Question: MUMmer plot error. How to resolve?
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gravatar for dan2010eve
7 weeks ago by
dan2010eve0
dan2010eve0 wrote:

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?

alignment software error • 283 views
ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by dan2010eve0

Hi dan2010eve

I'm deleting our previous conversation so this post can stay on track and address the problem you're facing.

ADD REPLYlink written 7 weeks ago by _r_am32k

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.

ADD REPLYlink written 7 weeks ago by _r_am32k
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