is.broadpeak FALSE 
[1] "Fix 40 stops\n"
[1] "Fix 13 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_2961622235/GEM-GABP-GM12878-Rep1.relaxed.narrowPeak_2961622235 :  39172 peaks
 39172 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_2961622235/GEM-GABP-GM12878-Rep2.relaxed.narrowPeak_2961622235 :  15147 peaks
 15147  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/GEM/idr/GEM-GABP-GM12878-Rep1_VS_GEM-GABP-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEM/idr/GEM-GABP-GM12878-Rep1_VS_GEM-GABP-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_2961622235/GEM-GABP-GM12878-Rep1.relaxed.narrowPeak_2961622235
/nfs/nobackup/ensembl/akundaje/tmp/idr_2961622235/GEM-GABP-GM12878-Rep2.relaxed.narrowPeak_2961622235
$p
[1] 0.7837102

$rho1
[1] 0.9311631

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEM/idr/GEM-GABP-GM12878-Rep1_VS_GEM-GABP-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] 3487.69

$x.mean2
[1] 6400.14

$y.mean1
[1] 3487.804

$y.mean2
[1] 6399.734

$x.sd1
[1] 2212.584

$x.sd2
[1] 1355.722

$y.sd1
[1] 2211.714

$y.sd2
[1] 1361.623