To answer one of my own questions:
NCBI is packaging their genome downloads as .gbff files. Mauve doesn't
like the extension so you have to change them to .gb or .gbk as stated
*four years ago* by Aaron at:
https://www.mail-archive.com/mauve-users@lists.sourceforge.net/msg00147.html
Apologies for not doing a good search ahead of my request.
Probably the JRE problem was answered four years ago also... I'll go
check now.
Peter
On 07/22/2014 2:01 PM, Peter Hoyt wrote:
Hi everyone. Sorry if this has been asked before, but I can't seem to
install the snapshot using the mauve_installer_20120303.exe: error
given is "Could not detect a suitable 64-it Java Runtime environment.
Mauve requires Java version 1.4 or later..."
I'm running JRE 6 for 64-bit and also have JRE 7 installed for 32-bit.
Is there a solution?
Also, our supercomputer setup is not liking my command-line scripts.
Would somebody correct my script below for doing a multiple alignment?
(the full path is used in this example)
java -Xmx12000m /opt/mauve/20120607/prebuilt/Mauve.jar
/opt/mauve/20120607/prebuilt/progressiveMauve --output=3bugs.xmfa
--output-guide-tree=3bugs.tree --backbone-output=3bugs.backbone
bug1.gbff bug2.gbff bug3.gbff
I'm trying to throw more RAM at the alignment but am getting errors
like "Exception in thread "main" java.lang.NoClassDefFoundError:
/opt/mauve/20120607/prebuilt/Mauve/jar
Caused by: java.lang.ClassNotFoundException:
.opt.mauve.20120607.prebuilt.Mauve.jar"
(yes I see the "Mauve/jar" in place of the "Mauve.jar" but assume it's
just an error message)
Thanks!
--
-
Peter R. Hoyt, Ph. D.
Graduate Program Director, Bioinformatics Certification
Oklahoma State University
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--
-
Peter R. Hoyt, Ph. D.
Graduate Program Director, Bioinformatics Certification
Oklahoma State University
Department of Biochemistry and Molecular Biology
110FB Henry Bellmon Research Center
(Shipping address: 246 Noble Research Center)
Stillwater, OK 74078
(405) 744-6206
------------------------------------------------------------------------------
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Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
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