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

[Hilmar Lapp]

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
>
>
> 		
> __________________________________
> Discover Yahoo!
> Have fun online with music videos, cool games, IM and more. Check it  
> out!
> http://discover.yahoo.com/ 
> online.html<load_seqdatabase.pl>_______________________________________ 
> ________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------