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Hello,<br>
<br>
I've no idea why now local ensembl 75 installation appears to be
working. Even if I got some small warnings:<br>
<br>
<pre>2014-07-21 16:51:45 - Read configuration from /share/apps/scripts/genomics/global/annotation/ensembl_75/vep_config/vep_template.config</pre>
<pre>2014-07-21 16:51:45 - Read existing cache info</pre>
<pre>2014-07-21 16:51:45 - Loaded plugin: Condel</pre>
<pre>2014-07-21 16:51:46 - Loaded plugin: Conservation</pre>
<pre>2014-07-21 16:51:46 - Fetching regulatory features for plugin: Conservation</pre>
<pre>2014-07-21 16:51:46 - Loaded plugin: Grantham</pre>
<pre>2014-07-21 16:51:46 - Output fields redefined (35 defined)</pre>
<pre>2014-07-21 16:51:46 - INFO: Database will be accessed when using --hgvs</pre>
<pre>2014-07-21 16:51:46 - Starting...</pre>
<pre>2014-07-21 16:51:47 - Read 25000 variants into buffer</pre>
<pre>2014-07-21 16:51:47 - Calculating consequences</pre>
<pre>2014-07-21 17:53:10 - Writing output</pre>
<pre>2014-07-21 17:53:10 - Processed 25000 total variants (7 vars/sec, 7 vars/sec total)</pre>
<pre>2014-07-21 17:53:11 - Read 25000 variants into buffer</pre>
<pre>2014-07-21 17:53:11 - Calculating consequences</pre>
<pre>2014-07-21 18:46:18 - Writing output</pre>
<pre>2014-07-21 18:46:18 - Processed 50000 total variants (8 vars/sec, 7 vars/sec total)</pre>
<pre>2014-07-21 18:46:20 - Read 25000 variants into buffer</pre>
<pre>2014-07-21 18:46:20 - Calculating consequences</pre>
<pre>2014-07-21 19:58:54 - Writing output</pre>
<pre>2014-07-21 19:58:54 - Processed 75000 total variants (6 vars/sec, 7 vars/sec total)</pre>
<pre>2014-07-21 19:58:55 - Read 25000 variants into buffer</pre>
<pre>2014-07-21 19:58:55 - Calculating consequences</pre>
<pre>2014-07-21 20:51:33 - Writing output</pre>
<pre>2014-07-21 20:51:34 - Processed 100000 total variants (8 vars/sec, 7 vars/sec total)</pre>
<pre>2014-07-21 20:51:35 - Read 25000 variants into buffer</pre>
<pre>2014-07-21 20:51:35 - Calculating consequences</pre>
<pre>2014-07-21 21:42:21 - Writing output</pre>
<pre>2014-07-21 21:42:21 - Processed 125000 total variants (8 vars/sec, 7 vars/sec total)</pre>
<pre>2014-07-21 21:42:22 - Read 25000 variants into buffer</pre>
<pre>2014-07-21 21:42:22 - Calculating consequences</pre>
<pre>2014-07-21 22:41:24 - Writing output</pre>
<pre>2014-07-21 22:41:25 - Processed 150000 total variants (7 vars/sec, 7 vars/sec total)</pre>
<pre>2014-07-21 22:41:27 - Read 25000 variants into buffer</pre>
<pre>2014-07-21 22:41:27 - Calculating consequences</pre>
<pre>2014-07-21 23:52:06 - Writing output</pre>
<pre>2014-07-21 23:52:07 - Processed 175000 total variants (6 vars/sec, 7 vars/sec total)</pre>
<pre>2014-07-21 23:52:08 - Read 25000 variants into buffer</pre>
<pre>2014-07-21 23:52:08 - Calculating consequences</pre>
<pre>2014-07-22 00:38:38 - Writing output</pre>
<pre>2014-07-22 00:38:38 - Processed 200000 total variants (9 vars/sec, 7 vars/sec total)</pre>
<pre>2014-07-22 00:38:40 - Read 25000 variants into buffer</pre>
<pre>2014-07-22 00:38:40 - Calculating consequences</pre>
<pre>
Use of uninitialized value in string eq at /share/apps/src/ensembl_75-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1078.</pre>
<pre>
</pre>
<pre>Use of uninitialized value in length at /share/apps/src/ensembl_75-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1081.</pre>
<pre>
2014-07-22 01:28:23 - Writing output</pre>
<pre>2014-07-22 01:28:24 - Processed 225000 total variants (8 vars/sec, 7 vars/sec total)</pre>
<pre>2014-07-22 01:28:25 - Read 25000 variants into buffer</pre>
<pre>2014-07-22 01:28:25 - Calculating consequences</pre>
<pre>2014-07-22 02:16:31 - Writing output</pre>
<br>
I now have to guess what's wrong with the uninitialized values with
ensembl_75-variation.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 07/21/2014 02:46 PM, Andy Yates
wrote:<br>
</div>
<blockquote
cite="mid:00EAD39C-B9CD-4036-B71C-A265F0160B5B@ebi.ac.uk"
type="cite">
<pre wrap="">Hi Guillermo,
Each release's set of files are loaded into a MySQL mirror database here at the EBI to detect these kinds of file regressions. I cannot report any problems with loaded any files from release 75. Could you elaborate on your error?
All the best,
Andy
------------
Andrew Yates - Ensembl Support Coordinator
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
Tel: +44-(0)1223-492538
Fax: +44-(0)1223-494468
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/">http://www.ensembl.org/</a>
On 18 Jul 2014, at 12:26, Guillermo Marco Puche <a class="moz-txt-link-rfc2396E" href="mailto:guillermo.marco@sistemasgenomicos.com"><guillermo.marco@sistemasgenomicos.com></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hello,
Could anyone confirm me that files I mentioned are working properly on local MySQL server?
I've been messing around with MySQL server config settings, have no problem with releases from 61 to 74 with installation. But 75 isn't working.
I'm very skeptical about server fault. I some mysql files inside homo_sapiens_variation could be different than previous versions. I would like to know if the mysql instructions to install DB have changed from 74 to 75. If any of Ensembl admins could confirm me this it would be great.
Thank you.
Best regards,
Guillermo.
On 07/17/2014 03:06 PM, Guillermo Marco Puche wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Dear developers,
Since two weeks I'm trying to install the ensembl 75 release on local MySQL server. (I've done this before since release 61 until release 74).
I always install the following schemes:
• ensembl_compara
• ensembl_ontology
• homo_sapiens_core
• homo_sapiens_funcgen
• homo_sapiens_otherfeatures
• homo_sapiens_variation
I'm experiencing a problem I've never encountered in the past. I'm getting installation problem on homo_sapiens_variation.
I've downloaded the sql *.tar.gz 4 times in the last two weeks. And I'm experiencing the mysql error install. With version 74 and older I've no problem.
Could you guys check if that file is corrupted on public mysql ftp server? Is the only logical explanation that comes to my mind.
Thank you.
Best regards,
Guillermo.
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</pre>
</blockquote>
<pre wrap="">
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</pre>
</blockquote>
<pre wrap="">
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</pre>
</blockquote>
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