[Bioperl-l] problems loading swissprot under mysql inmandrake 9.0

[Hilmar Lapp]

On Wednesday, February 19, 2003, at 02:53  AM, David Guzman wrote:

> DBD::mysql::st execute failed: Duplicate entry '6503-21203' for key 1 
> at
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm
> line 402, <GEN1> line 451975.

This is an "error" that is dealt with (the adaptors handle it, I just 
haven't disabled printing of those messages yet). You should not see 
this followed by a stack trace unless you enabled verbosity.

> DBD::mysql::st execute failed: Duplicate entry 'Pseudomonas fluorescens
> biotype--' for key 3 at
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BaseDriver.pm line 564,
> <GEN1> line 465986.
>

This will probably have caused failure to insert the bioentry, which 
you should see in a subsequent message with stack trace. There are a 
couple of swissprot entries with screwed up species line (e.g., in this 
case the token biotype should actually have been followed by the 
biotype ...). You can make the script continue by supplying --safe. 
With this flag, the script will roll back any failed sequences and 
continue.

	-hilmar

-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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