is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_1014317519/PeakSeq-GABP-HELAS3-Rep1.relaxed.narrowPeak_1014317519 :  15911 peaks
 15770 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_1014317519/PeakSeq-GABP-HELAS3-Rep2.relaxed.narrowPeak_1014317519 :  22822 peaks
 22674  peaks are left after cleaninghalf.width= reported 
significant measure= q.value 
URI is done
URI is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/PeakSeq/idr/PeakSeq-GABP-HELAS3-Rep1_VS_PeakSeq-GABP-HELAS3-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/PeakSeq/idr/PeakSeq-GABP-HELAS3-Rep1_VS_PeakSeq-GABP-HELAS3-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_1014317519/PeakSeq-GABP-HELAS3-Rep1.relaxed.narrowPeak_1014317519
/nfs/nobackup/ensembl/akundaje/tmp/idr_1014317519/PeakSeq-GABP-HELAS3-Rep2.relaxed.narrowPeak_1014317519
$p
[1] 0.5879074

$rho1
[1] 0.9599004

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/PeakSeq/idr/PeakSeq-GABP-HELAS3-Rep1_VS_PeakSeq-GABP-HELAS3-Rep2-overlapped-peaks.txt
Write number of peaks above IDR cutoff [0.01, 0.25]: npeaks-aboveIDR.txt
Marginal mean of two components:
$x.mean1
[1] 2881.441

$x.mean2
[1] 6226.958

$y.mean1
[1] 2934.241

$y.mean2
[1] 6151.948

$x.sd1
[1] 2018.086

$x.sd2
[1] 1520.14

$y.sd1
[1] 2099.897

$y.sd2
[1] 1524.638