[Bioperl-l] Muscle Alignment and Memory Allocation

[armendarez77 at hotmail.com]

That would be nice, but not possible right now :)



> Date: Tue, 13 Jul 2010 11:43:35 -0700
> From: randalls at bioinfo.wsu.edu
> To: armendarez77 at hotmail.com
> CC: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Muscle Alignment and Memory Allocation
> 
> 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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