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
twitter: @koadman
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