Gabri,
I have seen the similar
problem for XML output in mpiblast 1.4 before. However, I don’t know an
easy solution for this except modifying the code. But “-b” and “-v”
options for the XML output have been implemented in mpiblast 1.4-pio. You might
want to try to see if it works for you.
Thanks,
Heshan
From:
[EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Gabri Aparicio
Sent: Tuesday, May 30, 2006 5:55
PM
To:
[email protected]; [EMAIL PROTECTED]
Subject: [mpiblast-devel] Re:
[Mpiblast-users] NUMBER OF OUTPUT HITS DOES NOT MATCH WITH THE INPUT PARAMETERS
Thank you
again for you interest, Mike.
I can not especify what are the rules to show this bug. It is possible to be a
problem with blastp algorithm, but it is also possible to be a sequence
dependant bug. In the sequential blastall version it never occurs.
Someone else can contribute on the topic?
Can anybody confirm this bug? Has anybody a patch to it?
Thank you all.
2006/5/30, Mike Cariaso <[EMAIL PROTECTED]>:
I can confirm that mpiblast blastn does truncate to 20
hits as you wish. However as I lack a protein db and the blosum matricies I
lack a means to test blastp.
I have very vague memories of a bug where the system was behaving as if I was
getting back 20 hits per worker (or per DB fragment?) which might explain what
you are seeing.
Perhaps someone who works with protein seqs can take this a bit further?
----- Original Message ----
From: Gabri Aparicio < [EMAIL PROTECTED]>
To: [email protected]
Sent: Tuesday,
May 30, 2006 12:25:56 PM
Subject: Re: [Mpiblast-users] NUMBER OF OUTPUT HITS DOES NOT
MATCH WITH THE INPUT PARAMETERS
I am talking about the number of Hits. I have 274 Hits when I
execute this line:
mpirun -np 22 mpiblast -e 0.02 -m 7 -v 20 -b 20 -I -p blastp -d
nr -i prova.fas -o prova.xml
where prova.fas is this file:
>gi|23613525|ref|NP_704546.1| rifin [Plasmodium falciparum
3D7]
MKVHYINILLFALPLNILIYNQRNHNSTTHHTLKIPITRLLCECELYELANYDNDPEMKEVMQQFEDRTTQRFHEYDERM
KTTRQKCKDKCDKEIQKIILKDKLEKELMDKFATLHTDIQSDAIPTCICEKSLEDKMEKECLKCAQNLGGIVAPSTGVLG
EIAALAVNAWKTEAIAAATKAAIAKGTAKGLAAGAAKGVAEVIAQVESQFRLSTIGVKELGSIFNASNYTNETFISGYIY
AQYQGSQCGSLSMLLGKSKPFCTFVEGRIFATSVRVGRSFSPEDFIKTTVQTIVKNAKTTAEATKAQVASAEKAAVLETS
KKAIEATTTPYYTPIIVSIVAIVVIILIMVIIYKILRYRRKKKMKKKLQYIKLLKE
If I try to do the same with the blastall executable, I obtain
the requested 20 hits, and nothing more.
Thank you Mike for help me. Please try to execute the same file
with the same parameters than I am trying and comment me how are your results.
Thank you very much.
2006/5/30, Mike Cariaso <[EMAIL PROTECTED]>:
I use -b and -v successfully with mpiblast. Are you
perhaps counting the number of HSPs instead of the number of hits?
----- Original Message ----
From: Gabri Aparicio <[EMAIL PROTECTED]
>
To: [email protected]
Sent: Tuesday, May 30, 2006 10:43:54 AM
Subject: [Mpiblast-users] NUMBER OF OUTPUT HITS DOES NOT MATCH WITH THE INPUT
PARAMETERS
Hi,
I want to obtain only a certain number of hits in the output XML. In the
sequential BLASTALL I can solve it by using the -v and -b parameters, but the
same line in MPIBLAST does not work properly.
I just want to obtain 20 blast hits and MPIBLAST always give me 274 blast hits.
It seems MPIBLAST does not analize -v and -b parameters.
Do you have any idea of how to solve my problem?
Thanks.
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