[EMBOSS] Memory problem with extractseq

[michael watson (IAH-C)]

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