is.broadpeak FALSE 
[1] "Fix 25 stops\n"
[1] "Fix 63 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_825625473/GEM-POL2-H1ESC-Rep1.relaxed.narrowPeak_825625473 :  125000 peaks
 125000 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_825625473/GEM-POL2-H1ESC-Rep2.relaxed.narrowPeak_825625473 :  125000 peaks
 125000  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/GEM/idr/GEM-POL2-H1ESC-Rep1_VS_GEM-POL2-H1ESC-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEM/idr/GEM-POL2-H1ESC-Rep1_VS_GEM-POL2-H1ESC-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_825625473/GEM-POL2-H1ESC-Rep1.relaxed.narrowPeak_825625473
/nfs/nobackup/ensembl/akundaje/tmp/idr_825625473/GEM-POL2-H1ESC-Rep2.relaxed.narrowPeak_825625473
$p
[1] 0.6153798

$rho1
[1] 0.8504612

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEM/idr/GEM-POL2-H1ESC-Rep1_VS_GEM-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] 23283.18

$x.mean2
[1] 43988.68

$y.mean1
[1] 22779.11

$y.mean2
[1] 44794.54

$x.sd1
[1] 16110.95

$x.sd2
[1] 12922.02

$y.sd1
[1] 15952.35

$y.sd2
[1] 11860.93