is.broadpeak FALSE 
[1] "Fix 54 stops\n"
[1] "Fix 24 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_1898211976/dPeak-GABP-GM12878-Rep1.relaxed.narrowPeak_1898211976 :  116931 peaks
 116931 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_1898211976/dPeak-GABP-GM12878-Rep2.relaxed.narrowPeak_1898211976 :  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/dPeak/idr/dPeak-GABP-GM12878-Rep1_VS_dPeak-GABP-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/dPeak/idr/dPeak-GABP-GM12878-Rep1_VS_dPeak-GABP-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_1898211976/dPeak-GABP-GM12878-Rep1.relaxed.narrowPeak_1898211976
/nfs/nobackup/ensembl/akundaje/tmp/idr_1898211976/dPeak-GABP-GM12878-Rep2.relaxed.narrowPeak_1898211976
$p
[1] 0.4438573

$rho1
[1] 0.8544111

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/dPeak/idr/dPeak-GABP-GM12878-Rep1_VS_dPeak-GABP-GM12878-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] 12409.48

$x.mean2
[1] 21750.62

$y.mean1
[1] 12245.83

$y.mean2
[1] 21881.31

$x.sd1
[1] 9758.925

$x.sd2
[1] 8421.467

$y.sd1
[1] 9348.728

$y.sd2
[1] 8642.941