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='GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/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='GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/', 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 GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 4.73504400253 s
Creating peak regions... Creating peak regions took 60.7988660336 s
Estimating background... Estimating background took 14.5114250183 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 4.75197601318 s
Creating peak regions... Creating peak regions took 66.9601988792 s
Estimating background... Estimating background took 14.1181030273 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 4.55007505417 s
Creating peak regions... Creating peak regions took 53.0236620903 s
Estimating background... Estimating background took 12.1131298542 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 3.63104009628 s
Creating peak regions... Creating peak regions took 54.4635009766 s
Estimating background... Estimating background took 12.1101138592 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 3.50874018669 s
Creating peak regions... Creating peak regions took 52.89752388 s
Estimating background... Estimating background took 10.9805920124 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 4.14090895653 s
Creating peak regions... Creating peak regions took 50.7028560638 s
Estimating background... Estimating background took 10.819589138 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 3.05087184906 s
Creating peak regions... Creating peak regions took 42.4981110096 s
Estimating background... Estimating background took 9.41573786736 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 3.14777994156 s
Creating peak regions... Creating peak regions took 44.6776390076 s
Estimating background... Estimating background took 9.304708004 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 2.14556908607 s
Creating peak regions... Creating peak regions took 44.6540720463 s
Estimating background... Estimating background took 7.77453994751 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 2.82077789307 s
Creating peak regions... Creating peak regions took 40.7148478031 s
Estimating background... Estimating background took 8.61014986038 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 2.83331918716 s
Creating peak regions... Creating peak regions took 34.5726001263 s
Estimating background... Estimating background took 8.56260299683 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 3.30422091484 s
Creating peak regions... Creating peak regions took 36.4006719589 s
Estimating background... Estimating background took 8.99527096748 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 2.05664491653 s
Creating peak regions... Creating peak regions took 29.5717549324 s
Estimating background... Estimating background took 6.00347709656 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 2.2637181282 s
Creating peak regions... Creating peak regions took 28.1047899723 s
Estimating background... Estimating background took 6.06636500359 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 2.06109714508 s
Creating peak regions... Creating peak regions took 27.0185658932 s
Estimating background... Estimating background took 5.53074002266 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 1.66760611534 s
Creating peak regions... Creating peak regions took 25.9864308834 s
Estimating background... Estimating background took 5.14312291145 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 2.03710389137 s
Creating peak regions... Creating peak regions took 22.0235090256 s
Estimating background... Estimating background took 5.11189007759 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 1.75141811371 s
Creating peak regions... Creating peak regions took 23.1775209904 s
Estimating background... Estimating background took 4.67427206039 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 1.16472315788 s
Creating peak regions... Creating peak regions took 15.9238488674 s
Estimating background... Estimating background took 3.99402403831 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 1.63118100166 s
Creating peak regions... Creating peak regions took 16.2869038582 s
Estimating background... Estimating background took 4.17353701591 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 0.871229171753 s
Creating peak regions... Creating peak regions took 12.4431960583 s
Estimating background... Estimating background took 2.9608309269 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 0.867465019226 s
Creating peak regions... Creating peak regions took 12.7960629463 s
Estimating background... Estimating background took 1.69307112694 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 2.72089290619 s
Creating peak regions... Creating peak regions took 39.7690479755 s
Estimating background... Estimating background took 6.36082601547 s


Processing GM12383_VDR_ChIP-exo_VD_stimulated-GSM1889565/aligned.36mers.unique.bam
Reading in data... Reading data took 0.407673120499 s
Creating peak regions... Creating peak regions took 0.218069791794 s
Estimating background... Estimating background took 1.89100694656 s