[Bioperl-l] Muscle Alignment and Memory Allocation

[randalls at bioinfo.wsu.edu]

One suggestion is to use a computer with a lot more memory......

Randall Svancara
Systems Administrator/DBA/Developer
Main Bioinformatics Laboratory



----- Original Message -----
From: armendarez77 at hotmail.com
To: bioperl-l at lists.open-bio.org
Sent: Tuesday, July 13, 2010 11:00:27 AM
Subject: [Bioperl-l] Muscle Alignment and Memory Allocation

Hello,

I need to align 20-30 large full genome sequences (150,000+ bp each),
but I run out of memory. I've tried using -maxmb at the command line and
as an argument for Bio::Tools::Run::Alignment::Muscle, but I'm either
using it wrong or it's not working.

I've also tried aligning 2 sequences at a time and then aligning those
alignments using the -profile command, but it's still too much.

Do you have any advice on how to do such alignments? My attempts are
below.

Thank you,

Veronica


MUSCLE v3.6 by Robert C. Edgar

http://www.drive5.com/muscle This software is donated to the public
domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.

07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670
00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1
00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2
00:00:01 105 MB(-37%) Iter 1 6.25% Align node
*** OUT OF MEMORY ***
Memory allocated so far 3211.48 MB

Alignment not completed, cannot save.



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

MUSCLE v3.6 by Robert C. Edgar

http://www.drive5.com/muscle This software is donated to the public
domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.

07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670
00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1
00:00:00 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2
00:00:01 105 MB(-37%) Iter 1 6.25% Align node
*** OUT OF MEMORY ***
Memory allocated so far 3210.74 MB

Alignment not completed, cannot save.


Using Bio::Tools::Run::Alignment::Muscle and -maxmb

SCRIPT: my $inputFile = $ARGV[0];
my $factory = Bio::Tools::Run::Alignment::Muscle->new(-maxmb=>4000);

my $alnObj = $factory->align($inputFile);
my $output = "output.clw";
my $clwOut = Bio::AlignIO->new(-format=>'clustalw',
-file=>">$output.clw"); $clwOut->write_aln($alnObj);

OUTPUT:

MUSCLE v3.6 by Robert C. Edgar

http://www.drive5.com/muscle This software is donated to the public
domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.

07-13-2010_fullGenomes 17 seqs, max length 165101, avg length 152670
00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 1
00:00:01 26 MB(-9%) Iter 1 100.00% K-mer dist pass 2
00:00:01 105 MB(-37%) Iter 1 6.25% Align node
*** OUT OF MEMORY ***
Memory allocated so far 3210.9 MB

Alignment not completed, cannot save.

--------------------- WARNING ---------------------
MSG: Muscle call crashed: 512 [command /usr/bin/muscle -in
07-13-2010_fullGenomes.fasta -out /tmp/ubyNWLmbV8/GggmsmA0vA]

---------------------------------------------------






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