is.broadpeak FALSE 
[1] "Fix 1 stops\n"
[1] "Fix 9 stops\n"
read /nfs/nobackup/ensembl/akundaje/tmp/idr_306113038/Scripture-GABP-HELAS3-Rep1.relaxed.narrowPeak_306113038 :  25476 peaks
 25476 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_306113038/Scripture-GABP-HELAS3-Rep2.relaxed.narrowPeak_306113038 :  37771 peaks
 37771  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-GABP-HELAS3-Rep1_VS_Scripture-GABP-HELAS3-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Scripture/idr/Scripture-GABP-HELAS3-Rep1_VS_Scripture-GABP-HELAS3-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_306113038/Scripture-GABP-HELAS3-Rep1.relaxed.narrowPeak_306113038
/nfs/nobackup/ensembl/akundaje/tmp/idr_306113038/Scripture-GABP-HELAS3-Rep2.relaxed.narrowPeak_306113038
$p
[1] 0.5210209

$rho1
[1] 0.7285957

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/Scripture/idr/Scripture-GABP-HELAS3-Rep1_VS_Scripture-GABP-HELAS3-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] 5713.011

$x.mean2
[1] 5024.305

$y.mean1
[1] 5844.038

$y.mean2
[1] 4881.889

$x.sd1
[1] 3286.442

$x.sd2
[1] 2857.94

$y.sd1
[1] 3312.034

$y.sd2
[1] 2783.733