[Bioperl-l] Muscle Alignment and Memory Allocation
Kai Blin
kai.blin at biotech.uni-tuebingen.de
Tue Jul 13 18:42:58 UTC 2010
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
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