[Bioperl-l] blast Bio::Tools::Run::StandAloneBlast BlastFindWords returned non-zero status

[Jason Stajich]

And if you take bioperl out of the loop and run bl2seq on the cmd line
what does it do?

On Tue, 19 Aug 2003, Guido Dieterich wrote:

> Hi,
>
> i have a strange problem. I use
>
> $factory = Bio::Tools::Run::StandAloneBlast->new('program'  => 'blastp',
> 'outfile' => 'bl2seq.out');
>
> $report = $factory->bl2seq($query2, $query1);
>
> in case $query2->seq is "CMWDFDDXMPPADEDYSPWQLWLLA" Blast runs without
> warnings
>
> in case $query2->seq is "CMWDFDDXMPPADEDYSPWQLWLLS" Blast warns
> # last AA can also be T or G
> [bl2seq] WARNING:  [000.000]  BlastFindWords returned non-zero status
> [bl2seq] WARNING:  [000.000]  SetUpBlastSearch failed.
>
> ????????????
>
> Thanks
>
>
> Guido
>
>
>
>
>
>
>
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu