Re: [Gusdev-gusdev] Problem loading Pfam data into GUS

[<pj...@sa...>]

If I remember correctly I got an XML dump from CBIL with 
all of the ExternalDatabase table entries with the matching
ExternalDatabaseRelease rows. I added a few entries that GeneDB needed.

Is the ExternalReleaseTable populated with bootstrap data when a new GUS schema
is created?

I have a copy of those files that I can send to you but I can't access it right now.


Quoting Madhura Sharangpani <sma...@st...>:

> Hi
> 
> I am trying again to load Pfam data into GUS using LoadPfam plugin, but after
> registering the LoadPfam plugin successfully, when I try loading data into
> database, I get the following error:
> 
> ***************************************************
> elaine15:~/RA/pfam> ga
> GUS::Common::Plugin::LoadPfam --parse_only --flat_file=Pfam-A.full.gz --rele
> ase=13.0
> Reading properties from
> /afs/ir/users/s/m/smadhura/RA/GUS/config/GUS-PluginMgr.prop
> Reading properties from /afs/ir/users/s/m/smadhura/RA/GUS/.gus.properties
> ImportPfam: COMMIT OFF
> ImportPfam: reading Pfam release 13.0 from Pfam-A.full.gz
> 0: PF00244.7
> Unable to find most recent ExternalDatabaseRelease for ExternalDatabase
> medline at
> /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadPfam.pm
> line 417, <PFAM> line 590.
> 
> gunzip: stdout: Broken pipe
> ***************************************************
> 
> I have downloaded latest release 13.0 from website
> 
> Do I need to also specify external_database_release_id or something in the
> command?  
> 
> Thanks!
> 
> Madhura
>