How to align genomes on Mauve

Question

[hilalay3448]

Hello,

I am trying to align two draft genomes on Mauve and the program stops with error code 3.

How can I handle this problem.

[Sej Modha]

Have you followed the instructions available on http://darlinglab.org/mauve/user-guide/aligning.html

[GenoMax]

Are you using 32-bit or 64-bit Mauve? Past threads on mauve mailing list seem to indicate that this error code may refer to memory getting exhausted on a 32-bit system.

Answer 1

[Tm]

Similar issue is already discussed in sourceforge thread. Hopefull it will help resolving the error.

[hilalay3448]

I followed the instructions on the link above.

I use 64-bit Mauve and haven't fix the problem yet.

[Tm]

If you are using genbank file then try using fasta file too.

Answer 2

[hilalay3448]

Hello,

I still have problems with Mauve. The thread below is appearing when I try using Move Contings on Mauve. It seems alignment has done but I couldn't see any graphical image. It just says "Reading sequence 1 of 2" on Genome Alignment Visualization window. Does anyone have a solution for this problem? Thanks,

Hilal

The thread seen on console:

done.
Working set size: 400 Mb
Pagefile usage: 440 Mb
root alignment has 495 superintervals
root alignment length: 8716323
Organisms have 71.8% GC
Completed without error.
Alignment complete!
made reorder frame
shown
Oca 26, 2018 2:00:53 PM java.util.prefs.WindowsPreferences <init>
WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0x80000002. Windows RegCreateKeyEx(...) returned error code 5.
Exception in thread "Thread-7" org.biojava.bio.BioError: Unable to initialize DNATools
    at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:137)
    at org.biojava.bio.seq.io.SeqIOTools.getDNAParser(SeqIOTools.java:1045)
    at org.biojava.bio.seq.io.SeqIOTools.readFastaDNA(SeqIOTools.java:280)
    at org.gel.mauve.format.FastaFormat.readFile(Unknown Source)
    at org.gel.mauve.format.BaseFormat$2.<init>(Unknown Source)
    at org.gel.mauve.format.BaseFormat.makeIterator(Unknown Source)
    at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source)
    at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source)
    at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source)
    at org.gel.mauve.XmfaViewerModel.init(Unknown Source)
    at org.gel.mauve.XmfaViewerModel.<init>(Unknown Source)
    at org.gel.mauve.ModelBuilder.buildModel(Unknown Source)
    at org.gel.mauve.gui.FrameLoader.loadFile(Unknown Source)
    at org.gel.mauve.gui.FrameLoader.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
Caused by: org.biojava.bio.BioError: Unable to initialize RNATools
    at org.biojava.bio.seq.RNATools.<clinit>(RNATools.java:126)
    at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:130)
    ... 14 more
Caused by: org.biojava.bio.BioError: Couldn't parse TranslationTables.xml
    at org.biojava.bio.seq.RNATools.loadGeneticCodes(RNATools.java:529)
    at org.biojava.bio.seq.RNATools.<clinit>(RNATools.java:124)
    ... 15 more
Caused by: org.biojava.bio.symbol.IllegalSymbolException: Token `his' does not appear as a named symbol in alphabet `PROTEIN-TERM'
    at org.biojava.bio.seq.io.NameTokenization.parseToken(NameTokenization.java:110)
    at org.biojava.bio.seq.RNATools.loadGeneticCodes(RNATools.java:520)
    ... 16 more

[kloetzl]

For some reason bioJava wants to open or create Windows Registry Key (RegCreateKeyEx). However Access is denied (error code 5). Try running the command as Administrator. Or get yourself a Unix machine.