Re: cct test issue: blast: Error: Unknown argument: "query_gencode"

[ucko@debian.org (Aaron M. Ucko)]

Andreas Tille <andreas@an3as.eu> writes:

>   blastn [-h] [-help] [-import_search_strategy filename]
[...]
> DESCRIPTION
>    Nucleotide-Nucleotide BLAST 2.10.1+
[...]
> Error: Unknown argument: "query_gencode"

Please try simply dropping -query_gencode (and its argument) here --
because blastn performs direct nucleotide-nucleotide comparisons, it
doesn't care about genetic codes, and upstream evidently limited this
flag's use to the one tool for which it would be meaningful: tblastx.
(Likewise, only tblastn and tblastx support -db_gencode these days.)

Thanks for checking!

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu