is.broadpeak FALSE 
[1] "Fix 59 stops\n"
[1] "Fix 62 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_367816367/GEMv2-CTCF-GM12878-Rep1.relaxed.narrowPeak_367816367 :  65209 peaks
 65209 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_367816367/GEMv2-CTCF-GM12878-Rep2.relaxed.narrowPeak_367816367 :  65809 peaks
 65809  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/GEMv2/idr/GEMv2-CTCF-GM12878-Rep1_VS_GEMv2-CTCF-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEMv2/idr/GEMv2-CTCF-GM12878-Rep1_VS_GEMv2-CTCF-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_367816367/GEMv2-CTCF-GM12878-Rep1.relaxed.narrowPeak_367816367
/nfs/nobackup/ensembl/akundaje/tmp/idr_367816367/GEMv2-CTCF-GM12878-Rep2.relaxed.narrowPeak_367816367
$p
[1] 0.8787743

$rho1
[1] 0.9625694

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEMv2/idr/GEMv2-CTCF-GM12878-Rep1_VS_GEMv2-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] 23755.51

$x.mean2
[1] 15759.16

$y.mean1
[1] 22866.73

$y.mean2
[1] 22152.12

$x.sd1
[1] 13047.15

$x.sd2
[1] 11666.25

$y.sd1
[1] 13141.69

$y.sd2
[1] 13190.18