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

[Jason Stajich]

easier for us to debug if you send an example script and some example
sequences that cause the problem.

On Wed, 16 Jan 2002, Simon Chan wrote:

> 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!
>
>
> #########
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu