Re: [Mauve-users] stripsubsetLCBs error

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Hi Prabh,

I was never able to work around the error and visualize the core extraction.  I can import the fasta into geneious and look at the alignment that way but when I do that my annotations are lost.  Sorry I can’t be of assistance.

-S

From: Prabh Basra [mailto:bas...@gm...]
Sent: Tuesday, February 09, 2016 11:08 AM
To: Susan Beth Fogelson
Cc: mau...@li...
Subject: Re: [Mauve-users] stripsubsetLCBs error

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 <fo...@ug...<mailto:fo...@ug...>> 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:aar...@ut...]
Sent: Sunday, January 24, 2016 7:58 PM
To: mau...@li...<mailto:mau...@li...>
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

http://darlinglab.org<http://darlinglab.org/>

twitter: @koadman

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