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
------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Mauve-users mailing list
Mauve-users@lists.sourceforge.net<mailto:Mauve-users@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/mauve-users
--
Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
________________________________
UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any
accompanying attachments may contain confidential information. If you are not
the intended recipient, do not read, use, disseminate, distribute or copy this
message or attachments. If you have received this message in error, please
notify the sender immediately and delete this message. Any views expressed in
this message are those of the individual sender, except where the sender
expressly, and with authority, states them to be the views of the University of
Technology Sydney. Before opening any attachments, please check them for
viruses and defects. Think. Green. Do. Please consider the environment before
printing this email.
------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
_______________________________________________
Mauve-users mailing list
Mauve-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mauve-users
