[ensembl-dev] Exonerate "protein2dna:bestfit" problem in 64 Bit Computer

B Enn witch.of.agnessi at gmail.com
Tue Aug 27 18:12:52 BST 2013

Hello all,

I'm having a problem to run the "protein2dna:bestfit" model in my 64 bit
computer and under both Linux Cluster and Cygwin. For the Linux Cluster
I've tried both the readymade executable and compiled source code. I
downloaded the sources from ensemble CVS as well as the tarball from EBI


Program details: ./exonerate -v

exonerate from exonerate version 2.2.0
Using glib version 2.22.5
Built on Aug 26 2013

The simple command I used :

./exonerate -m p2d:b -q test_protein.fasta -t test_dna.fasta --exhaustive yes

The program just quits without producing any output as follows:

** (process:1922): WARNING **: Exhaustively generating suboptimal
alignments will be VERY SLOW
-- completed exonerate analysis

****However it runs fine with my old 32 bit Ubuntu.*****Also it runs fine
if the 'bestfit' part is dropped i.e when only "protein2dna" model is used.

The Pastebin Protein and DNA file links are here:




Did anybody face the same problem and any suggestions to solve it?

I'm approaching a deadline fast, and by 32 bit Ubuntu can't handle the big
data I've to process. So, any help is much appreciated
Thanks in advance
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