is.broadpeak FALSE 
[1] "Fix 1 stops\n"
[1] "Fix 2 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_2772429733/SPP-CTCF-GM12878-Rep2.relaxed.narrowPeak_2772429733 :  125000 peaks
 125000 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_2772429733/SPP-CTCF-GM12878-Rep1.relaxed.narrowPeak_2772429733 :  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/SPP/idr/SPP-CTCF-GM12878-Rep2_VS_SPP-CTCF-GM12878-Rep1-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/SPP/idr/SPP-CTCF-GM12878-Rep2_VS_SPP-CTCF-GM12878-Rep1-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_2772429733/SPP-CTCF-GM12878-Rep2.relaxed.narrowPeak_2772429733
/nfs/nobackup/ensembl/akundaje/tmp/idr_2772429733/SPP-CTCF-GM12878-Rep1.relaxed.narrowPeak_2772429733
$p
[1] 0.7296057

$rho1
[1] 0.9465995

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/SPP/idr/SPP-CTCF-GM12878-Rep2_VS_SPP-CTCF-GM12878-Rep1-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] 31926.48

$x.mean2
[1] 66915.48

$y.mean1
[1] 33034.1

$y.mean2
[1] 63930.98

$x.sd1
[1] 20052.6

$x.sd2
[1] 11550.19

$y.sd1
[1] 20157.42

$y.sd2
[1] 17851.79