[Bioperl-l] error running load_seqdatabase.pl

[Hilmar Lapp]

Why don't you just ask your sysadmin - he'll know where to look. It's 
actually in a config file, and the default installation of Postgres 
makes this config file unreadable for every one except the pg-admin 
user chosen at installation time.

	-hilmar

On Dec 30, 2005, at 3:15 PM, Angshu Kar wrote:

> I've no clue about my Pg setup! It has been done by the sysadmin! :(
> Could you please tell me the commands and I can run and let you know 
> the reports?
>
> thanks,
> angshu
>
> On 12/30/05, Hilmar Lapp <hlapp at gmx.net> wrote:
>>
>> 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 Lappemail: lapp at gnf.org
>> >> GNF, San Diego, Ca. 92121phone: +1-858-812-1757
>> >> -------------------------------------------------------------
>> >>
>> >>
>> >
>> >
>> --
>> -------------------------------------------------------------
>> 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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