est2genome complains that stack ran out of memory

[Peter Rice]

Chan Chee Seng wrote:

> I have recently installed emboss version 2.6.  When my one of my users 
> ran estgenome, she got the following error messages.
> 
> ~>  est2genome
> Align EST and genomic DNA sequences
> EST sequence(s): park2musdowngene.txt
> Genomic sequence: park2mousecontig.txt
> Output file [mus.est2genome]: hope7.estgenome
> Error: rpairs 2500001 beyond maximum 2500000
> Error: increase space threshold to repeat this search
> Error: stack ran out of memory, returning NULL
> Error: rpairs 2500001 beyond maximum 2500000

> Is there a configuration file to tweak so as to increase the stack?  Do 
> I have to recompile emboss with some special settings?  Any help would 
> be most appreciated.  Thanks.

est2genome has a command line option "-space" to increase the "stack", 
for example:

est2genome -space 20

The default value is 10 (Mbytes).

The error message is rather confusing, and should be improved. But also, 
est2genome should be able to check for stack space limits and use an 
alternative algorithm.

Can you please send the two input sequence files (park2musdowngene.txt 
and park2mousecontig.txt) so we can check why the program ran out of 
stack space.

Hope this helps,

Peter