is.broadpeak FALSE 
read /nfs/nobackup/ensembl/akundaje/tmp/idr_1590616370/MOSAiCS-GABP-HELAS3-Rep1.relaxed.narrowPeak_1590616370 :  109836 peaks
 109836 peaks are left after cleaning
 /nfs/nobackup/ensembl/akundaje/tmp/idr_1590616370/MOSAiCS-GABP-HELAS3-Rep2.relaxed.narrowPeak_1590616370 :  114085 peaks
 114085  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-HELAS3-Rep1_VS_MOSAiCS-GABP-HELAS3-Rep2-uri.sav 
EM is done

EM is saved at: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-GABP-HELAS3-Rep1_VS_MOSAiCS-GABP-HELAS3-Rep2-em.sav 
EM estimation for the following files
/nfs/nobackup/ensembl/akundaje/tmp/idr_1590616370/MOSAiCS-GABP-HELAS3-Rep1.relaxed.narrowPeak_1590616370
/nfs/nobackup/ensembl/akundaje/tmp/idr_1590616370/MOSAiCS-GABP-HELAS3-Rep2.relaxed.narrowPeak_1590616370
$p
[1] 0.4455691

$rho1
[1] 0.9400866

$rho2
[1] 0

Write overlapped peaks and local idr to: /net/isilon5/encode/work/akundaje/work/encode3/phase1_results/origWidth/MOSAICS/idr/MOSAiCS-GABP-HELAS3-Rep1_VS_MOSAiCS-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] 11962.35

$x.mean2
[1] 23505.48

$y.mean1
[1] 12194.64

$y.mean2
[1] 23318.69

$x.sd1
[1] 10061.82

$x.sd2
[1] 7865.716

$y.sd1
[1] 9812.366

$y.sd2
[1] 8371.989