Hi Amarin, Ray,
In addition to changing the the -Xmx parameter for the java heap size,
in this case you'll also need to change a parameter in the class
org.gel.mauve.SimilarityIndex (2.3.1 release) or the class
org.gel.mauve.histogram.ZoomHistogram (current svn trunk). The specific
variable is max_
Ray,
I am using the Linux version. I've already adjusted that parameter to
account for the RAM capacity of the workstation. I'm wondering if there is
a similar parameter for max similarity index that can be adjusted. If so
adjusted to what?
-Amarin
On Thu, Oct 9, 2014 at 12:45 AM, Raymond W
Hi Amarin,
I'm not sure if this will solve your problem, but are you running the Linux
version? If you are and running the script called "Mauve", it is actually a
bash script that in turn calls Java. You can view it and adjust the memory
requirements.
For example, in the script, I see:
JAVA_A
Is there value I can adjust to allow more memory for this function? I
aligned 3 1.2GB genomes but am unable to open the alignment file in the
mauve GUI. If this is not possible could anyone recommend a different
application to use for visualization? Thanks.
Exception in thread "Thread-1" java.l
