Antwort: Re: [EMBOSS] water exception

[Graziano P.]

Hi David,
I tried launching "limit" and these are the results:

127 /home/life> limit
cputime         unlimited
filesize        unlimited
datasize        unlimited
stacksize       unlimited
coredumpsize    0 kbytes
memoryuse       unlimited
vmemoryuse      unlimited
descriptors     1024
memorylocked    unlimited
maxproc         6132

Both memoryuse and vmemoryuse are unlimited. I am not
obliged to use water, but I am curious to understand
why the EBI-SRS server is able to perform this
alignment and my server not.

Best regards
Graziano

P.S. I am having troubles in sending mail to this
mailing list; I regularly receive mails but I cannot
send mails using outlook. Has the EMBOSS mailing list
got an IP blacklist?


 --- David.Bauer at SCHERING.DE ha scritto: 
> 
> Hi Graziano,
> 
> with the command "limit"  (in tcsh or bash) you can
> see if memoryuse and/or
> vmemoryuse is limited.
> You can try to increase the limit or set it to
> "unlimited".
> 
> Regards,
> David.
> 
> 
> 
> Hi Graziano,
> 
> > I have to align two complete mitochondrial genome
> > sequences (about 16500 nt long) using water
> (emboss
> > version 2.7.1). I have tried this alignment on a
> linux
> > server with 2 Gbytes of RAM and water returns this
> > error:
> >
> > "Uncaught exception:  Allocation failed,
> insufficient
> > memory available, raised at water.c:126"
> 
> It will be virtual memory rather than RAM. Something
> in your shell will
> limit how much memory you can have for water, and it
> is not limited to (or
> by) the physical RAM in the machine.
> 
> But this is a huge alignment problem - just to get a
> "best local match".
> 
> You could get fast results with dottup or (perhaps
> better) polydot. You
> need a large wordsize (the shortest identical
> sequence you expect in a
> real match). Polydot can save the best matches as
> feature tables.
> 
> hope this halps,
> 
> Peter
> 
> 
> 
> 
> 
>  


		
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