[EMBOSS] Stretcher & custom scoring matrix

[Ryan Golhar]

I'm using stretcher with a custom scoring matrix I created.  It works
for 99% of my sequence.  Occassionally, I get the waring:

Warning: stretcher CheckScore failed

I'm using a gapopen penalty of 160000 and gapextend of 40000.  This is
because I need to normalize my matrix from floating point to integer.  I
suspect this has something to do with it.  

What does this error mean?

Ryan