[Bioperl-l] error running load_seqdatabase.pl

[Angshu Kar]

You mean the ' use lib ' in my perl script to point to the .pm folder?
Yes I've done that! Else how it should have failed at the first step.Isn't
it?


On 12/30/05, Hilmar Lapp <hlapp at gmx.net> wrote:
>
> Did you set your PERL5LIB appropriately?
>
> On some Windows platforms there are known problems with dynamically
> loaded perl modules. The module quoted below does 'use
> Bio::Root::Root;', so the absence of that is not the problem.
>
>         -hilmar
>
> On Dec 30, 2005, at 5:28 PM, Angshu Kar wrote:
>
> > A new error:
> >
> > I installed bioperl-db in my own WinXP m/c following instructions in
> > CVS by Chris Fields. I'm trying to run the same command from this m/c
> > (the postgres db resides in the linux box) and getting the error:
> >
> > Loading NC_003076.gbk ...
> > Undefined subroutine &Bio::Root::Root::debug called at
> > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 1537,
> > <GEN0> line 766536.
> >
> > Any inputs on this?
> >
> >
> >
> > On 12/30/05, Hilmar Lapp <hlapp at gmx.net> wrote:
> >> incompatibility.
> >>
> >> You haven't yet run the bioperl-db test suite, have you? Please don't
> >> ask for more help before you haven't done that.
> >>
> >> Also, you do remember my earlier answer to a similar report from you,
> >> right?
> >> http://portal.open-bio.org/pipermail/bioperl-l/2005-December/
> >> 020389.html
> >>
> >> The two first things to do is to check whether you run out of shared
> >> memory and to run the tests and see whether the location where the
> >> process gets killed can be narrowed down. If it's not a bug (which it
> >> is unlikely to be - but the tests will provide more evidence) then the
> >>  next step would be to recompile your own perl, DBI and DBD::Pg, and
> >> PostgreSQL, in that order.
> >>
> >> -hilmar
> >>
> >> On Dec 30, 2005, at 4:13 PM, Angshu Kar wrote:
> >>
> >> > 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:
> >> >> 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 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
> -------------------------------------------------------------
>
>
>