Antwort: [EMBOSS] eprimer3

[David.Bauer at SCHERING.DE]

Hi Caroline,

there seems to be a problem that may be architecture and/or memory
dependent.

I did a test with a 2.3 Mb sequence and got an totally empty output list.
So I tested a bit with different sequence length:
It works OK up to:
-numreturn 10 -pickanyway -sbegin 1 -send 2100000
But I get an empty output with:
-numreturn 10 -pickanyway -sbegin 1 -send 2200000
And the output is OK again with
-numreturn 10 -pickanyway -sbegin 100000 -send 2200000

The system is FreeBSD on Intel with 768 Mb RAM.

Here is the debug ouput in case I get an empty output list:
The negative numbers for memory use do not look really healthy to me :-(
Final Summary
=============
String usage (bytes): -1556553655 allocated, 17 freed, -1554743706 in use
String usage (number): 160768 allocated, 0 freed 159728 in use
Regexp usage (bytes): 112 allocated, 0 freed, 0 in use
Regexp usage (number): 28 allocated, 0 freed 0 in use
Table usage : 3 opened, 0 closed, 251 maxsize, 24 maxmem
List usage : 11 opened, 8 closed, 0 maxsize 5970 nodes
List iterator usage : 11 opened, 11 closed, 0 maxsize
Regexp usage (bytes): 112 allocated, 0 freed, 0 in use
Regexp usage (number): 28 allocated, 0 freed 0 in use
File usage : 1 opened, 5 closed, 3 max, 6 total
ajNamExit done
Memory usage (bytes): -1553262663 allocated, 17 reallocated 8390208 zeroed
Memory usage (number): 368042 allocates, 0 frees, 365811 resizes, 0 in use


In case the output was OK the memory allocation looks much better and is
very close to what I have available as physical RAM.
Final Summary
=============
String usage (bytes): 711486205 allocated, 16 freed, 713296154 in use
String usage (number): 158674 allocated, 0 freed 157634 in use
Regexp usage (bytes): 112 allocated, 0 freed, 0 in use
Regexp usage (number): 28 allocated, 0 freed 0 in use
Table usage : 3 opened, 0 closed, 251 maxsize, 24 maxmem
List usage : 11 opened, 8 closed, 0 maxsize 5970 nodes
List iterator usage : 11 opened, 11 closed, 0 maxsize
Regexp usage (bytes): 112 allocated, 0 freed, 0 in use
Regexp usage (number): 28 allocated, 0 freed 0 in use
File usage : 1 opened, 5 closed, 3 max, 6 total
ajNamExit done
Memory usage (bytes): 714748493 allocated, 16 reallocated 8390208 zeroed
Memory usage (number): 364254 allocates, 0 frees, 362023 resizes, 0 in use

Gary, I hope you have an idea how to fix this ;-)

Cheers,
David.



                                                                                                                    
                      "Barretto,Caroline,LAUSAN                                                                     
                      NE,NRC/BAS"                                                                                   
                      <Caroline.Barretto at rdls.n         An:      <emboss at hgmp.mrc.ac.uk>                            
                      estle.com>                        Kopie:                                                      
                      Gesendet von:                     Thema:   [EMBOSS] eprimer3                                  
                      owner-emboss at hgmp.mrc.ac.                                                                     
                      uk                                                                                            
                                                                                                                    
                                                                                                                    
                      09.08.2004 12:22                                                                              
                                                                                                                    
                                                                                                                    




Hello,


Is it possible to use eprimer3 on a complete bacterial genome or do we have
to give a smaller sequence? I have tried with a genome of 2,3Mbases but I
never get any result.


Many thanks,


Caroline.