is.broadpeak FALSE 
read /broad/hptmp/anshul/idr_53272324/MOSAiCS3-CTCF-GM12878-Rep1.relaxed.narrowPeak_53272324 :  108708 peaks
 108708 peaks are left after cleaning
 /broad/hptmp/anshul/idr_53272324/MOSAiCS3-CTCF-GM12878-Rep2.relaxed.narrowPeak_53272324 :  122445 peaks
 122445  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/MOSAICS3/idr/MOSAiCS3-CTCF-GM12878-Rep1_VS_MOSAiCS3-CTCF-GM12878-Rep2-uri.sav 
EM is done

EM is saved at: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/MOSAICS3/idr/MOSAiCS3-CTCF-GM12878-Rep1_VS_MOSAiCS3-CTCF-GM12878-Rep2-em.sav 
EM estimation for the following files
/broad/hptmp/anshul/idr_53272324/MOSAiCS3-CTCF-GM12878-Rep1.relaxed.narrowPeak_53272324
/broad/hptmp/anshul/idr_53272324/MOSAiCS3-CTCF-GM12878-Rep2.relaxed.narrowPeak_53272324
$p
[1] 0.8140821

$rho1
[1] 0.9101343

$rho2
[1] 0

Write overlapped peaks and local idr to: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/MOSAICS3/idr/MOSAiCS3-CTCF-GM12878-Rep1_VS_MOSAiCS3-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] 36014.4

$x.mean2
[1] 59790.38

$y.mean1
[1] 34567.84

$y.mean2
[1] 66108.25

$x.sd1
[1] 21436.01

$x.sd2
[1] 21418.46

$y.sd1
[1] 21196.25

$y.sd2
[1] 12406.09