is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_2748425896/PeakSeq-POL2-H1ESC-Rep1.relaxed.narrowPeak_2748425896 :  89560 peaks
 89185 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_2748425896/PeakSeq-POL2-H1ESC-Rep2.relaxed.narrowPeak_2748425896 :  125000 peaks
 124689  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-POL2-H1ESC-Rep1_VS_PeakSeq-POL2-H1ESC-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/PeakSeq/idr/PeakSeq-POL2-H1ESC-Rep1_VS_PeakSeq-POL2-H1ESC-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_2748425896/PeakSeq-POL2-H1ESC-Rep1.relaxed.narrowPeak_2748425896
/nfs/nobackup/ensembl/akundaje/tmp/idr_2748425896/PeakSeq-POL2-H1ESC-Rep2.relaxed.narrowPeak_2748425896
$p
[1] 0.6035104

$rho1
[1] 0.8581297

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/PeakSeq/idr/PeakSeq-POL2-H1ESC-Rep1_VS_PeakSeq-POL2-H1ESC-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] 19097.05

$x.mean2
[1] 35561.9

$y.mean1
[1] 19362.94

$y.mean2
[1] 35157.52

$x.sd1
[1] 13385.16

$x.sd2
[1] 10756.76

$y.sd1
[1] 13708.28

$y.sd2
[1] 10744.24