Persons who have used this program, How do you overcome the slowness problem? I have also see that when i do not used the "--bestn" command wich gives the best aligned secuence the code runs perfeclty.
Did you check that you're not running out of memory ? --bestn is supposed to speed up exonerate. However, you're using quite a high value for it which may make exonerate work more than needed. Since --model est2genome uses essentially a Smith-Waterman alignment algorithm, --bestn 70 probably forces exonerate to run this for quite a lot of sequences.
If the problem is due to the --bestn option then you may be better off not using it and then post processing the output. Also look at the section on 'Strategies for speed' in the man pages.
Oh, Thank you very much for you answer i use --bestn 1 i dont know what i put it that way on my question, Does you answer still the same? Im trying to map cDNA from Drosophila virilis to the Drosophila melanogaster genome, this with the goal to obtain an anotation for both species... for rna seq analyses. Im open to suggestions.
The debian man-pagel also lists a --cores parameter. You can also try setting the --score parameter and setting --fsmmemory to be close to physical RAM.
Using GMAP could be an alternative.
From the manual:
STRATEGIES FOR SPEED
Keep all data on local disks.
Apply the highest acceptable score thresholds using a combination of
--score, --percent and --bestn.
Repeat mask and dust the genomic (target) sequence. (Softmask these
sequences and use --softmasktarget).
Increase the --fsmmemory option to allow more query multiplexing.
Increase the value for --seedrepeat
When using an alignment model containing introns, set --geneseed as
high as possible.
If you are compiling exonerate yourself, see the README file supplied
with the source code for details of compile-time optimisations.
How did you install the versions of Exonerate you used?
Following the user guide, ./configure, make, make installl, Do you have an idea about making the programing runnning faster?
Hi I havent find an answer yet
Did you check that you're not running out of memory ? --bestn is supposed to speed up exonerate. However, you're using quite a high value for it which may make exonerate work more than needed. Since --model est2genome uses essentially a Smith-Waterman alignment algorithm, --bestn 70 probably forces exonerate to run this for quite a lot of sequences. If the problem is due to the --bestn option then you may be better off not using it and then post processing the output. Also look at the section on 'Strategies for speed' in the man pages.
Oh, Thank you very much for you answer i use --bestn 1 i dont know what i put it that way on my question, Does you answer still the same? Im trying to map cDNA from Drosophila virilis to the Drosophila melanogaster genome, this with the goal to obtain an anotation for both species... for rna seq analyses. Im open to suggestions.
Thanks!!