[ensembl-dev] mfetch / pfetch executables

[William Spooner]

Hi Paolo,

You will be unable to run the LoadUniProt analysis without replacing mfetch with some other way of accessing the UniProt sequences. However, the UniProt analysis is related to the ensembl family (tribe-mcl) data, which is not required for the GeneTree. Just comment the UniProt stuff out of your compara config file or delete the analysis/jobs from the database.

Will

On 10 Feb 2011, at 08:36, Paolo Cozzi wrote:

> 
> Dear all
> 
> I'm trying to do the genetree tutorial of the ensembl-compara pipeline.
> During the execution of the LoadUniProt analysis, the worker dies with
> this message:
> 
> mfetch returned nothing, mole server probably down at
> /home/pcozzi/ensembl-libraries/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/LoadUniProt.pm
> line 195
> 
> By looking into LoadUniProt.pm module, I see that this module dies if
> the "mfetch" execution returns no lines. In my local installation, I
> don't have this executable.
> 
> Where I can get "mfetch" code or binary file?
> 
> Thanks for your attention
> 
> Best regards,
> 
> Paolo.
> 
> 
> -- 
> 
> Dott. Paolo Cozzi
> National Research Council, Institute for Biomedical Technologies
> Via Fratelli Cervi 93, 20090 Segrate (MI) Italy
> Office: +39 02 264 22600
> Mobile: +39 338 5451244
> Fax: +39 02 264 22660
> Mail: paolo.cozzi at itb.cnr.it
> skype: paolo.cozzi81
> 
> 
> 
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--
William Spooner
whs at eaglegenomics.com
http://www.eaglegenomics.com