is.broadpeak FALSE 
[1] "Fix 3 stops\n"
[1] "Fix 14 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_223746240/GPS-P300-K562-Rep1.relaxed.narrowPeak_223746240 :  72502 peaks
 72502 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_223746240/GPS-P300-K562-Rep2.relaxed.narrowPeak_223746240 :  82659 peaks
 82659  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-P300-K562-Rep1_VS_GPS-P300-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPS/idr/GPS-P300-K562-Rep1_VS_GPS-P300-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_223746240/GPS-P300-K562-Rep1.relaxed.narrowPeak_223746240
/nfs/nobackup/ensembl/akundaje/tmp/idr_223746240/GPS-P300-K562-Rep2.relaxed.narrowPeak_223746240
$p
[1] 0.6958423

$rho1
[1] 0.8152248

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPS/idr/GPS-P300-K562-Rep1_VS_GPS-P300-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] 18286.85

$x.mean2
[1] 30181.49

$y.mean1
[1] 18722.57

$y.mean2
[1] 29186.76

$x.sd1
[1] 12033.51

$x.sd2
[1] 9807.73

$y.sd1
[1] 12246.95

$y.sd2
[1] 10324.78