... Estimating background took 0.453629970551 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.218753099442 s
Creating peak regions... Creating peak regions took 11.145840168 s
Estimating background... Estimating background took 0.55838394165 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.238354921341 s
Creating peak regions... Creating peak regions took 11.7329518795 s
Estimating background... Estimating background took 0.44718503952 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.592129945755 s
Creating peak regions... Creating peak regions took 34.7069120407 s
Estimating background... Estimating background took 0.437674999237 s


Processing GM19235_VDR_ChIP-exo_VD_stimulated-GSM1889576/aligned.36mers.unique.bam
Reading in data... Reading data took 0.150027990341 s
Creating peak regions... Creating peak regions took 0.113663196564 s
Estimating background... Estimating background took 4.06770300865 s