[BioSQL-l] load_seqdatabase.pl warnings and errors

[Hilmar Lapp]

On May 19, 2009, at 4:17 AM, michael watson (IAH-C) wrote:

> [...]
> -------------------- WARNING ---------------------
>
> MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values  
> were
> ("AY312586S1","32307407","AY312586","Foot-and-mouth disease virus O
> isolate O/SKR/2000 S fragment, complete
>
> 1,9762)
>
> Duplicate entry 'AY312586-1-1' for key 2
>
> ---------------------------------------------------

This suggests that a sequence with the above accession or GI number  
was already in the database, or occurs in the file twice.

If this situation is possible, you will have to pass the --lookup (or  
--flatlookup) flag to the script, and specify how you want updates to  
take place when they are necessary (options --noupdate, --remove, and  
--mergeobjs).

> -------------------- WARNING ---------------------
>
> MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,
> values were ("","1") FKs (324,3,4)
>
> Duplicate entry '324-3-4-1' for key 2
> ---------------------------------------------------

I suspect that 324 is the primary key of the sequence record that  
raised the duplicate entry warning above. Can you check that?

If the insert is turned into an update, these warnings should go away  
too.

> [...]
> -------------------- WARNING ---------------------
>
> MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,
> values were ("","1") FKs (323,3,4)
>
> Duplicate entry '323-3-4-1' for key 2
>
> ---------------------------------------------------

Similar to before, except 323 is probably the primary key for AY312587.

> [...]
> -------------------- WARNING ---------------------
>
> MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,
> values were ("","1") FKs (325,3,4)
>
> Duplicate entry '325-3-4-1' for key 2
>
> ---------------------------------------------------

And if the order of messages is preserved correctly, 325 would be the  
primary key of AY312589.

> [...]
> -------------------- WARNING ---------------------
>
> MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed,  
> values
> were ("","Direct Submission","Submitted (12-AUG-2004) National Center
> for Biotechnology Information, NIH,
>
> C-E8D3CBBD80002FA1","1","8170","") FKs (<NULL>)
>
> Duplicate entry 'CRC-E8D3CBBD80002FA1' for key 3
>
> ---------------------------------------------------

This one is odd. Can you check which existing entry you have with  
reference.crc = 'CRC-E8D3CBBD80002FA1'?

	-hilmar
-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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