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='GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/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='GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/', 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 GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 1.04384994507 s
Creating peak regions... Creating peak regions took 58.0343170166 s
Estimating background... Estimating background took 0.761296987534 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 1.08429098129 s
Creating peak regions... Creating peak regions took 54.8915569782 s
Estimating background... Estimating background took 0.61863899231 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.904046773911 s
Creating peak regions... Creating peak regions took 41.5643601418 s
Estimating background... Estimating background took 0.498613119125 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.73316693306 s
Creating peak regions... Creating peak regions took 41.6019511223 s
Estimating background... Estimating background took 0.544934034348 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.762670993805 s
Creating peak regions... Creating peak regions took 41.7317378521 s
Estimating background... Estimating background took 0.510611057281 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.831531047821 s
Creating peak regions... Creating peak regions took 37.8836019039 s
Estimating background... Estimating background took 5.44978690147 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.575600862503 s
Creating peak regions... Creating peak regions took 36.2518801689 s
Estimating background... Estimating background took 0.582619190216 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.730172157288 s
Creating peak regions... Creating peak regions took 33.0856230259 s
Estimating background... Estimating background took 0.557629108429 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.484758853912 s
Creating peak regions... Creating peak regions took 32.4537398815 s
Estimating background... Estimating background took 0.476947069168 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.505414009094 s
Creating peak regions... Creating peak regions took 30.8999528885 s
Estimating background... Estimating background took 0.562297105789 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.659610033035 s
Creating peak regions... Creating peak regions took 29.538766861 s
Estimating background... Estimating background took 0.553803920746 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.585513830185 s
Creating peak regions... Creating peak regions took 31.1266200542 s
Estimating background... Estimating background took 0.555938959122 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.32063794136 s
Creating peak regions... Creating peak regions took 25.4951848984 s
Estimating background... Estimating background took 0.460336923599 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.313170194626 s
Creating peak regions... Creating peak regions took 25.192497015 s
Estimating background... Estimating background took 0.454147100449 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.319410085678 s
Creating peak regions... Creating peak regions took 23.6900529861 s
Estimating background... Estimating background took 0.465904951096 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.446691036224 s
Creating peak regions... Creating peak regions took 20.7257080078 s
Estimating background... Estimating background took 0.441169977188 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.293324947357 s
Creating peak regions... Creating peak regions took 19.0334999561 s
Estimating background... Estimating background took 0.559631109238 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.411108016968 s
Creating peak regions... Creating peak regions took 18.3965890408 s
Estimating background... Estimating background took 0.459663152695 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.256083011627 s
Creating peak regions... Creating peak regions took 13.7948970795 s
Estimating background... Estimating background took 0.54890704155 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.391951084137 s
Creating peak regions... Creating peak regions took 14.9428730011 s
Estimating background... Estimating background took 0.466421842575 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.164236068726 s
Creating peak regions... Creating peak regions took 11.712515831 s
Estimating background... Estimating background took 0.446717023849 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.166130065918 s
Creating peak regions... Creating peak regions took 12.3833959103 s
Estimating background... Estimating background took 0.333346128464 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.527228116989 s
Creating peak regions... Creating peak regions took 36.1647360325 s
Estimating background... Estimating background took 0.378039121628 s


Processing GM12752_VDR_ChIP-exo_VD_stimulated-GSM1889568/aligned.36mers.unique.bam
Reading in data... Reading data took 0.188979148865 s
Creating peak regions... Creating peak regions took 0.123725175858 s
Estimating background... Estimating background took 4.30284714699 s