is.broadpeak FALSE 
[1] "Fix 4 stops\n"
[1] "Fix 11 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_1234018296/GPSv2-CTCF-GM12878-Rep1.relaxed.narrowPeak_1234018296 :  54791 peaks
 54791 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_1234018296/GPSv2-CTCF-GM12878-Rep2.relaxed.narrowPeak_1234018296 :  55220 peaks
 55220  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-CTCF-GM12878-Rep1_VS_GPSv2-CTCF-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPSv2/idr/GPSv2-CTCF-GM12878-Rep1_VS_GPSv2-CTCF-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_1234018296/GPSv2-CTCF-GM12878-Rep1.relaxed.narrowPeak_1234018296
/nfs/nobackup/ensembl/akundaje/tmp/idr_1234018296/GPSv2-CTCF-GM12878-Rep2.relaxed.narrowPeak_1234018296
$p
[1] 0.8714356

$rho1
[1] 0.9700222

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPSv2/idr/GPSv2-CTCF-GM12878-Rep1_VS_GPSv2-CTCF-GM12878-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] 22206.52

$x.mean2
[1] 20336.4

$y.mean1
[1] 21223.83

$y.mean2
[1] 26947.45

$x.sd1
[1] 12400.94

$x.sd2
[1] 14306.49

$y.sd1
[1] 12462.85

$y.sd2
[1] 12994.01