<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Jan<div><br></div><div>I noticed warnings as well patching from 66->73 for compara for a few tables ( I don't quite remember which ones ). </div><div><br></div><div>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.</div><div><br></div><div>again doesn't really help you I guess.</div><div><br></div><div>Will</div><div><br></div><div><div>On 17 Jan 2014, at 06:49, Jan Vogel <<a href="mailto:jan.vogel@gmail.com">jan.vogel@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div>Hi there, </div><div><br></div><div>i'm trying to patch our ensembl 67 compara database up to schema 74. </div><div><br></div><div>It fails :-( when applying the <b>ensembl-compara/sql/patch_67_68.sql</b> patch as in the 67 schema there are duplicate member ids in the <span style="font-family: Menlo; ">sequence_exon_bounded table. Any idea how to fix this and patch my e67 up to e68 ? </span></div><div><span style="font-family: Menlo; "><br></span></div><div><span style="font-family: Menlo; ">Thanks,</span></div><div><span style="font-family: Menlo; "><br></span></div><div><span style="font-family: Menlo; "> Jan Vogel</span></div><div><br></div><div><div><br></div><div>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' : </div><div><br></div><div>--------------</div><div>SET session sql_mode='TRADITIONAL'</div><div>--------------</div><div>……</div><div>…..</div><div><br></div><div><br></div><div>--------------</div><div>ALTER TABLE sequence_exon_bounded </div><div>DROP PRIMARY KEY, DROP KEY member_id, </div><div>DROP COLUMN sequence_exon_bounded_id, </div><div>ADD PRIMARY KEY (member_id)</div><div>--------------</div><div><br></div><div>Failed to apply patch 'patch_67_68.sql' to database 'ensembl_compara_67'!</div><div>In non-interative mode; aborting current run at schema_patcher.pl line 643.</div></div><div><br></div><div><br></div><div>Looking into the sequence_exon_bounded table, it looks that some member ids are duplicated: </div><div><br></div><div><div><font face="Menlo">mysql> select count(distinct(member_id)) from sequence_exon_bounded limit 10 ; </font></div><div><font face="Menlo">+----------------------------+</font></div><div><font face="Menlo">| count(distinct(member_id)) |</font></div><div><font face="Menlo">+----------------------------+</font></div><div><font face="Menlo">| 1371152 | </font></div><div><font face="Menlo">+----------------------------+</font></div><div><font face="Menlo">1 row in set (10.55 sec)</font></div><div><font face="Menlo"><br></font></div><div><font face="Menlo">mysql> select count(member_id) from sequence_exon_bounded limit 10 ; </font></div><div><font face="Menlo">+------------------+</font></div><div><font face="Menlo">| count(member_id) |</font></div><div><font face="Menlo">+------------------+</font></div><div><font face="Menlo">| 1373719 | </font></div><div><font face="Menlo">+------------------+</font></div></div><div><br></div><div><br></div><div><br></div></div>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></blockquote></div><br></body></html>