is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_26799148/MOSAiCS-GABP-GM12878-Rep1.relaxed.narrowPeak_26799148 :  103711 peaks
 103711 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_26799148/MOSAiCS-GABP-GM12878-Rep2.relaxed.narrowPeak_26799148 :  125000 peaks
 125000  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-GABP-GM12878-Rep1_VS_MOSAiCS-GABP-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-GABP-GM12878-Rep1_VS_MOSAiCS-GABP-GM12878-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_26799148/MOSAiCS-GABP-GM12878-Rep1.relaxed.narrowPeak_26799148
/nfs/nobackup/ensembl/akundaje/tmp/idr_26799148/MOSAiCS-GABP-GM12878-Rep2.relaxed.narrowPeak_26799148
$p
[1] 0.3788343

$rho1
[1] 0.9042755

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-GABP-GM12878-Rep1_VS_MOSAiCS-GABP-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] 10955.98

$x.mean2
[1] 21557.31

$y.mean1
[1] 11261.01

$y.mean2
[1] 21371

$x.sd1
[1] 9391.253

$x.sd2
[1] 8282.95

$y.sd1
[1] 9093.31

$y.sd2
[1] 8708.018