[ensembl-dev] Patching an Ensembl compare database from 67 to 74
Will Chow
wc2 at sanger.ac.uk
Fri Jan 17 10:08:11 GMT 2014
Hi Jan
I noticed warnings as well patching from 66->73 for compara for a few tables ( I don't quite remember which ones ).
Of course this doesn't really help you or solve your issues, but since our group doesn't use those tables I just ignored the patch warnings and for our purposes, it seems to work. I do notice in the meta table the patch keys for the updates are not there below e70 even though the patches are in the sql directory.
again doesn't really help you I guess.
Will
On 17 Jan 2014, at 06:49, Jan Vogel <jan.vogel at gmail.com> wrote:
>
> Hi there,
>
> i'm trying to patch our ensembl 67 compara database up to schema 74.
>
> It fails :-( when applying the ensembl-compara/sql/patch_67_68.sql patch as in the 67 schema there are duplicate member ids in the sequence_exon_bounded table. Any idea how to fix this and patch my e67 up to e68 ?
>
> Thanks,
>
> Jan Vogel
>
>
> ERROR 1062 (23000) at line 28 in file: '/gnet/resfiles3/resapps/apps/ensembl/ensembl-74/ensembl-compara/sql/patch_67_68.sql': Duplicate entry '2012449' for key 'PRIMARY' :
>
> --------------
> SET session sql_mode='TRADITIONAL'
> --------------
> ……
> …..
>
>
> --------------
> ALTER TABLE sequence_exon_bounded
> DROP PRIMARY KEY, DROP KEY member_id,
> DROP COLUMN sequence_exon_bounded_id,
> ADD PRIMARY KEY (member_id)
> --------------
>
> Failed to apply patch 'patch_67_68.sql' to database 'ensembl_compara_67'!
> In non-interative mode; aborting current run at schema_patcher.pl line 643.
>
>
> Looking into the sequence_exon_bounded table, it looks that some member ids are duplicated:
>
> mysql> select count(distinct(member_id)) from sequence_exon_bounded limit 10 ;
> +----------------------------+
> | count(distinct(member_id)) |
> +----------------------------+
> | 1371152 |
> +----------------------------+
> 1 row in set (10.55 sec)
>
> mysql> select count(member_id) from sequence_exon_bounded limit 10 ;
> +------------------+
> | count(member_id) |
> +------------------+
> | 1373719 |
> +------------------+
>
>
>
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