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='GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/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='GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/', 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 GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 3.65543699265 s
Creating peak regions... Creating peak regions took 58.5790388584 s
Estimating background... Estimating background took 11.3540220261 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 4.0541100502 s
Creating peak regions... Creating peak regions took 67.0803999901 s
Estimating background... Estimating background took 10.938587904 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 3.17742419243 s
Creating peak regions... Creating peak regions took 49.5354430676 s
Estimating background... Estimating background took 9.14618206024 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 2.94244003296 s
Creating peak regions... Creating peak regions took 45.6887991428 s
Estimating background... Estimating background took 8.05522990227 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 2.67236614227 s
Creating peak regions... Creating peak regions took 43.2567150593 s
Estimating background... Estimating background took 8.17375397682 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 2.75868010521 s
Creating peak regions... Creating peak regions took 44.2128448486 s
Estimating background... Estimating background took 8.83046293259 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 2.52201795578 s
Creating peak regions... Creating peak regions took 36.6013700962 s
Estimating background... Estimating background took 7.83824300766 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 2.4208688736 s
Creating peak regions... Creating peak regions took 36.1135399342 s
Estimating background... Estimating background took 6.64946484566 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 1.6618039608 s
Creating peak regions... Creating peak regions took 35.8137068748 s
Estimating background... Estimating background took 6.03711104393 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 2.33860707283 s
Creating peak regions... Creating peak regions took 39.3799219131 s
Estimating background... Estimating background took 6.44147205353 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 2.04152703285 s
Creating peak regions... Creating peak regions took 38.0344891548 s
Estimating background... Estimating background took 7.58660507202 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 2.09112596512 s
Creating peak regions... Creating peak regions took 34.7076480389 s
Estimating background... Estimating background took 6.56141495705 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 1.77029085159 s
Creating peak regions... Creating peak regions took 33.6022069454 s
Estimating background... Estimating background took 5.1524951458 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 1.42256999016 s
Creating peak regions... Creating peak regions took 28.0575199127 s
Estimating background... Estimating background took 5.08313417435 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 1.51068401337 s
Creating peak regions... Creating peak regions took 25.6307549477 s
Estimating background... Estimating background took 4.63789486885 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 1.33355998993 s
Creating peak regions... Creating peak regions took 22.093337059 s
Estimating background... Estimating background took 4.45671701431 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 1.62409186363 s
Creating peak regions... Creating peak regions took 20.3358409405 s
Estimating background... Estimating background took 4.58918809891 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 1.22997498512 s
Creating peak regions... Creating peak regions took 20.4365799427 s
Estimating background... Estimating background took 3.92611193657 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 1.17824912071 s
Creating peak regions... Creating peak regions took 15.6467218399 s
Estimating background... Estimating background took 3.62921595573 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 1.00845313072 s
Creating peak regions... Creating peak regions took 15.7584400177 s
Estimating background... Estimating background took 3.67962813377 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 0.686913013458 s
Creating peak regions... Creating peak regions took 11.9604940414 s
Estimating background... Estimating background took 1.30001401901 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 0.62341594696 s
Creating peak regions... Creating peak regions took 12.794080019 s
Estimating background... Estimating background took 1.50385499001 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 1.88119912148 s
Creating peak regions... Creating peak regions took 41.0099289417 s
Estimating background... Estimating background took 5.66163015366 s


Processing GM12489_VDR_ChIP-exo_VD_stimulated-GSM1889566/aligned.36mers.unique.bam
Reading in data... Reading data took 0.311710834503 s
Creating peak regions... Creating peak regions took 0.200319051743 s
Estimating background... Estimating background took 1.29223203659 s