[Bioperl-l] error running load_seqdatabase.pl

[Angshu Kar]

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:
>
> I suspect it's either a (out-of-)memory error or a binary
> 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 Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
>