[ensembl-dev] Ensembl 75 MySQL problem

Tue Jul 22 07:13:55 BST 2014

Hello,

I've no idea why now local ensembl 75 installation appears to be 
working. Even if I got some small warnings:

2014-07-21 16:51:45 - Read configuration from /share/apps/scripts/genomics/global/annotation/ensembl_75/vep_config/vep_template.config

2014-07-21 16:51:45 - Read existing cache info

2014-07-21 16:51:45 - Loaded plugin: Condel

2014-07-21 16:51:46 - Loaded plugin: Conservation

2014-07-21 16:51:46 - Fetching regulatory features for plugin: Conservation

2014-07-21 16:51:46 - Loaded plugin: Grantham

2014-07-21 16:51:46 - Output fields redefined (35 defined)

2014-07-21 16:51:46 - INFO: Database will be accessed when using --hgvs

2014-07-21 16:51:46 - Starting...

2014-07-21 16:51:47 - Read 25000 variants into buffer

2014-07-21 16:51:47 - Calculating consequences

2014-07-21 17:53:10 - Writing output

2014-07-21 17:53:10 - Processed 25000 total variants (7 vars/sec, 7 vars/sec total)

2014-07-21 17:53:11 - Read 25000 variants into buffer

2014-07-21 17:53:11 - Calculating consequences

2014-07-21 18:46:18 - Writing output

2014-07-21 18:46:18 - Processed 50000 total variants (8 vars/sec, 7 vars/sec total)

2014-07-21 18:46:20 - Read 25000 variants into buffer

2014-07-21 18:46:20 - Calculating consequences

2014-07-21 19:58:54 - Writing output

2014-07-21 19:58:54 - Processed 75000 total variants (6 vars/sec, 7 vars/sec total)

2014-07-21 19:58:55 - Read 25000 variants into buffer

2014-07-21 19:58:55 - Calculating consequences

2014-07-21 20:51:33 - Writing output

2014-07-21 20:51:34 - Processed 100000 total variants (8 vars/sec, 7 vars/sec total)

2014-07-21 20:51:35 - Read 25000 variants into buffer

2014-07-21 20:51:35 - Calculating consequences

2014-07-21 21:42:21 - Writing output

2014-07-21 21:42:21 - Processed 125000 total variants (8 vars/sec, 7 vars/sec total)

2014-07-21 21:42:22 - Read 25000 variants into buffer

2014-07-21 21:42:22 - Calculating consequences

2014-07-21 22:41:24 - Writing output

2014-07-21 22:41:25 - Processed 150000 total variants (7 vars/sec, 7 vars/sec total)

2014-07-21 22:41:27 - Read 25000 variants into buffer

2014-07-21 22:41:27 - Calculating consequences

2014-07-21 23:52:06 - Writing output

2014-07-21 23:52:07 - Processed 175000 total variants (6 vars/sec, 7 vars/sec total)

2014-07-21 23:52:08 - Read 25000 variants into buffer

2014-07-21 23:52:08 - Calculating consequences

2014-07-22 00:38:38 - Writing output

2014-07-22 00:38:38 - Processed 200000 total variants (9 vars/sec, 7 vars/sec total)

2014-07-22 00:38:40 - Read 25000 variants into buffer

2014-07-22 00:38:40 - Calculating consequences

Use of uninitialized value in string eq at /share/apps/src/ensembl_75-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1078.

Use of uninitialized value in length at /share/apps/src/ensembl_75-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1081.

2014-07-22 01:28:23 - Writing output

2014-07-22 01:28:24 - Processed 225000 total variants (8 vars/sec, 7 vars/sec total)

2014-07-22 01:28:25 - Read 25000 variants into buffer

2014-07-22 01:28:25 - Calculating consequences

2014-07-22 02:16:31 - Writing output

I now have to guess what's wrong with the uninitialized values with 
ensembl_75-variation.

Best regards,
Guillermo.

On 07/21/2014 02:46 PM, Andy Yates wrote:
> 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
> http://www.ensembl.org/
>
> On 18 Jul 2014, at 12:26, Guillermo Marco Puche <guillermo.marco at sistemasgenomicos.com> wrote:
>
>> 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:
>>> 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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>>
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