Aaron,
I was in a hurry and ran Mauve with some DNASTAR format .seq files without
converting them to .fas or .gbk first. The alignment seems to have run fine, so
the files were correctly recognized, but the display did not load. Here is part
of the console log:
OS name is: Windows 7 arch: amd64
Executing:
win64\progressiveMauve
--output=C:\Users\plunkettg\Documents\Assemblies\RS218\testing
--output-guide-tree=C:\Users\plunkettg\Documents\Assemblies\RS218\testing.guide_tree
--backbone-output=C:\Users\plunkettg\Documents\Assemblies\RS218\testing.backbone
C:\Users\plunkettg\Documents\Assemblies\RS218\missing-in-454.seq
C:\Users\plunkettg\Documents\Assemblies\RS218\RS218_v20-chromosome.seq
Storing raw sequence at C:\Users\PLUNKE~1\AppData\Local\Temp\raw6EBA.tmp
Sequence loaded successfully.
C:\Users\plunkettg\Documents\Assemblies\RS218\missing-in-454.seq 10138 base
pairs.
Storing raw sequence at C:\Users\PLUNKE~1\AppData\Local\Temp\raw6EE9.tmp
Sequence loaded successfully.
C:\Users\plunkettg\Documents\Assemblies\RS218\RS218_v20-chromosome.seq 5089232
base pairs.
... [omitted for brevity] ...
done.
root alignment has 1 superintervals
root alignment length: 5089232
Organisms have 50.6% GC
Completed without error.
Exception in thread "Thread-8" java.lang.RuntimeException: Unexpected format:
DNAstar
at
org.gel.mauve.format.SupportedFormatFactory.formatNameToFormat(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)
If I try loading the alignment file, I get the last part of the above (from
Exception in thread). The actual alignment file notes that the files are in the
DNAstar format:
#FormatVersion Mauve1
#Sequence1File C:\Users\plunkettg\Documents\Assemblies\RS218\missing-in-454.seq
#Sequence1Format DNAstar
#Annotation1File
C:\Users\plunkettg\Documents\Assemblies\RS218\missing-in-454.seq
#Annotation1Format DNAstar
#Sequence2File
C:\Users\plunkettg\Documents\Assemblies\RS218\RS218_v20-chromosome.seq
#Sequence2Format DNAstar
#Annotation2File
C:\Users\plunkettg\Documents\Assemblies\RS218\RS218_v20-chromosome.seq
#Annotation2Format DNAstar
#BackboneFile C:\Users\plunkettg\Documents\Assemblies\RS218\testing.bbcols
> 1:1-10138 + C:\Users\plunkettg\Documents\Assemblies\RS218\missing-in-454.seq
====
So my question is, if the alignment engine can recognize and deal with DNASTAR
format sequences, how hard would it be to have the display engine read them as
well?
Partial disclaimer: I do work for DNASTAR now, but this question is not for
them.
Cheers,
Guy
Dr. Guy Plunkett III
Senior Scientist, Laboratory of Genetics & Genome Center, UW-Madison
Senior Scientist, DNASTAR
Laboratory of Genetics, University of Wisconsin DNASTAR, Inc.
425G Henry Mall Rm 5428 3801 Regent Street
Madison, WI 53706-1580 Madison, WI 53705
(608) 890-0189 phone (608) 237-3081 phone
(608) 262-2976 fax (608) 258-7439 fax
g...@genome.wisc.edu plunke...@dnastar.com
web: http://www.genome.wisc.edu/information/gplunkett.html
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