MUMmer plot error. How to resolve?
My third year comp sci friend got me this far, I hope you guys can help me with the last inch! For the record, I have practically no coding experience. I am using the 3.9.4 alpha version of MUMmer.
Here is the manual I have been following: http://mummer.sourceforge.net/examples/
I am at part 2.2.2 Running the Mummer plot, and I type in the final line to generate the plot.
dansterboy@DESKTOP-57RMBGG:/mnt/c/mummer/MUMmer-3.9.4alpha$ mummerplot -x "[0,8666124]" -y "[0,9025608]" -postscript -p mummer mummer.mums
Can't use 'defined(%hash)' (Maybe you should just omit the defined()?) at /usr/bin/mummerplot line 884.
So I go to investigate the error and I dont know how to proceed from here (this is the line I get once I ctrl x dash and enter 884).
if ( defined (%$rref) ) {
#-- skip reference sequence or set atts from hash
if ( !exists ($rref->{$idR}) ) { next; }
else { ($refoff, $reflen, $refdir) = @{$rref->{$idR}}; }
What should I do?
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Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image or the HTML embed code, not the link to the webpage that has the image embedded (which is what you have used here)
Sorry! I believe I fixed it.
No, you still need to use the image embedding control, not just paste the link. Please read the post I linked to.
The pictures appear for me now. No links.
The images are showing up now but they seem to be screenshots of plain text content, which is counterproductive. You could just paste the content here - especially the error message. It's really hard to read as it is now.
You can copy-paste the content directly here (using the code formatting option shown below), or use a GitHub Gist if the content volume exceeds allowed length here.
I posted the code. I hope this really helps.
Sorry about the back and forth, but it was necessary to get your post into shape so people read it enough to provide input.
Hi dan2010eve
I'm deleting our previous conversation so this post can stay on track and address the problem you're facing.
Hello dan2010eve!
It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/14990/mummer-plot-error-line-884-what-to-do
This is typically not recommended as it runs the risk of annoying people in both communities.