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='ERalpha_ChIP-exo_replicate_2-GSM2994889/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='ERalpha_ChIP-exo_replicate_2-GSM2994889/', 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 ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 4.70463895798 s
Creating peak regions... Creating peak regions took 60.2222020626 s
Estimating background... Estimating background took 18.6611180305 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 5.11331701279 s
Creating peak regions... Creating peak regions took 70.187443018 s
Estimating background... Estimating background took 17.0988709927 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 5.21877598763 s
Creating peak regions... Creating peak regions took 56.6511640549 s
Estimating background... Estimating background took 19.7406778336 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 3.23271393776 s
Creating peak regions... Creating peak regions took 59.1421399117 s
Estimating background... Estimating background took 9.7890059948 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 3.77684593201 s
Creating peak regions... Creating peak regions took 47.3330979347 s
Estimating background... Estimating background took 12.5912418365 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 3.54963898659 s
Creating peak regions... Creating peak regions took 42.5857510567 s
Estimating background... Estimating background took 13.0181059837 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 3.59673810005 s
Creating peak regions... Creating peak regions took 46.1677749157 s
Estimating background... Estimating background took 12.4313800335 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 3.66893005371 s
Creating peak regions... Creating peak regions took 37.58010602 s
Estimating background... Estimating background took 12.2511880398 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 2.60097694397 s
Creating peak regions... Creating peak regions took 40.1502912045 s
Estimating background... Estimating background took 10.5317051411 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 2.82140398026 s
Creating peak regions... Creating peak regions took 42.9931969643 s
Estimating background... Estimating background took 9.99638199806 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 2.55704498291 s
Creating peak regions... Creating peak regions took 36.2521648407 s
Estimating background... Estimating background took 9.33366107941 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 3.09716510773 s
Creating peak regions... Creating peak regions took 39.9016520977 s
Estimating background... Estimating background took 10.9930639267 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 1.51866698265 s
Creating peak regions... Creating peak regions took 30.7920329571 s
Estimating background... Estimating background took 5.4318780899 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 2.94880890846 s
Creating peak regions... Creating peak regions took 32.1054029465 s
Estimating background... Estimating background took 9.50824904442 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 2.23686003685 s
Creating peak regions... Creating peak regions took 27.8386280537 s
Estimating background... Estimating background took 8.36049795151 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 2.12503695488 s
Creating peak regions... Creating peak regions took 28.6525189877 s
Estimating background... Estimating background took 8.21933603287 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 3.18164920807 s
Creating peak regions... Creating peak regions took 23.4713830948 s
Estimating background... Estimating background took 20.0213010311 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 1.06276702881 s
Creating peak regions... Creating peak regions took 19.1030302048 s
Estimating background... Estimating background took 2.05757498741 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 1.69554901123 s
Creating peak regions... Creating peak regions took 15.4952321053 s
Estimating background... Estimating background took 5.62395000458 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 3.23794007301 s
Creating peak regions... Creating peak regions took 19.700109005 s
Estimating background... Estimating background took 21.7156720161 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 0.89138007164 s
Creating peak regions... Creating peak regions took 12.9517459869 s
Estimating background... Estimating background took 2.95284795761 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 0.703146934509 s
Creating peak regions... Creating peak regions took 13.0579390526 s
Estimating background... Estimating background took 1.93693614006 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 2.73531913757 s
Creating peak regions... Creating peak regions took 39.5813479424 s
Estimating background... Estimating background took 7.2817261219 s


Processing ERalpha_ChIP-exo_replicate_2-GSM2994889/aligned.36mers.unique.bam
Reading in data... Reading data took 0.0905749797821 s
Creating peak regions... Creating peak regions took 0.161261081696 s
Estimating background... Estimating background took 0.701857089996 s