[Bioperl-l] error running load_seqdatabase.pl

[Hilmar Lapp]

If it didn't happen for a different input file, can you tell what is 
special about this one? The file name lets me guess the input is a 
contig or even a full chromosome? Is the input on which the process 
wasn't killed of the same nature? Are the sequences of comparable or 
vastly different lengths? Is there only a single contig in the 
offending input? Can you reproduce the problem on an empty database 
with input containing a single entry? If so, let me know where I can 
get that file from and I'll try to reproduce it locally.

	-hilmar

On Dec 30, 2005, at 2:29 PM, Angshu Kar wrote:

> Any clues why my load_seqdatabase.pl (./load_seqdatabase.pl 
> --dbname=USBA --dbuser=postgres --format=genbank  --driver=Pg --debug  
> NC_003076.gbk)
>  is getting killed after the follwoing step?
>
>  Using Bio::DB::BioSQL::Pg::BiosequenceAdaptorDriver as driver peer 
> for Bio::DB::BioSQL::BiosequenceAdaptor
> preparing SELECT statement: SELECT bioentry_id FROM biosequence WHERE 
> bioentry_id = ?
>
> Killed
>
> I'm using a linux box. This didn't happen for a different i/p file!
>
> Thanks,
> Angshu
>
>
> On 12/29/05, Angshu Kar <angshu96 at gmail.com> wrote: I'm sorry that I 
> missed it! Thanks for pointing it out.
>> Also thanks Hilmar for the update.
>>
>> Angshu
>>
>>
>> On 12/29/05, Torsten Seemann < torsten.seemann at infotech.monash.edu.au 
>> > wrote:> I'm getting the following error while trying to run :
>>> > ./load_seqdatabase.pl -host localhost -dbname USBA -dbuser 
>>> postgres -format
>>> > genbank NC_003076.gbk
>>> > MSG: failed to open connection: Can't connect to local MySQL 
>>> server through
>>> > socket '/var/lib/mysql/mysql.sock' (2)
>>> > But I've a postgreSQL db and not a MySQL one...could anyone please 
>>> guide me
>>> > troubleshoot this?
>>>
>>> Did you read the documentation for the load_seqdatabase.pl script?
>>>
>>> It's in the script itself!
>>>
>>>     =item --driver $driver
>>>     the DBI driver name for the RDBMS e.g., mysql, Pg, or Oracle 
>>> [mysql]
>>>
>>> The default DBI driver is [mysql].
>>>
>>> I think you want the option "-driver Pg".
>>>
>>> --
>>> Torsten Seemann
>>> Victorian Bioinformatics Consortium, Monash University, Australia
>>>  http://www.vicbioinformatics.com/
>>
>>
-- 
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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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