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. [email protected] 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 > > > > > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
