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='GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/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='GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/', 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 GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 15.607981205 s
Creating peak regions... Creating peak regions took 77.4178118706 s
Estimating background... Estimating background took 96.6179580688 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 20.5510449409 s
Creating peak regions... Creating peak regions took 98.7039060593 s
Estimating background... Estimating background took 102.955631971 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 17.6476237774 s
Creating peak regions... Creating peak regions took 83.518018961 s
Estimating background... Estimating background took 87.6569981575 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 16.5028791428 s
Creating peak regions... Creating peak regions took 79.1685380936 s
Estimating background... Estimating background took 78.5898449421 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 13.7485809326 s
Creating peak regions... Creating peak regions took 68.2083849907 s
Estimating background... Estimating background took 76.3217160702 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 15.4524328709 s
Creating peak regions... Creating peak regions took 73.4955289364 s
Estimating background... Estimating background took 74.0811610222 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 11.2335281372 s
Creating peak regions... Creating peak regions took 53.6329541206 s
Estimating background... Estimating background took 64.0661680698 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 12.939925909 s
Creating peak regions... Creating peak regions took 61.4106678963 s
Estimating background... Estimating background took 60.8624250889 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 9.95112919807 s
Creating peak regions... Creating peak regions took 54.5991520882 s
Estimating background... Estimating background took 46.4292469025 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 10.773072958 s
Creating peak regions... Creating peak regions took 53.7452609539 s
Estimating background... Estimating background took 53.8093669415 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 11.7664659023 s
Creating peak regions... Creating peak regions took 53.4826369286 s
Estimating background... Estimating background took 53.9984459877 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 12.5275399685 s
Creating peak regions... Creating peak regions took 54.5550730228 s
Estimating background... Estimating background took 59.9160180092 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 8.68209314346 s
Creating peak regions... Creating peak regions took 43.1497690678 s
Estimating background... Estimating background took 41.6184670925 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 8.29335999489 s
Creating peak regions... Creating peak regions took 41.2153439522 s
Estimating background... Estimating background took 41.0069570541 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 8.16117501259 s
Creating peak regions... Creating peak regions took 42.1896438599 s
Estimating background... Estimating background took 38.6064531803 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 7.4216799736 s
Creating peak regions... Creating peak regions took 36.0024390221 s
Estimating background... Estimating background took 33.7649178505 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 7.48137807846 s
Creating peak regions... Creating peak regions took 33.399600029 s
Estimating background... Estimating background took 35.0625319481 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 7.71969008446 s
Creating peak regions... Creating peak regions took 33.1957399845 s
Estimating background... Estimating background took 34.2746691704 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 5.39560699463 s
Creating peak regions... Creating peak regions took 25.5613598824 s
Estimating background... Estimating background took 23.0446789265 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 5.44955801964 s
Creating peak regions... Creating peak regions took 26.6603550911 s
Estimating background... Estimating background took 27.3298239708 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 4.09291195869 s
Creating peak regions... Creating peak regions took 19.941947937 s
Estimating background... Estimating background took 16.5650060177 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 3.09344410896 s
Creating peak regions... Creating peak regions took 19.8477900028 s
Estimating background... Estimating background took 14.7830219269 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 6.62086796761 s
Creating peak regions... Creating peak regions took 60.8975479603 s
Estimating background... Estimating background took 22.0369491577 s


Processing GM19213_VDR_ChIP-exo_VD_stimulated-GSM1889573/aligned.36mers.unique.bam
Reading in data... Reading data took 2.36636590958 s
Creating peak regions... Creating peak regions took 0.368771076202 s
Estimating background... Estimating background took 2.44225502014 s