[Bioperl-l] Error while parsing

Steve Chervitz sac at bioperl.org
Sat Feb 10 22:56:10 EST 2007


Your report may be lacking HSP alignments for the hit you are attempting to
process. Note that by default, blast will report twice as many one-line
descriptions as it will alignments:

  -v  Number of database sequences to show one-line descriptions for (V)
[Integer]
    default = 500
  -b  Number of database sequence to show alignments for (B) [Integer]
    default = 250

Verify that this isn't the case for your error. If not, go ahead and file a
bug report. Attach the report (zipped if big) as well as the relevant
portion of your processing script.

Steve

On 2/10/07, George Heller <george.heller at yahoo.com> wrote:
>
> Hi all,
>
>   I am in the process of parsing a few files, actually blast results, but
> happen to get the following error:
>
>   ------------- EXCEPTION  -------------
> MSG: Can't get HSPs: data not collected.
> STACK Bio::Search::Hit::GenericHit::hsp
> /usr/lib/perl5/site_perl/5.8.5/Bio/Search/Hit/GenericHit.pm:649
> STACK toplevel parser.pl:31
>   --------------------------------------
>
>   I am not sure if this is a bug, or is there something I am doing wrong.
> Any pointers are appreciated.
>
>   Thanks!
>   George.
>
>
> ---------------------------------
> No need to miss a message. Get email on-the-go
> with Yahoo! Mail for Mobile. Get started.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


More information about the Bioperl-l mailing list