[Bioperl-l] error running load_seqdatabase.pl

[Angshu Kar]

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:
>
> 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 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
> -------------------------------------------------------------
>
>
>