is.broadpeak FALSE 
[1] "Fix 8 stops\n"
[1] "Fix 6 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_275684209/GEMv2-GABP-GM12878-Rep1.relaxed.narrowPeak_275684209 :  13813 peaks
 13813 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_275684209/GEMv2-GABP-GM12878-Rep2.relaxed.narrowPeak_275684209 :  7257 peaks
 7257  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-GABP-GM12878-Rep1_VS_GEMv2-GABP-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEMv2/idr/GEMv2-GABP-GM12878-Rep1_VS_GEMv2-GABP-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_275684209/GEMv2-GABP-GM12878-Rep1.relaxed.narrowPeak_275684209
/nfs/nobackup/ensembl/akundaje/tmp/idr_275684209/GEMv2-GABP-GM12878-Rep2.relaxed.narrowPeak_275684209
$p
[1] 0.8913222

$rho1
[1] 0.9179731

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEMv2/idr/GEMv2-GABP-GM12878-Rep1_VS_GEMv2-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] 2219.85

$x.mean2
[1] 3531.637

$y.mean1
[1] 2228.308

$y.mean2
[1] 3467.657

$x.sd1
[1] 1347.522

$x.sd2
[1] 904.7445

$y.sd1
[1] 1347.981

$y.sd2
[1] 986.1153