is.broadpeak FALSE 
[1] "Fix 4 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_1532115666/GPSv2-P300-K562-Rep1.relaxed.narrowPeak_1532115666 :  14792 peaks
 14792 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_1532115666/GPSv2-P300-K562-Rep2.relaxed.narrowPeak_1532115666 :  25685 peaks
 25685  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/GPSv2/idr/GPSv2-P300-K562-Rep1_VS_GPSv2-P300-K562-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPSv2/idr/GPSv2-P300-K562-Rep1_VS_GPSv2-P300-K562-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_1532115666/GPSv2-P300-K562-Rep1.relaxed.narrowPeak_1532115666
/nfs/nobackup/ensembl/akundaje/tmp/idr_1532115666/GPSv2-P300-K562-Rep2.relaxed.narrowPeak_1532115666
$p
[1] 0.7766315

$rho1
[1] 0.7661616

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPSv2/idr/GPSv2-P300-K562-Rep1_VS_GPSv2-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] 5149.982

$x.mean2
[1] 5791.788

$y.mean1
[1] 5035.536

$y.mean2
[1] 6183.839

$x.sd1
[1] 3162.188

$x.sd2
[1] 2603.803

$y.sd1
[1] 3184.744

$y.sd2
[1] 2363.802