Did you provide -parse_seqids in the header?
Peter dealt with related things here:
On Apr 19, 2013, at 1:05 PM, shalu sharma
> Thanks everyone for you inputs.
> I got really excited when i saw that you can even get super kingdom, but
> when i tried to test it i just got taxa ids but not the super kingdom. Do
> you have any idea whats going wrong?
> my command:
> blastx -query test.fas -db /db/ncbiblast/refseq/latest/refseq_protein
> -max_target_seqs 1 -outfmt "6 staxids sskingdoms"
> 246200 N/A
> 246200 N/A
> On Thu, Apr 18, 2013 at 3:52 PM, Smithies, Russell <
> [email protected]> wrote:
>> I agree they have finally listened and added features requested by users
>> but I've been suggesting they have a compressed output format available
>> from eutils or genbank for years but have made no headway ;- (
>> What's so hard about gzip'ping the output? I'm sure it would go a long
>> toward solving all the problems we get with truncated replies from
>> -----Original Message-----
>> From: [email protected] [mailto:
>> bio[email protected]] On Behalf Of Fields, Christopher J
>> Sent: Friday, 19 April 2013 6:26 a.m.
>> To: Peter Cock
>> Cc: [email protected]; shalu sharma; shalabh sharma
>> Subject: Re: [Bioperl-l] Taxa Id from blast report
>> On Apr 18, 2013, at 11:48 AM, Peter Cock
>>> On Thu, Apr 18, 2013 at 5:32 PM, shalabh sharma
>>>> Hey Peter,
>>>> Thanks a lot, I really appreciate it. I wanted these things
>>>> implemented in blast from long time.
>>> Me too. You can get the descriptions from the plain text BLAST or XML
>>> output already of course, but they're not so nice to work with.
>> NCBI has been much more receptive of user input over the last several
>> years, much more so than in the past. I understand the reasoning for
>> dropping BLAST support (though there were definitely needless bumps in
>> Bioperl-l mailing list
>> [email protected]
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