Hi,
I hope this is the correct place to post this.
I'm trying to run the assembly scoring script as found on:
http://code.google.com/p/ngopt/wiki/How_To_Score_Genome_Assemblies_with_Mauve<https://bio-exch.bio.tamu.edu/owa/14.1.339.1/scripts/premium/redir.aspx?C=8602e16ee8fb4451820afd2b5147c90d&URL=http%3a%2f%2fcode.google.com%2fp%2fngopt%2fwiki%2fHow_To_Score_Genome_Assemblies_with_Mauve>
on Mac osx 10.6.8
The example files eventually fail with the message:
...
...
Getting broken CDS...numCDS: 0
done!
Printing GC contents of gaps < 100nt!
shown
/Users/rsw3284/read_simulation_76bp/mauveAssemblyMetrics.R
./assembly2_scores/alignment2 ./assembly3_scores/alignment3
Error in read.table(mcname) : no lines available in input
Calls: plotMissingGC -> read.table
Execution halted
Furthermore, if I try to run the script with my own files: assembly 1-3 are
FASTA format and around 290kb, while the reference is also FASTA format at
around 300kb --> I get the reoccurring error:
java.lang.ArrayIndexOutOfBoundsException: -1
at org.gel.mauve.assembly.AssemblyScorer.computeContigSizeStats(Unknown
Source)
at org.gel.mauve.assembly.AssemblyScorer.loadInfo(Unknown Source)
at org.gel.mauve.assembly.AssemblyScorer.completeAlignment(Unknown
Source)
at org.gel.mauve.contigs.ContigOrderer.fireAlignmentEvent(Unknown
Source)
at org.gel.mauve.contigs.ContigOrderer.reorderDone(Unknown Source)
at org.gel.mauve.contigs.ContigReorderer.initModelData(Unknown
Source)
at org.gel.mauve.contigs.ContigReorderer.loadFile(Unknown Source)
at org.gel.mauve.gui.AlignFrame.completeAlignment(Unknown Source)
at org.gel.mauve.gui.AlignWorker.finished(Unknown Source)
at org.gel.mauve.gui.SwingWorker$1.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
at java.awt.EventQueue.access$000(EventQueue.java:85)
I'm not very well versed in java, but I attempted to run the java debugger,
with a catch for :
java.lang.ArrayIndexOutOfBoundsException
> catch java.lang.ArrayIndexOutOfBoundsException
Set all java.lang.ArrayIndexOutOfBoundsException
> resume
All threads resumed.
>
Exception occurred: java.lang.ArrayIndexOutOfBoundsException (to be caught
at: org.gel.mauve.ModelBuilder.buildModel(), line=-1
bci=66)"thread=AWT-EventQueue-0", org.gel.mauve.ModelBuilder.buildModel(),
line=-1 bci=57
Is it perhaps looking for XMFA format? My files are all regular FASTA
format.
I'm currently using Mauve-snapshot_2011-12-01.dmg.
Any idea as to how I might be able to fix this?
Also, is there a hard limit as to how many assemblies I could potentially
compare at once?
Rgds,
Roy W.
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