is.broadpeak FALSE 
[1] "Fix 38 stops\n"
[1] "Fix 85 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_2897812592/GEM-CTCF-GM12878-Rep1.relaxed.narrowPeak_2897812592 :  102801 peaks
 102801 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_2897812592/GEM-CTCF-GM12878-Rep2.relaxed.narrowPeak_2897812592 :  125000 peaks
 125000  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-CTCF-GM12878-Rep1_VS_GEM-CTCF-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEM/idr/GEM-CTCF-GM12878-Rep1_VS_GEM-CTCF-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_2897812592/GEM-CTCF-GM12878-Rep1.relaxed.narrowPeak_2897812592
/nfs/nobackup/ensembl/akundaje/tmp/idr_2897812592/GEM-CTCF-GM12878-Rep2.relaxed.narrowPeak_2897812592
$p
[1] 0.7641159

$rho1
[1] 0.9521492

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/GEM/idr/GEM-CTCF-GM12878-Rep1_VS_GEM-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] 32967.06

$x.mean2
[1] 57303.79

$y.mean1
[1] 31837.06

$y.mean2
[1] 60957.37

$x.sd1
[1] 19894.82

$x.sd2
[1] 19552.77

$y.sd1
[1] 19759.88

$y.sd2
[1] 14293.45