I'm running "CuffDiff For CummeRbund" on test data to optimize my analysis workflow. I've chosen "CD For CB" because the output is several text tables of data rather than just the datafile for CummeRbund. I had my BAM files sliced to just chromosome 6 and was working with those to get to where I felt "CD For CB" worked well. However, when I moved over to using the full BAM files, the tool processes all the way through with no error, but produces 'empty' tables - nothing to download. Because it's processing fully to the green I have no error messages to show. I'm using replicates for 2 conditions, and at this point all settings for the tool are at default. What's going on here?