[ensembl-dev] DumpMultiAlign.pl Problem

[Javier Herrero]

Dear Fenix

You are using the wrong version of the API. The error message you get 
says you are using the API version 69. This will be the next API version 
and it is still under development. Importantly, the script relies on the 
API version to find the matching core databases. In this case, the 
script is trying to connect to the human database 69 when this does not 
exist yet.

You can easily fix this problem by "updating" your CVS version to the 67 
API (remember that we always recommend to use matching API and database 
version). This command (run in each main API directory) should do the trick:

cvs up -r branch-ensembl-67

I hope this helps

Javier

On 20/08/12 05:55, ???? wrote:
> Dear all,
>
> I used the DumpMultiAlign.pl normally on compara_67 few months ago, 
> but I failed to fetch it now.
>
> Here is my cmd
> perl ensembl-compara/scripts/dumps/DumpMultiAlign.pl --compara_url 
> mysql://anonymous@ensembldb.ensembl.org:5306/ensembl_compara_67 
> <http://anonymous@ensembldb.ensembl.org:5306/ensembl_compara_67> 
> --species human --seq_region 2 --seq_region_start 106709742 
> --seq_region_end 106709769 --seq_region_strand 1 --alignment_type EPO 
> --set_of_species mammals --restrict --output_format clustalw
>
> But the error occurred,
>
> -------------------- WARNING ----------------------
> MSG: human is not a valid species name (check DB and API version)
> FILE: Bio/EnsEMBL/Registry.pm LINE: 1187
> CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 972
> Date (localtime)    = Mon Aug 20 11:52:13 2012
> Ensembl API version = 69
> ---------------------------------------------------
>
> -------------------- EXCEPTION --------------------
> MSG: Can not find internal name for species 'human'
> STACK Bio::EnsEMBL::Registry::get_adaptor 
> /ensembl/ensembl/modules//Bio/EnsEMBL/Registry.pm:974
> STACK toplevel 
> /ensembl/ensembl-compara/scripts/dumps/DumpMultiAlign.pl:453
> Date (localtime)    = Mon Aug 20 11:52:13 2012
> Ensembl API version = 69
> ---------------------------------------------------
>
> Could anyone help me?
>
> Sincerely,
> Thanks,
>
> Fenix
>
>
>
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-- 
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK

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