is.broadpeak FALSE 
[1] "Fix 12 stops\n"
[1] "Fix 41 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_1266828145/GPSv2-POL2-H1ESC-Rep1.relaxed.narrowPeak_1266828145 :  15835 peaks
 15835 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_1266828145/GPSv2-POL2-H1ESC-Rep2.relaxed.narrowPeak_1266828145 :  43360 peaks
 43360  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-POL2-H1ESC-Rep1_VS_GPSv2-POL2-H1ESC-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPSv2/idr/GPSv2-POL2-H1ESC-Rep1_VS_GPSv2-POL2-H1ESC-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_1266828145/GPSv2-POL2-H1ESC-Rep1.relaxed.narrowPeak_1266828145
/nfs/nobackup/ensembl/akundaje/tmp/idr_1266828145/GPSv2-POL2-H1ESC-Rep2.relaxed.narrowPeak_1266828145
$p
[1] 0.9255629

$rho1
[1] 0.8707031

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPSv2/idr/GPSv2-POL2-H1ESC-Rep1_VS_GPSv2-POL2-H1ESC-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] 5593.871

$x.mean2
[1] 4873.582

$y.mean1
[1] 5502.727

$y.mean2
[1] 5947.292

$x.sd1
[1] 3219.433

$x.sd2
[1] 2833.987

$y.sd1
[1] 3259.94

$y.sd2
[1] 2288.158