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Dear Fenix<br>
<br>
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.<br>
<br>
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:<br>
<br>
cvs up -r branch-ensembl-67<br>
<br>
I hope this helps<br>
<br>
Javier<br>
<br>
<div class="moz-cite-prefix">On 20/08/12 05:55, 八號風球 wrote:<br>
</div>
<blockquote
cite="mid:CAEJ3sUys1bGxF6xNoaPeDE22A3+Kvq-JVzpZhERq35E+oVfBDA@mail.gmail.com"
type="cite">Dear all,
<div><br>
</div>
<div>I used the DumpMultiAlign.pl normally on compara_67 few
months ago, but I failed to fetch it now.</div>
<div><br>
</div>
<div>Here is my cmd</div>
<div>perl ensembl-compara/scripts/dumps/DumpMultiAlign.pl
--compara_url mysql://<a moz-do-not-send="true"
href="http://anonymous@ensembldb.ensembl.org:5306/ensembl_compara_67">anonymous@ensembldb.ensembl.org:5306/ensembl_compara_67</a>
--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</div>
<div><br>
</div>
<div>But the error occurred,</div>
<div><br>
</div>
<div>
<div>-------------------- WARNING ----------------------</div>
<div>MSG: human is not a valid species name (check DB and API
version)</div>
<div>FILE: Bio/EnsEMBL/Registry.pm LINE: 1187</div>
<div>CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 972</div>
<div>Date (localtime) = Mon Aug 20 11:52:13 2012</div>
<div>Ensembl API version = 69</div>
<div>---------------------------------------------------</div>
<div><br>
</div>
<div>-------------------- EXCEPTION --------------------</div>
<div>MSG: Can not find internal name for species 'human'</div>
<div>STACK Bio::EnsEMBL::Registry::get_adaptor
/ensembl/ensembl/modules//Bio/EnsEMBL/Registry.pm:974</div>
<div>STACK toplevel
/ensembl/ensembl-compara/scripts/dumps/DumpMultiAlign.pl:453</div>
<div>Date (localtime) = Mon Aug 20 11:52:13 2012</div>
<div>Ensembl API version = 69</div>
<div>---------------------------------------------------</div>
</div>
<div><br>
</div>
<div>Could anyone help me?</div>
<div><br>
</div>
<div>Sincerely,</div>
<div>Thanks,</div>
<div><br>
</div>
<div>Fenix</div>
<div><br>
</div>
<br>
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<br>
<pre wrap="">_______________________________________________
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK</pre>
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