MMR stops working after the first iteration with -S option on

[bkffadia]

I launch MMR using the following command line :

./mmr2 -b -S -v -o /Path/MMR5839sTS.Human.Heart.2ypb.Male.sorted.bam /Path/5839sTS.Human.Heart.2ypb.Male.sorted.bam

the work progresses until the first iteration is finished then MMR doesn't stop or exit but it doesn't proceed either. when I tried MMR without the -S option I didn't face this issue.