[BioSQL-l] Re: A problem in using load_seqdatabase.pl

[Hilmar Lapp]

Dennis,

which version of biosql do you use? Could you please post the entire 
error message. After how many entries does that happen? Is it 
reproducible? Would it always hit the same entry?

	-hilmar

BTW you should always post to the mailing list(s), biosql-l or 
bioperl-l in this case. Otherwise you may not reach the right people, 
or nor the right email addresses.

On Thursday, August 28, 2003, at 12:12  AM, Dennis Chen wrote:

> Dear sir,
>  
>  
> I am an user in using load_seqdatabase.pl you released before.  I 
> tried several ways to figure out a problem in using the script, but I 
> still can not run it appropriately.  I tried to load 
> decompressed SWISSPROT data (Release 41.13 of 21-Jun-2003, 
> "sprot.dat") into ORACLE database Server (ver 9.2.0.1.0 in Linux 9.0) 
> by using the load_seqdatabase.pl script. Hardware environment: 2 AMD 
> 2000+ CPU, 4 GB RAM, 80 GB HDD, Virtual swap 6G space.  Perl v.5.8, 
> BioPerl v.1.22, DBI v.1.37, DBD::Oracle v.1.14 and newest bioperl-db 
> nodule were installed in system.  In addition, I made some 
> modification in the load_seqdatabase.pl for parameter setting:
> my $remove_flag = 1;
> my $lookup_flag = 0;
> my $no_update_flag = 0;
> my $safe_flag = 0;
>  
> Other parameters would set as default. Then I run the script as: perl 
> load_seqdatabase.pl sorot.dat.
>  
> Howerer, I always got the warning of "Out of memory..."
> Could you please give me some advise to overcome this trouble?  Thank 
> you very much.
>  
> Best regards,
>  
>  
> Dennis 08/29/2003
>  
>  
>
> __________________________________________________
> Bioinformatics
>
> Dennis, Kuang-DenChen
>
> Research Scientist
>
> Tel: +886-2-8976-9123 ext.7703
>
> Fax: +886-2-8976-9523
>
> Mobile: +886-916-992-455
>
> mailto:dennis.chen at vitagenomics.com
>
>
>
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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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