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='GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/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='GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/', 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 GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 1.45546793938 s
Creating peak regions... Creating peak regions took 73.3463029861 s
Estimating background... Estimating background took 6.33242797852 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 1.46859788895 s
Creating peak regions... Creating peak regions took 67.8445599079 s
Estimating background... Estimating background took 6.60420680046 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 1.27157092094 s
Creating peak regions... Creating peak regions took 62.4129290581 s
Estimating background... Estimating background took 6.09000515938 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 1.15501093864 s
Creating peak regions... Creating peak regions took 51.9542961121 s
Estimating background... Estimating background took 0.981673002243 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 1.21337604523 s
Creating peak regions... Creating peak regions took 54.222181797 s
Estimating background... Estimating background took 5.26588201523 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 1.09751582146 s
Creating peak regions... Creating peak regions took 48.7721590996 s
Estimating background... Estimating background took 1.08271813393 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 1.06038713455 s
Creating peak regions... Creating peak regions took 44.883551836 s
Estimating background... Estimating background took 4.59783220291 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.801847934723 s
Creating peak regions... Creating peak regions took 40.9660170078 s
Estimating background... Estimating background took 4.19714999199 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.631380081177 s
Creating peak regions... Creating peak regions took 39.2858309746 s
Estimating background... Estimating background took 0.681926012039 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.989133834839 s
Creating peak regions... Creating peak regions took 38.2005450726 s
Estimating background... Estimating background took 3.99622583389 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.847321033478 s
Creating peak regions... Creating peak regions took 37.8015649319 s
Estimating background... Estimating background took 0.801933050156 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.946556091309 s
Creating peak regions... Creating peak regions took 40.9372091293 s
Estimating background... Estimating background took 4.13941407204 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.62813782692 s
Creating peak regions... Creating peak regions took 30.7080619335 s
Estimating background... Estimating background took 0.690629005432 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.632658958435 s
Creating peak regions... Creating peak regions took 29.3148860931 s
Estimating background... Estimating background took 0.72007894516 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.594580173492 s
Creating peak regions... Creating peak regions took 31.2829239368 s
Estimating background... Estimating background took 0.599813938141 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.525763034821 s
Creating peak regions... Creating peak regions took 24.9111230373 s
Estimating background... Estimating background took 0.695449113846 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.541389942169 s
Creating peak regions... Creating peak regions took 22.4830560684 s
Estimating background... Estimating background took 0.696553945541 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.491912126541 s
Creating peak regions... Creating peak regions took 21.5846579075 s
Estimating background... Estimating background took 0.603176116943 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.379446983337 s
Creating peak regions... Creating peak regions took 17.8407139778 s
Estimating background... Estimating background took 0.620126008987 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.432887077332 s
Creating peak regions... Creating peak regions took 20.9561369419 s
Estimating background... Estimating background took 0.585360050201 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.259726047516 s
Creating peak regions... Creating peak regions took 13.9275779724 s
Estimating background... Estimating background took 0.576349020004 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.280984163284 s
Creating peak regions... Creating peak regions took 14.5084781647 s
Estimating background... Estimating background took 0.493859052658 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.848978042603 s
Creating peak regions... Creating peak regions took 47.4650959969 s
Estimating background... Estimating background took 0.62068605423 s


Processing GM19214_VDR_ChIP-exo_VD_stimulated-GSM1889574/aligned.36mers.unique.bam
Reading in data... Reading data took 0.368093013763 s
Creating peak regions... Creating peak regions took 0.150129079819 s
Estimating background... Estimating background took 5.08895993233 s