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='GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/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='GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/', 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 GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 3.76712393761 s
Creating peak regions... Creating peak regions took 57.4554810524 s
Estimating background... Estimating background took 9.2531478405 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 4.00027298927 s
Creating peak regions... Creating peak regions took 60.086992979 s
Estimating background... Estimating background took 9.21569514275 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 3.13787817955 s
Creating peak regions... Creating peak regions took 53.7271010876 s
Estimating background... Estimating background took 7.86815404892 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 3.49391198158 s
Creating peak regions... Creating peak regions took 51.1437520981 s
Estimating background... Estimating background took 7.09148812294 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 2.57341980934 s
Creating peak regions... Creating peak regions took 46.1058368683 s
Estimating background... Estimating background took 7.04560804367 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 2.73364496231 s
Creating peak regions... Creating peak regions took 44.49218297 s
Estimating background... Estimating background took 7.45413398743 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 2.34464406967 s
Creating peak regions... Creating peak regions took 39.622439146 s
Estimating background... Estimating background took 6.22383594513 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 2.08059978485 s
Creating peak regions... Creating peak regions took 44.3349819183 s
Estimating background... Estimating background took 6.27111196518 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 2.15435504913 s
Creating peak regions... Creating peak regions took 41.3898899555 s
Estimating background... Estimating background took 5.79828095436 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 2.55767703056 s
Creating peak regions... Creating peak regions took 38.5427241325 s
Estimating background... Estimating background took 6.00020813942 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 2.17953181267 s
Creating peak regions... Creating peak regions took 35.0092289448 s
Estimating background... Estimating background took 6.51010394096 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 2.30551791191 s
Creating peak regions... Creating peak regions took 35.1420669556 s
Estimating background... Estimating background took 5.93627715111 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 1.82280611992 s
Creating peak regions... Creating peak regions took 31.7858588696 s
Estimating background... Estimating background took 4.45329594612 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 1.50127410889 s
Creating peak regions... Creating peak regions took 27.334597826 s
Estimating background... Estimating background took 4.644313097 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 1.32824087143 s
Creating peak regions... Creating peak regions took 30.2460048199 s
Estimating background... Estimating background took 4.90369200706 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 1.88635087013 s
Creating peak regions... Creating peak regions took 33.0845630169 s
Estimating background... Estimating background took 4.81990599632 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 1.82072305679 s
Creating peak regions... Creating peak regions took 26.7852458954 s
Estimating background... Estimating background took 4.25978398323 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 1.0842628479 s
Creating peak regions... Creating peak regions took 21.4242370129 s
Estimating background... Estimating background took 3.88703894615 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 0.97248506546 s
Creating peak regions... Creating peak regions took 15.2517290115 s
Estimating background... Estimating background took 3.16764998436 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 1.31174588203 s
Creating peak regions... Creating peak regions took 15.7018489838 s
Estimating background... Estimating background took 3.3038687706 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 0.737220048904 s
Creating peak regions... Creating peak regions took 12.8242628574 s
Estimating background... Estimating background took 1.14662790298 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 0.709160089493 s
Creating peak regions... Creating peak regions took 15.0465831757 s
Estimating background... Estimating background took 1.23775696754 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 2.42097687721 s
Creating peak regions... Creating peak regions took 49.3954701424 s
Estimating background... Estimating background took 5.38396811485 s


Processing GM10847_VDR_ChIP-exo_VD_stimulated-GSM1889559/aligned.36mers.unique.bam
Reading in data... Reading data took 0.249053955078 s
Creating peak regions... Creating peak regions took 0.189810037613 s
Estimating background... Estimating background took 1.23244714737 s