[Bioperl-l] error running load_seqdatabase.pl

[Hilmar Lapp]

PERL5LIB is an environment variable. 'use lib '/path/to/whatever';' 
should have the same effect though, apart from the fact that it 
requires you to modify the software.

The path should point to the directories where you installed your 
add-on packages.

You are correct, if the path is wrong then 'use Bio::Root::Root;' will 
fail - unless there is a system-default installed version of Bioperl 
older than 1.5.x.

	-hilmar

On Dec 30, 2005, at 8:20 PM, Angshu Kar wrote:

> 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
>> -------------------------------------------------------------
>>
>>
>>
-- 
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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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