is.broadpeak FALSE 
[1] "Fix 7 stops\n"
[1] "Fix 34 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_1158312993/GEMv2-POL2-H1ESC-Rep1.relaxed.narrowPeak_1158312993 :  14680 peaks
 14680 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_1158312993/GEMv2-POL2-H1ESC-Rep2.relaxed.narrowPeak_1158312993 :  43478 peaks
 43478  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEMv2/idr/GEMv2-POL2-H1ESC-Rep1_VS_GEMv2-POL2-H1ESC-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEMv2/idr/GEMv2-POL2-H1ESC-Rep1_VS_GEMv2-POL2-H1ESC-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_1158312993/GEMv2-POL2-H1ESC-Rep1.relaxed.narrowPeak_1158312993
/nfs/nobackup/ensembl/akundaje/tmp/idr_1158312993/GEMv2-POL2-H1ESC-Rep2.relaxed.narrowPeak_1158312993
$p
[1] 0.9214048

$rho1
[1] 0.8690556

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEMv2/idr/GEMv2-POL2-H1ESC-Rep1_VS_GEMv2-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] 5175.032

$x.mean2
[1] 5114.162

$y.mean1
[1] 5115.131

$y.mean2
[1] 5779.175

$x.sd1
[1] 3018.888

$x.sd2
[1] 2573.32

$y.sd1
[1] 3041.901

$y.sd2
[1] 2161.572