is.broadpeak FALSE 
[1] "Fix 44 stops\n"
[1] "Fix 54 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_1365219895/Scripture-CTCF-GM12878-Rep1.relaxed.narrowPeak_1365219895 :  79451 peaks
 79451 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_1365219895/Scripture-CTCF-GM12878-Rep2.relaxed.narrowPeak_1365219895 :  93461 peaks
 93461  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/Scripture/idr/Scripture-CTCF-GM12878-Rep1_VS_Scripture-CTCF-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Scripture/idr/Scripture-CTCF-GM12878-Rep1_VS_Scripture-CTCF-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_1365219895/Scripture-CTCF-GM12878-Rep1.relaxed.narrowPeak_1365219895
/nfs/nobackup/ensembl/akundaje/tmp/idr_1365219895/Scripture-CTCF-GM12878-Rep2.relaxed.narrowPeak_1365219895
$p
[1] 0.4584861

$rho1
[1] 0.9506993

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Scripture/idr/Scripture-CTCF-GM12878-Rep1_VS_Scripture-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] 18805.65

$x.mean2
[1] 21997.95

$y.mean1
[1] 15843.14

$y.mean2
[1] 24507.24

$x.sd1
[1] 10414.65

$x.sd2
[1] 12766.06

$y.sd1
[1] 10233.52

$y.sd2
[1] 11678.57