<font size=2 face="Arial">un subscribe me please.</font>
<br>
<br><font size=2 face="Arial">Yinyan</font>
<br>
<br><font size=2 face="sans-serif"> </font>
<br>
<br>
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<td><font size=1 color=#5f5f5f face="sans-serif">From:</font>
<td><font size=1 face="sans-serif">William Spooner <whs@eaglegenomics.com></font>
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<td><font size=1 color=#5f5f5f face="sans-serif">To:</font>
<td><font size=1 face="sans-serif">Jianguo Lu <jianguonk@gmail.com></font>
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<td valign=top><font size=1 color=#5f5f5f face="sans-serif">Cc:</font>
<td><font size=1 face="sans-serif">dev@ensembl.org</font>
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<td><font size=1 color=#5f5f5f face="sans-serif">Date:</font>
<td><font size=1 face="sans-serif">2011-07-29 16:10</font>
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<td><font size=1 color=#5f5f5f face="sans-serif">Subject:</font>
<td><font size=1 face="sans-serif">Re: [ensembl-dev] Question on using
ensembl-compara to extract        homology
alignment</font>
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<td><font size=1 color=#5f5f5f face="sans-serif">Sent by:</font>
<td><font size=1 face="sans-serif">dev-bounces@ensembl.org</font></table>
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<hr noshade>
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<br>
<br><tt><font size=2>Can you try updating your Perl DBI and DBD::mysql
modules to the latest versions from CPAN? This looks a lot like a problem
we had a few years back with those modules.<br>
<br>
Best,<br>
<br>
Will<br>
<br>
On 29 Jul 2011, at 20:40, Jianguo Lu wrote:<br>
<br>
> Hello, <br>
> <br>
> I used this command to do the homology alignment and got some error
information. I am sure there is the GenomeDBAdaptor in my computer. Could
you help me to fix this problem? Appreciate it!<br>
> <br>
> Best Regards,<br>
> Jianguo Lu<br>
> -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br>
> perl getHomologyAlignment.pl -dbhost ensembldb.ensembl.org -dbname
ensembl_compara_51 -dbuser anonymous -dbport 5306 -sp sapiens -g ENSG00000004059<br>
> <br>
> -------------------- WARNING ----------------------<br>
> MSG: Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor cannot be found.<br>
> Exception Bareword "SQL_VARCHAR" not allowed while "strict
subs" in use at /home/catfish/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm
line 278.<br>
> Bareword "SQL_VARCHAR" not allowed while "strict subs"
in use at /home/catfish/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm
line 279.<br>
> Bareword "SQL_INTEGER" not allowed while "strict subs"
in use at /home/catfish/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm
line 280.<br>
> Bareword "SQL_TINYINT" not allowed while "strict subs"
in use at /home/catfish/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm
line 281.<br>
> Bareword "SQL_VARCHAR" not allowed while "strict subs"
in use at /home/catfish/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm
line 282.<br>
> Bareword "SQL_VARCHAR" not allowed while "strict subs"
in use at /home/catfish/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/GenomeDBAdaptor.pm
line 283.<br>
> Compilation failed in require at (eval 46) line 3.<br>
> <br>
> <br>
> FILE: Bio/EnsEMBL/Registry.pm LINE: 502<br>
> CALLED BY: EnsEMBL/DBSQL/DBAdaptor.pm  LINE: 713<br>
> ---------------------------------------------------<br>
> <br>
> -------------------- WARNING ----------------------<br>
> MSG: Could not find GenomeDB adaptor in the registry for DEFAULT compara<br>
> <br>
> FILE: EnsEMBL/DBSQL/DBAdaptor.pm LINE: 719<br>
> CALLED BY: EnsEMBL/Compara/Member.pm  LINE: 488<br>
> ---------------------------------------------------<br>
> Can't call method "fetch_by_dbID" on an undefined value
at /home/catfish/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/Member.pm
line 489.<br>
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<br>
--<br>
William Spooner<br>
whs@eaglegenomics.com<br>
</font></tt><a href=http://www.eaglegenomics.com/><tt><font size=2>http://www.eaglegenomics.com</font></tt></a><tt><font size=2><br>
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