Hi Aaron,
On Tue, Dec 20, 2016 at 12:31:07PM -0500, Aaron M. Ucko wrote:
> Andreas Tille <ti...@debian.org> writes:
>
> > ncbi-blast+-legacy (>= 2.5.0-2~) | blast2
>
> Yes, this is an appropriate dependency for anything that historically
> listed blast2 and continues to use legacy command names such as bl2seq.
OK.
> > Could you give some hint for a patch to fix this test suite error:
>
> Good question. The error from the underlying blastn command (buried in
> the middle of the log) is
>
> BLAST engine error: Error: Gap existence and extension values 0 and 0 are
> not supported for substitution scores 1 and -1
> 3 and 2 are supported existence and extension values
> 2 and 2 are supported existence and extension values
> 1 and 2 are supported existence and extension values
> 0 and 2 are supported existence and extension values
> 4 and 1 are supported existence and extension values
> 3 and 1 are supported existence and extension values
> 2 and 1 are supported existence and extension values
> 4 and 2 are supported existence and extension values
> Any values more stringent than 4 and 2 are supported
>
> I've tried fiddling with parameters to address this error, but so far
> haven't been able to get blastn to report *any* hits for these test
> cases, perhaps because the sequences are too short.
>
> I'm also concerned that pynast.util.blast_align_unaligned_seqs invokes
> bl2seq with the -VT flag, which historically requested the old BLAST
> engine.
When thinking about this just disabling the affected test might be a
reasonable thing to do. I'm not sure about the consequences and I can
report this upstream but the last code changes were 3 years ago the
latest issue in Github issue tracker was opened about 2 years ago.
In any case it is one of the more freqently used programs in the Debian
Med scope.
Kind regards
Andreas.
--
http://fam-tille.de
