Hi Mike,
Unfornately, i've got any error message. All the job run without
complains about such a problem.
But thank's you for investigate with this special case.
Mike Cariaso wrote:
> The problem occurs when a workers sees that no GIs apply to it, and then
> decides that it should do no GI filtering. Nodes which match some GIs,
> stil respect the filter. The problem occurs in the ncbi toolbox, not the
> pure mpiBLAST code, since it assumes that running on a single node with
> a filter that matches none of the GIs is illogical.
>
> Please confirm that your runs produce this message on STDERR:
> BlastCreateVirtualOIDList: Missing oidlists to attach virtual_oidlist
>
> If so the problem occurs in ncbi/tools/blastool.c at line 2727
> /* attach mask to appropriate place */
> if (oidlist_forall_rdfp && real_ngis > 0) {
> rdfp_chain->oidlist = virtual_oidlist;
> } else {
> if (mask_rdfp)
> mask_rdfp->oidlist = virtual_oidlist;
> else {
> /* Should never happen */
> ErrPostEx(SEV_ERROR, 0, 0, "BlastCreateVirtualOIDList: Missing "
> "oidlists to attach virtual_oidlist");
> OIDListFree(virtual_oidlist);
> return NULL;
> }
> }
>
>
>
> Unfortunately, simply replacing the /* Should never happen */ block
> with another
> mask_rdfp->oidlist = virtual_oidlist;
> or
> mask_rdfp->oidlist = NULL;
> seems to result in crashes when there are no GIs for a particular worker.
>
>
> Presumably the worker can be told to look for this case, and return a
> correct "No results found" response to the master. Doing so, is a bit
> beyond my abilities tonight, and before I attempt anything of the sort
> I'd welcome input from others. While the problem is most visible in
> Jerome's extreme case, this could be an issue any time the filter
> removes more GIs than are present on a single worker. That pathological
> case is certainly rare, but not impossible.
>
>
>
>
>
> --
> Mike Cariaso * Bioinformatics Software * http://www.cariaso.com
>
>
> ----- Original Message ----
> From: Mike Cariaso <[EMAIL PROTECTED]>
> To: [email protected]
> Sent: Wednesday, March 14, 2007 8:57:46 PM
> Subject: Re: [Mpiblast-users] Strange issue in mpiBlast limiting by "Gi"
>
>
> By having so few GIs, it becomes likely that at least one of the workers
> is given 0 sequences to analyze. This seems like a rather special case,
> and I would imagine it is where the bug hunt should begin. I'll try to
> do a few tests this evening.
>
>
> --
> Mike Cariaso * Bioinformatics Software * http://www.cariaso.com
>
>
> ----- Original Message ----
> From: Jerome <[EMAIL PROTECTED]>
> To: [email protected]
> Sent: Wednesday, March 14, 2007 8:43:23 PM
> Subject: Re: [Mpiblast-users] Strange issue in mpiBlast limiting by "Gi"
>
> Hi Mike,
> Yes, i understand our remark, and you are rigth in the way that the
> number of sequence's reference is very big.
> But in my special case, the end user are using genome sequence for
> bacteria, that have just one reference (or two for ribozomal ciclic
> sequence) for all of the genome. And, searching for just two or three
> special bacterias, i found this issue.
> With the other databases as nt, and i've never use filter of 2 or 3 Gi.
> Take my question more like a desie to understand why this problem.
> Best regards.
>
> Mike Cariaso wrote:
> > Jerome,
> >
> > What you are describing may be true (if so, its worth pursing), but my
> > your usage sounds very strange to me.
> >
> > Having 7 fragments would be reasonable for a small cluster with 7 nodes.
> > But for your GI filter file to only have 7 lines, would mean that you
> > would only be searching 7 sequences. When I search a database such as
> > NCBI's 'nt', my filterfile usually has more than 4,000,000 GIs.
> >
> > The GI filter is used to include/exclude individual sequences when
> > searching your blastable database. This is done with the "-l
> > filterfilename "(lowercase L) command line switch, where filterfilename
> > is (usually) a text file of GI #s, one per line. Typically a blastable
> > database will have thousands to millions of sequences, and therefore
> > thousands to millions of GIs.
> >
> > The number of fragments refers to the number of pieces you split your
> > blastable database into. Commonly this will be the same size as the
> > number of workers in your cluster, or perhaps a multiple such as 2x or
> > 3x larger.
> >
> > In most cases the number of sequences in the database is many thousands
> > of times larger than the number of fragments. Otherwise each worker
> > would have very little work to do, and mpiBLAST probably wouldn't make
> > much sense.
> >
> > Does it sound like you and I are describing the same thing?
> >
> > --
> > Mike Cariaso * Bioinformatics Software * http://www.cariaso.com
> >
> >
> > ----- Original Message ----
> > From: Jerome <[EMAIL PROTECTED]>
> > To: [email protected]
> > Sent: Wednesday, March 14, 2007 7:55:28 PM
> > Subject: [Mpiblast-users] Strange issue in mpiBlast limiting by "Gi"
> >
> > Hi all,
> > ive just instal a Mpiblast to running on our cluster. And it's a verya
> > fast program that i can thank's you!
> > For justa few day, some user want's to limit the search in a database of
> > bacterians genome. And i could notice that, if the number of "gi"
> > entries in the filter file is less or equivalent of the number of
> > fragments of the initial database, i don't matter about this filter file.
> > I mean that, for example, if i format the databases in 7 fragments, and
> > ask with a filter file size of >7 lines, i don't use it and answer the
> > similar response as if i don't use this filter.
> > Could someone help me in this issue?
> >
> > --
> > -- Jérôme
> > Le vase donne une forme au vide, et la musique au silence.
> > (Georges Braque)
> >
--
-- Jérôme
En essayant continuellement, on finit par réussir. Donc:
Plus ça rate, plus on a de chance que ça marche.
(Devise Shadok)
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