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='GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/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='GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/', 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 GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 7.57028317451 s
Creating peak regions... Creating peak regions took 80.3686380386 s
Estimating background... Estimating background took 24.8963229656 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 8.19329690933 s
Creating peak regions... Creating peak regions took 91.7354500294 s
Estimating background... Estimating background took 26.1151609421 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 6.74317979813 s
Creating peak regions... Creating peak regions took 62.6921129227 s
Estimating background... Estimating background took 21.4155359268 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 5.98602199554 s
Creating peak regions... Creating peak regions took 66.2299458981 s
Estimating background... Estimating background took 20.5240180492 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 6.00876808167 s
Creating peak regions... Creating peak regions took 66.2200899124 s
Estimating background... Estimating background took 19.1678378582 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 6.2790749073 s
Creating peak regions... Creating peak regions took 60.6337239742 s
Estimating background... Estimating background took 18.7065370083 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 5.01710700989 s
Creating peak regions... Creating peak regions took 53.4997189045 s
Estimating background... Estimating background took 15.9280760288 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 5.22774505615 s
Creating peak regions... Creating peak regions took 54.929049015 s
Estimating background... Estimating background took 15.8710651398 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 4.1478228569 s
Creating peak regions... Creating peak regions took 54.6699571609 s
Estimating background... Estimating background took 12.1373710632 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 4.25829982758 s
Creating peak regions... Creating peak regions took 42.0336050987 s
Estimating background... Estimating background took 13.8670940399 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 4.5927491188 s
Creating peak regions... Creating peak regions took 40.0765810013 s
Estimating background... Estimating background took 14.2765347958 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 4.68117308617 s
Creating peak regions... Creating peak regions took 48.3336269855 s
Estimating background... Estimating background took 14.2696049213 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 3.27448606491 s
Creating peak regions... Creating peak regions took 37.6167469025 s
Estimating background... Estimating background took 9.9879219532 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 3.55755996704 s
Creating peak regions... Creating peak regions took 34.7305870056 s
Estimating background... Estimating background took 10.022605896 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 2.86071300507 s
Creating peak regions... Creating peak regions took 36.0085690022 s
Estimating background... Estimating background took 9.33668398857 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 2.58712291718 s
Creating peak regions... Creating peak regions took 30.9827609062 s
Estimating background... Estimating background took 8.58800292015 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 3.25198602676 s
Creating peak regions... Creating peak regions took 25.3485410213 s
Estimating background... Estimating background took 8.34960889816 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 3.47076797485 s
Creating peak regions... Creating peak regions took 27.4821550846 s
Estimating background... Estimating background took 8.14736890793 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 1.91069889069 s
Creating peak regions... Creating peak regions took 19.5402472019 s
Estimating background... Estimating background took 6.07268095016 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 2.34582614899 s
Creating peak regions... Creating peak regions took 19.5382730961 s
Estimating background... Estimating background took 6.5995221138 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 1.61245417595 s
Creating peak regions... Creating peak regions took 16.9570670128 s
Estimating background... Estimating background took 4.59165811539 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 1.17812180519 s
Creating peak regions... Creating peak regions took 16.2008221149 s
Estimating background... Estimating background took 4.1049079895 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 4.14063978195 s
Creating peak regions... Creating peak regions took 49.3089661598 s
Estimating background... Estimating background took 11.623128891 s


Processing GM19190_VDR_ChIP-exo_VD_stimulated-GSM1889571/aligned.36mers.unique.bam
Reading in data... Reading data took 0.698805093765 s
Creating peak regions... Creating peak regions took 0.295485019684 s
Estimating background... Estimating background took 1.64605593681 s