[Bioperl-l] error/warning messages while using pSW.pm

[Simon Chan]

Hi All,
        
I'm hoping someone out there can share their experience with this young newbie ;-)
        
 I'm writing a program which inputs one large sequence of DNA into one  array of an element.  Using a foreach loop embedded inside a while  loop, I use Ewan's Bio::Tools::pSW to compare each sequence with another.  So if I have 4 sequences (and thus 4 elements in the array),  Seq1 compared to Seq2, and then Seq1 compared to Seq3, Seq1 to Seq4, then Seq2
 to Seq3, etc, etc, etc.
        
 I have tested my loops, so I am quite sure that they work.  However I get an error  message that looks like this:
        
________________________________________________
Error Message:

Warning Error
In ProteinSW hidden read off, between 999:887,1003:891 - gone past start cell (now in 998,888,2), can't be good news!.
Warning Error
  In full dc, at 999:887,1003:891 got a bad hidden explicit read off...
Warning Error
 In recaluclating PackAln with state MATCH, from [1,3,3], got a bad source state. Error!
Warning Error
  Between state [998,886,3] and [999,889,0] got no labels... labelling as UNKNOWN
Warning Error
 Got an uninterpretable label, UNKNOWN_LABEL
Warning Error
 Got an uninterpretable label, UNKNOWN_LABEL
   ________________________________________________
        
  I agree with the error message: this can't be good news :) !
  I've searched through some of the archives, but with little luck.  Any help would be appreicated.
 Many thanks!
 

#########