is.broadpeak FALSE 
[1] "Fix 37 stops\n"
[1] "Fix 61 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_1897314516/GPS-CTCF-GM12878-Rep1.relaxed.narrowPeak_1897314516 :  101299 peaks
 101299 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_1897314516/GPS-CTCF-GM12878-Rep2.relaxed.narrowPeak_1897314516 :  119721 peaks
 119721  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-CTCF-GM12878-Rep1_VS_GPS-CTCF-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPS/idr/GPS-CTCF-GM12878-Rep1_VS_GPS-CTCF-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_1897314516/GPS-CTCF-GM12878-Rep1.relaxed.narrowPeak_1897314516
/nfs/nobackup/ensembl/akundaje/tmp/idr_1897314516/GPS-CTCF-GM12878-Rep2.relaxed.narrowPeak_1897314516
$p
[1] 0.7518582

$rho1
[1] 0.9623947

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GPS/idr/GPS-CTCF-GM12878-Rep1_VS_GPS-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] 33156.04

$x.mean2
[1] 56766.98

$y.mean1
[1] 32055.2

$y.mean2
[1] 60096.7

$x.sd1
[1] 19791.34

$x.sd2
[1] 20939.23

$y.sd1
[1] 19784.7

$y.sd2
[1] 16348.02