Question: How to align genomes on Mauve
0
gravatar for hilalay3448
22 months ago by
hilalay34480 wrote:

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.

alignment genome • 1.4k views
ADD COMMENTlink modified 21 months ago • written 22 months ago by hilalay34480

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

ADD REPLYlink modified 22 months ago • written 22 months ago by Sej Modha4.5k

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.

ADD REPLYlink written 22 months ago by genomax74k
0
gravatar for toralmanvar
22 months ago by
toralmanvar820
toralmanvar820 wrote:

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

ADD COMMENTlink written 22 months ago by toralmanvar820

I followed the instructions on the link above.

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

ADD REPLYlink written 22 months ago by hilalay34480

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

ADD REPLYlink written 22 months ago by toralmanvar820
0
gravatar for hilalay3448
21 months ago by
hilalay34480 wrote:

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
ADD COMMENTlink modified 21 months ago by genomax74k • written 21 months ago by hilalay34480
1

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.

ADD REPLYlink written 21 months ago by kloetzl1.1k
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