is.broadpeak FALSE 
[1] "Fix 2 stops\n"
[1] "Fix 4 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_458726539/GPSv2-GABP-HELAS3-Rep1.relaxed.narrowPeak_458726539 :  5450 peaks
 5450 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_458726539/GPSv2-GABP-HELAS3-Rep2.relaxed.narrowPeak_458726539 :  6268 peaks
 6268  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-GABP-HELAS3-Rep1_VS_GPSv2-GABP-HELAS3-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPSv2/idr/GPSv2-GABP-HELAS3-Rep1_VS_GPSv2-GABP-HELAS3-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_458726539/GPSv2-GABP-HELAS3-Rep1.relaxed.narrowPeak_458726539
/nfs/nobackup/ensembl/akundaje/tmp/idr_458726539/GPSv2-GABP-HELAS3-Rep2.relaxed.narrowPeak_458726539
$p
[1] 0.9050767

$rho1
[1] 0.9447562

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPSv2/idr/GPSv2-GABP-HELAS3-Rep1_VS_GPSv2-GABP-HELAS3-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] 1898.327

$x.mean2
[1] 2935.645

$y.mean1
[1] 1893.085

$y.mean2
[1] 2980.434

$x.sd1
[1] 1143.255

$x.sd2
[1] 827.7201

$y.sd1
[1] 1134.683

$y.sd2
[1] 869.939