[Bioperl-l] error running load_seqdatabase.pl

[Angshu Kar]

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:
>
> If it didn't happen for a different input file, can you tell what is
> 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 Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
>