[BioSQL-l] Re: [Bioperl-l] Error loading sequence with load_seqdatabase.pl

[Duangdaow Kanhasiri]

The 

OS: Rocks Cluster v 3.3 
Total Memory: 2 GB
DBD::Pg version: 1.42
DBI version: 1.48


--- Hilmar Lapp <hlapp at gmx.net> wrote:

> What OS are you running this on? How much memory
> have you got on the  
> machine on which you run the script, and on the
> machine on which you  
> run the database? Are these the same or not? Which
> version of DBI and  
> DBD::Pg?
> 
> This hasn't been reported by anyone else really so I
> suspect it's  
> either due to too limited memory, or a problem in
> the DBD driver or in  
> the DBI compiled code. Can you watch the process
> (using, e.g., top) and  
> see how fast it increases in memory consumption?
> Since you can continue  
> when you restart it's not something specific to one
> sequence that would  
> trigger the problem; rather it appears whenever you
> have run through a  
> certain number of entries the process dies.
> 
> 	-hilmar
> 
> On Jun 8, 2005, at 7:43 PM, Duangdaow Kanhasiri
> wrote:
> 
> > Hi,
> >
> > I've used the bioperl script load_seqdatabase.pl
> (came
> > with the biosql' scripts) to load the bacterial
> > sequence in genbank format(*.gbk) into PostgreSQL
> 8.0
> > database on Linux machine as:
> >
> > $perl load_seqdatabase.pl /export/Bacteria/*/*.gbk
> &
> >
> > Where  under the /export/Bacteria/ path are the
> > Bacteria's name path e.g. Acinetobacter_sp_ADP1
> and
> > the file name are like NC_006824.gbk.
> >
> > Previously it used to load some sequences in to
> some
> > tables in biosql database (count from table
> bioentry)
> >
> > bioseq=# select count(*) from bioentry;
> >  count
> > -------
> >    33
> > (1 row)
> >
> >
> > However, after a while it then stopped with the
> the
> > error:
> >
> > [1]+  Segmentation fault      perl
> load_seqdatabase.pl
> > /export/Bacteria/*/*.gbk &
> >
> > I then checked and removed the *.gbk file that
> have
> > already been loaded in to the table, leaving only
> the
> > unloaded ones and ran the scripted again.  It
> > continued to work for some times and stopped
> again.  I
> > repeated the process several times until 173
> sequences
> > were loaded into the table:
> >
> > bioseq=# select count(*) from bioentry;
> >  count
> > -------
> >    173
> > (1 row)
> >
> > The program then stopped again and this time it
> > wouldn't run anymore even I tried with only on
> file.
> > The error is still the same like:
> >
> > $ perl load_seqdatabase.pl
> >
>
/export/Bacteria/Lactobacillus_johnsonii_NCC_533/NC_005362.gbk
> > Segmentation fault
> > $
> >
> > Now I couldn't load the rest of my sequences into
> the
> > database anymore.  I would be very apprecialed if
> any
> > one knows how to solve the "Segmentation fault"
> > problem?
> >
> > Regards,
> >
> > Davina
> >
> >
> > 		
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>
online.html<load_seqdatabase.pl>_______________________________________
> 
> > ________
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> >
>
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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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