Re: [Gusdev-gusdev] LoadBlastSimFast error

[Dave B. <db...@pc...>]

Hi Poliana,

Just as a first cut, make sure you have generated your perl GUS objects 
recently.  Make sure the file

{$GUS_HOME}/lib/perl/GUS/Model/DoTS/ExternalAASequence.pm

exists.

Also, I saw your other comment about the similarity file having the 
sequences source ids instead of GUS IDs.  That is not a problem if, in the 
DoTS.ExternalAASequence table, those sequence source ids show up in the 
'name' attribute.  Unless you consciously loaded them that way though, 
that may not be the case, and you should probably substitute the ids with 
GUS Ids in the blast file (I find I have to do that a lot when running 
this plugin.)

However, even if the sequence source ids are not in the 'name' attribute 
of that table, I don't think that is the reason for the error you mention 
when running the plugin.

Dave




On Wed, 2 Mar 2005, Poliana Mateus wrote:

> Hello All,
>
> I'm trying to run the LoadBlastSimFast...
>
> And I get the following error message:
>
> ----------------------------------------------------------------------------------------------------------------------
> [poliana@phytomonas Plugin]$ ga GUS::Common::Plugin::LoadBlastSimFast
> --file=/usr/local/GUS/Blast/scripts/8saida.out
> --queryTable=DoTS::ExternalAASequence
> --subjectTable="DoTS::ExternalAASequence" --commit
>
> Wed Mar  2 15:07:11 2005        ARGS    algoinvo        1
> Wed Mar  2 15:07:11 2005        ARGS    batchSize       1000
> Wed Mar  2 15:07:11 2005        ARGS    comment
> Wed Mar  2 15:07:11 2005        ARGS    commit  1
> Wed Mar  2 15:07:11 2005        ARGS    debug
> Wed Mar  2 15:07:11 2005        ARGS    file
> /usr/local/GUS/Blast/scripts/8saida.out
> Wed Mar  2 15:07:11 2005        ARGS    group
> Wed Mar  2 15:07:11 2005        ARGS    gusconfigfile
> /usr/local/GUS/gus_home/.gus.properties
> Wed Mar  2 15:07:11 2005        ARGS    hspMatchLength
> Wed Mar  2 15:07:11 2005        ARGS    hspPctIdent
> Wed Mar  2 15:07:11 2005        ARGS    hspPvalue
> Wed Mar  2 15:07:11 2005        ARGS    hspsLimit
> Wed Mar  2 15:07:11 2005        ARGS    maxSubjects
> Wed Mar  2 15:07:11 2005        ARGS    minSubjects
> Wed Mar  2 15:07:11 2005        ARGS    noHSPs  0
> Wed Mar  2 15:07:11 2005        ARGS    project
> Wed Mar  2 15:07:11 2005        ARGS    queryTable      DoTS::ExternalAASequence
> Wed Mar  2 15:07:11 2005        ARGS    restartAlgInvs
> Wed Mar  2 15:07:11 2005        ARGS    sqlVerbose
> Wed Mar  2 15:07:11 2005        ARGS    subjectMatchLength
> Wed Mar  2 15:07:11 2005        ARGS    subjectPctIdent
> Wed Mar  2 15:07:11 2005        ARGS    subjectPvalue
> Wed Mar  2 15:07:11 2005        ARGS    subjectTable    DoTS::ExternalAASequence
> Wed Mar  2 15:07:11 2005        ARGS    subjectsLimit
> Wed Mar  2 15:07:11 2005        ARGS    testnumber
> Wed Mar  2 15:07:11 2005        ARGS    usage
> Wed Mar  2 15:07:11 2005        ARGS    user
> Wed Mar  2 15:07:11 2005        ARGS    verbose
> Wed Mar  2 15:07:11 2005        ARGS    veryVerbose
> Wed Mar  2 15:07:11 2005        COMMIT  commit on
>
> Can't locate object method "new" via package
> "DoTS::ExternalAASequence" (perhaps you forgot to load
> "DoTS::ExternalAASequence"?) at
> /usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadBlastSimFast.pm
> line 381, <GEN0> line 563.
>
> ---------------------------------------------------------------------------------------------------------------------------------
>
> My table DoTS::ExternalAASequence already was loaded.
> ??
>
> Poliana
>
>
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