[Bioperl-l] Clustalw && large sequence number

[Sally Li]

Hi, there,

I received some messages related to this issue. Let me
explain this problem in a more detail.

Hardware: IBM eServer 
          Memory: 6 G
          processors: 4 X 700 MH
Software:

    bioperl
    clustalw 1.82

Problem:
  If the sequences number is large, like 4000
sequences the program was running . But after a long
run, it is hanging there for ever. No error messages
appear.

Notes: clustalw is ok to process less than 1000
sequences. I have aligned 500 sequences ( Mouse
genome) and it works fine. The performance and results
are good to me. If some one can solve this problem, I
believe it will help me and other people who are
intersed in aligment for the huge sequence file.

Thank you very much for your help.

Sally


--- Christopher J Moressi
<cmoressi@engineering.uiowa.edu> wrote:
> Mrs Li.
> 
> That is a large amount of sequences all right. I was
> wondering if you could
> give me the version of Clustalw you are using. I
> know one of the older
> version had some memory problems which in some
> operation systems would cause
> a core dump. Also, what are the error/debug
> information are you receiving
> from the program?
> 
> If you feel ambitious, you might try using gdb to
> check were the problem may
> be. It wont take much time to figure out what piece
> of code is causing the
> problem, however, figuring out what it is doing and
> why will take some
> time..
> 
> 	-Chris
> 
> 
> -----Original Message-----
> From: bioperl-l-admin@bioperl.org
> [mailto:bioperl-l-admin@bioperl.org]On
> Behalf Of Sally Li
> Sent: Thursday, January 16, 2003 2:54 PM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] Clustalw && large sequence
> number
> 
> 
> Hi,
> 
>  I have clustalw run in my Red Hat 8.0 of IBM
> eServer
>  which has 6 G memory. But I failed to get the
> aligment
> done if sequence number is big, like, 4000
> sequences.
>  Any  idea?
> 
>  Thank you very much.
> 
>  Sally
> 
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