Hi Antony,
thanks a lot for report!
Actually, GUI might have some additional bugs issues, since command line version is used more frequently, and GUI is not used too often.
Command line has more detailed reports and better error processing.
Several questions:
1) Which Qualimap version did you use? Which operating system?
2) Did you try running analysis for the same BAM file using command line? More details here:
3) Is it possible for you to share the BAM file (or subsample from the BAM file) so I can check it carefully?
How to create subsample using samtools:
--
Konstantin