[Bioperl-l] error running load_seqdatabase.pl

[Angshu Kar]

oops! he is not present now!
anyways, if you have some time could you please if there are any reasons for
the script to get killed with the .gbk file?

Thanks,
Angshu

On 12/30/05, Hilmar Lapp <hlapp at gmx.net> wrote:
>
> 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 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
> -------------------------------------------------------------
>
>
>