[Bioperl-l] error running load_seqdatabase.pl

[Hilmar Lapp]

Did you empty the database after the previous runs?

Also, you haven't reported your hw setup. In particular, how much 
memory and swap do you have, is Pg running locally (your command line 
suggests it does), and how much memory have you allocated to Pg?

	-hilmar

On Dec 30, 2005, at 3:01 PM, Angshu Kar wrote:

> Yes Hilmar its indeed a full sequence of chromosome. I got it from 
> ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/CHR_V/
> I tried with the .faa and .fna files and they ran successfully.
> Also I missed a line (may be relevant) in the debug o/p:
> no adaptor found for class Bio::Annotation::TypeManager
>
> Thanks,
> Angshu
>
>
> On 12/30/05, Hilmar Lapp < hlapp at gmx.net> wrote:
>> 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/
>> >>
>> >>
>> --
>> -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>> -------------------------------------------------------------
>>
>>
>
>
-- 
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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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