[EMBOSS] Antwort: Memory problem with extractseq

[david.bauer at bayerhealthcare.com]

Hi,

I tested this on a larger machine and the job growth to  ~7.3 Gb before it 
outputs the requested sequence part.
The memory size is the same for extractseq and seqret.
Chromosome 1 fasta file size is ~250 Mb so it seems that EMBOSS is not 
very memory efficient  ;-)

David.

emboss-bounces at lists.open-bio.org schrieb am 18/03/2010 10:11:59:

> Hi
> 
> I'm using EMBOSS 6.1.0 on a fairly small Linux VM which has about 3Gb of 
RAM.
> 
> I find it strange that extractseq reports a memory problem:
> 
> -bash-3.00# /usr/local/EMBOSS-6.1.0/bin/extractseq  -sequence chr1.
> fasta -outseq chr1_.1.fasta -regions '34415690-34415711'
> Extract regions from a sequence
> Uncaught exception:  Allocation failed, insufficient memory 
> available, raised at ajstr.c:2406
> 
> Whereas if I write a Bioperl script using SeqIO and the trunk() 
> function, it works perfectly.
> 
> I'd have thought EMBOSS would be more streamlined and memory 
> efficient than Bioperl?
> 
> Thanks
> Mick
> 
> 
> 
> 
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