[Bioperl-l] Muscle Alignment and Memory Allocation

[Kai Blin]

On Tue, 2010-07-13 at 11:00 -0700, armendarez77 at hotmail.com wrote:

Hi Veronica,

> I need to align 20-30 large full genome sequences  (150,000+ bp each), but I run out of memory. 

The fact that this also fails on the command line tells me that you're
not running into a BioPerl problem. See my comments inline below:

[...]

> 00:00:01  105 MB(-37%)  Iter   1    6.25%  Align node
> *** OUT OF MEMORY ***
> Memory allocated so far 3211.48 MB
                         ^^^^^^^^^^
[...]

> Using -maxmb at the command line:
> 
> $ muscle -in 07-13-2010_fullGenomes.fasta -clwout 07-13-2010_fullGenomes.clw -maxiters 1 -diags1 -sv -maxmb 4000
                                                                                                      ^^^^^^^^^^^^
You're running out of memory at 3211.48 MB, but you're telling muscle
it's fine to use 4000 MB. Maybe you might want to provide less memory to
-maxmb .....

Cheers,
Kai

-- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Interfakultäres Institut für Mikrobiologie und Infektionsmedizin
Abteilung Mikrobiologie/Biotechnologie
Eberhard-Karls-Universität Tübingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 Tübingen                        Fax :   ++49 7071 29-5979
Deutschland
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben