Hi Susan
I was wondering if you were able to visualize the care alignment in the GUI. It
continues to give me the following error:
Exception in thread "Thread-4" java.lang.ArrayIndexOutOfBoundsException: genome
E.fergusonii_ATCC.fasta position 1
at org.gel.mauve.XMFAAlignment.getLCB(Unknown Source)
at org.gel.mauve.XMFAAlignment.getRange(Unknown Source)
at org.gel.mauve.SimilarityIndex.calculateIndex(Unknown Source)
at org.gel.mauve.SimilarityIndex.<init>(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(Thread.java:745)
Thanks
Prabh
> On Jan 25, 2016, at 4:45 PM, Susan Beth Fogelson <foge...@uga.edu> wrote:
>
> Hi Aaron,
>
>
> My first issue is that I ran the alignment on my PC using the windows
> version, which in turn used my local/external hard drive for the path’s. I
> didn’t realize that when I ran the alignment so to fix it I tried to write a
> substitution statement to replace the paths so that it would be pointing to
> the correct directory when I moved the file into my linux server to extract
> the core alignment. I finally just broke down and re-ran the alignment using
> the linux version so that the paths would be consistent throughout the whole
> process. The original alignments were run using each genome in its own file.
>
>
> Once I ran the alignments on the linux server I was easily able to extract
> the LCBs and build a core alignment. Once you extract the LCB’s and
> concatenate them into one file, are you able to visualize the resultant core
> file in the Mauve windows GUI? When I try to do this the program says it is
> reading the sequences but nothing ever appears on the screen.
>
>
> -Susan
>
> From: Aaron Darling [mailto:aaron.darl...@uts.edu.au]
> Sent: Sunday, January 24, 2016 7:58 PM
> To: mauve-users@lists.sourceforge.net
> Subject: Re: [Mauve-users] stripsubsetLCBs error
>
> Hi Susan, what operating system are you using, and what operating system was
> the alignment done with?
> Have you tried moving the sequence files, alignment file, and .bbcols to be
> located in the same directory?
> If done carefully, it should be possible to do a total search & replace on
> pathnames to strip them out of the XMFA (e.g. to replace the directory name
> with nothing), which might help if there are some troublesome characters in
> the path names. It might also help us help you if you were to copy & paste
> the paths involved into the next email.
>
> The suggestion to improve the error message about which file failed to open
> is a good one, I agree it's unfortunately generic and vague. Chances are high
> that it's failing on the first sequence file in your alignment.
>
> One last question, did you run the original alignment from a single
> multifasta, or with each genome sequence in its own file?
>
> Best,
> -Aaron
>
> On Fri, 2016-01-22 at 18:53 +0000, Susan Beth Fogelson wrote:
> Hello,
>
>
>
> I am attempting to extract the LCBs from my genome alignment and I am getting
> the common error message:
>
> Exception FileNotOpened thrown from
>
> Unknown() in gnFileSource.cpp 67
>
> Called by Unknown()
>
> Read 28814 backbone entries
>
> seq_count is: 0
>
>
>
> From previous post this means that one of the paths in my xmfa file is not
> correct so the files cannot be opened. I have been through the file 5 times
> now and cannot find an abnormality in the paths to my files. Is there a way
> to get more information about which file the program can’t open just to give
> me a more focused search for the error in my file? Thank you for your time
>
>
>
> -Susan
>
>
>
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> Aaron E. Darling, Ph.D.
> Associate Professor, ithree institute
> University of Technology Sydney
> Australia
>
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