[EMBOSS] einverted- file size limits?
jison at ebi.ac.uk
Thu Jun 26 07:24:40 UTC 2008
The short answer is you need more memory and a faster computer.
Check there are no system limits on memory usage (do an "unlimit"
or some such). EMBOSS has no arbitrary memory limits, it is just
that einverted uses full dynamic programming which is necessarily
very memory and CPU intensive, especially for larger sequences.
You could try running palindrome which does a similar thing and is
is faster and less memory intensive.
> I am attempting to use einverted on a relatively large set of
> sequences. I've noticed that when I run just a few sequences, einverted
> seems to run just fine. However, when I use the same parameters on a
> large set of sequences, the program quits before it has finished
> analyzing all of the data. Are there known file size limits or sequence
> length limits for einverted? If so, how can I run large sequences
> (>300kb) or large numbers of sequences (1000+)?
> I'm running einverted from EMBOSS 5.0.0 on a Sun machine running Solaris
> 9 for SPARC.
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