is.broadpeak FALSE 
[1] "Fix 24 stops\n"
[1] "Fix 24 stops\n"
read /broad/hptmp/anshul/idr_3269020012/dPeak3-GABP-HELAS3-Rep1.relaxed.narrowPeak_3269020012 :  111797 peaks
 111797 peaks are left after cleaning
 /broad/hptmp/anshul/idr_3269020012/dPeak3-GABP-HELAS3-Rep2.relaxed.narrowPeak_3269020012 :  113247 peaks
 113247  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/dPeak3/idr/dPeak3-GABP-HELAS3-Rep1_VS_dPeak3-GABP-HELAS3-Rep2-uri.sav 
EM is done

EM is saved at: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/dPeak3/idr/dPeak3-GABP-HELAS3-Rep1_VS_dPeak3-GABP-HELAS3-Rep2-em.sav 
EM estimation for the following files
/broad/hptmp/anshul/idr_3269020012/dPeak3-GABP-HELAS3-Rep1.relaxed.narrowPeak_3269020012
/broad/hptmp/anshul/idr_3269020012/dPeak3-GABP-HELAS3-Rep2.relaxed.narrowPeak_3269020012
$p
[1] 0.4143327

$rho1
[1] 0.9095147

$rho2
[1] 0

Write overlapped peaks and local idr to: /broad/compbio/anshul/projects/encode3/evaluation/tfs/phase1/idrResults/origWidth/dPeak3/idr/dPeak3-GABP-HELAS3-Rep1_VS_dPeak3-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] 8030.906

$x.mean2
[1] 18108.61

$y.mean1
[1] 8378.729

$y.mean2
[1] 17862.23

$x.sd1
[1] 6517.937

$x.sd2
[1] 6185.805

$y.sd1
[1] 6801.794

$y.sd2
[1] 6356.53