IGV memory on Windows

Question

[liorglic]

Hi there,
I am trying to load a bunch of pretty-heavy gff3 files to IGV. The machine is a Windows10 one, with 16GB RAM.
All gff files are zipped and indexed, but still loading the files kills IGV - it is just loading forever, unable to display anything.
I've tried reducing the visibility range to 20kb, but this simply resulted in IGV getting stuck when I zoom in.
I suspect that the issue is memory allocation. Is there a way to tell IGV to take up more memory? It looks like by default it only takes 1.2GB. Or any other idea on how to get this to work?
Thanks!

[Jim Robinson]

How did you install IGV, what version are you using, and how are you starting it? Just double clicking the jar file will result in what you describe. Also what version are you using? Our windows installers sets the max at 4 GB by default.

[liushaorui]

hi, just add one more for java script with : -Xms4g

[Ram]

"java script" is an ambiguous phrase as JavaScript is a language of its own. Please just use "Java".

Answer 1

[Noah]

I ran into this issue too, so although this question was already answered, I would like to put the solution here, as this is the first page that came up in Google.

According to the readme included with IGV, you can edit the file at:

Mac and Linux: $HOME/.igv/java_arguments

Windows: %USERPROFILE%/.igv/java_arguments

You just need to remove the pound sign (#) from the beginning of the line with the -Xmx argument, like so:

-Xmx8g

If you would like, you can even increase the 8g to something larger, like 12g if your computer has enough RAM. I would recommend leaving a few GB of RAM for your operating system, as you don't want to use memory it needs and cause a crash.

Answer 2

[Pierre Lindenbaum]

Is there a way to tell IGV to take up more memory? It looks like by default it only takes 1.2GB

change the -Xmx<12345>m in the igv.bat file.

[liorglic]

Thanks. Changed from 4gb to 10gb, but it doesn't seem to change anything. Interestingly, I found out that things work very well using IGV web, so I'm going to use that until a better solution is found.

[phenomata]

Sorry to add this up but did you happen to find a solution to this behavior (other than using IGV web)? Changing the java -Xmx option in the igv.bat file doesn't do anything to the maximum memory usage limit.

[liorglic]

Nope /: Switched to IGV web (which has its own issues)

[phenomata]

Thanks for the reply lior. Hope for the best!

[Noah]

If you're using the GUI version of IGV, I think you would need to edit the igv-launcher.bat file instead. However, IGV recommends you instead put the arguments in your user profile here:

%HOMEPATH%\.igv\java_arguments

You can see my answer for more detail.