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_1-GSM2994888/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_1-GSM2994888/', 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_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 5.00397610664 s
Creating peak regions... Creating peak regions took 61.8235728741 s
Estimating background... Estimating background took 27.3412458897 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 5.83334493637 s
Creating peak regions... Creating peak regions took 73.2710089684 s
Estimating background... Estimating background took 25.2087230682 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 5.16532993317 s
Creating peak regions... Creating peak regions took 64.2144830227 s
Estimating background... Estimating background took 27.382748127 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 3.31601905823 s
Creating peak regions... Creating peak regions took 61.0001349449 s
Estimating background... Estimating background took 13.6281781197 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 4.81160593033 s
Creating peak regions... Creating peak regions took 54.1711390018 s
Estimating background... Estimating background took 20.2017168999 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 4.05145716667 s
Creating peak regions... Creating peak regions took 52.7106339931 s
Estimating background... Estimating background took 18.2804338932 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 3.59104585648 s
Creating peak regions... Creating peak regions took 41.3616061211 s
Estimating background... Estimating background took 16.8997159004 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 4.15928697586 s
Creating peak regions... Creating peak regions took 39.7139160633 s
Estimating background... Estimating background took 16.6646330357 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 3.14561200142 s
Creating peak regions... Creating peak regions took 37.1477849483 s
Estimating background... Estimating background took 14.0355470181 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 3.28666210175 s
Creating peak regions... Creating peak regions took 39.1919329166 s
Estimating background... Estimating background took 14.7664079666 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 2.91521692276 s
Creating peak regions... Creating peak regions took 36.274941206 s
Estimating background... Estimating background took 12.6043169498 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 3.51224994659 s
Creating peak regions... Creating peak regions took 35.470236063 s
Estimating background... Estimating background took 14.750838995 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 1.55087018013 s
Creating peak regions... Creating peak regions took 31.5965340137 s
Estimating background... Estimating background took 7.49170184135 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 2.74132704735 s
Creating peak regions... Creating peak regions took 27.9524691105 s
Estimating background... Estimating background took 12.8255648613 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 1.99194693565 s
Creating peak regions... Creating peak regions took 27.599047184 s
Estimating background... Estimating background took 12.1104991436 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 2.33076500893 s
Creating peak regions... Creating peak regions took 24.7665479183 s
Estimating background... Estimating background took 11.6460828781 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 3.76640295982 s
Creating peak regions... Creating peak regions took 27.4922180176 s
Estimating background... Estimating background took 25.1943979263 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 1.25564694405 s
Creating peak regions... Creating peak regions took 21.9985108376 s
Estimating background... Estimating background took 5.21179318428 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 1.60128211975 s
Creating peak regions... Creating peak regions took 15.9438960552 s
Estimating background... Estimating background took 7.16881084442 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 3.74178886414 s
Creating peak regions... Creating peak regions took 19.1182549 s
Estimating background... Estimating background took 28.1637969017 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 1.35122013092 s
Creating peak regions... Creating peak regions took 15.0225260258 s
Estimating background... Estimating background took 6.32400894165 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 0.737773895264 s
Creating peak regions... Creating peak regions took 14.134098053 s
Estimating background... Estimating background took 4.02932596207 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 2.33003997803 s
Creating peak regions... Creating peak regions took 46.7891089916 s
Estimating background... Estimating background took 9.30030298233 s


Processing ERalpha_ChIP-exo_replicate_1-GSM2994888/aligned.36mers.unique.bam
Reading in data... Reading data took 0.098424911499 s
Creating peak regions... Creating peak regions took 0.200897932053 s
Estimating background... Estimating background took 0.685107946396 s