[ensembl-dev] mfetch / pfetch executables

Paolo Cozzi paolo.cozzi at itb.cnr.it
Fri Feb 11 08:45:15 GMT 2011


Thank you for your reply, William.

But what is mfetch? is a tool for downloading uniprot data?

best regards

Paolo.



Il 10/02/2011 15:05, William Spooner ha scritto:
> 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
>
>
>


-- 

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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