is.broadpeak FALSE 
[1] "Fix 1 stops\n"
[1] "Fix 2 stops\n"
read SPP-300K-G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM-Rep1/G1E-ER4-24h-TAL1-Rep1-ENCFF001MTO.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.regionPeak :  181065 peaks
 181065 peaks are left after cleaning
 SPP-300K-G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM-Rep2/G1E-ER4-24h-TAL1-Rep2-ENCFF001MTM.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.regionPeak :  255134 peaks
 255134  peaks are left after cleaninghalf.width= reported 
significant measure= signal.value 
URI is done
URI is saved at: IDR-SPP-G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM-uri.sav 
EM is done

EM is saved at: IDR-SPP-G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM-em.sav 
EM estimation for the following files
SPP-300K-G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM-Rep1/G1E-ER4-24h-TAL1-Rep1-ENCFF001MTO.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep1-ENCFF001MSM.mm10.36mers.unique.regionPeak
SPP-300K-G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM-Rep2/G1E-ER4-24h-TAL1-Rep2-ENCFF001MTM.mm10.36mers.unique_VS_G1E-ER4-24h-Control-Rep2-ENCFF001MSW.mm10.36mers.unique.regionPeak
$p
[1] 0.2771346

$rho1
[1] 0.7278674

$rho2
[1] 0

Write overlapped peaks and local idr to: IDR-SPP-G1E-ER4-24h-TAL1-ENCFF001MTO-vs-ENCFF001MTM-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] 4650.47

$x.mean2
[1] 10344.11

$y.mean1
[1] 4832.02

$y.mean2
[1] 10274.06

$x.sd1
[1] 4409.564

$x.sd2
[1] 4347.807

$y.sd1
[1] 4666.63

$y.sd2
[1] 4333.965