is.broadpeak FALSE 
[1] "Fix 2 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_211716462/GPS-ZNF274-K562-Rep1.relaxed.narrowPeak_211716462 :  15099 peaks
 15099 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_211716462/GPS-ZNF274-K562-Rep2.relaxed.narrowPeak_211716462 :  37439 peaks
 37439  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/GPS/idr/GPS-ZNF274-K562-Rep1_VS_GPS-ZNF274-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPS/idr/GPS-ZNF274-K562-Rep1_VS_GPS-ZNF274-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_211716462/GPS-ZNF274-K562-Rep1.relaxed.narrowPeak_211716462
/nfs/nobackup/ensembl/akundaje/tmp/idr_211716462/GPS-ZNF274-K562-Rep2.relaxed.narrowPeak_211716462
$p
[1] 0.6141847

$rho1
[1] 0.862828

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPS/idr/GPS-ZNF274-K562-Rep1_VS_GPS-ZNF274-K562-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] 809.9181

$x.mean2
[1] 1306.028

$y.mean1
[1] 930.9364

$y.mean2
[1] 1117.72

$x.sd1
[1] 574.1149

$x.sd2
[1] 443.4383

$y.sd1
[1] 604.7007

$y.sd2
[1] 518.7765