Question: IGV memory on Windows
0
gravatar for liorglic
9 months ago by
liorglic340
liorglic340 wrote:

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!

igv gff • 651 views
ADD COMMENTlink modified 13 days ago by Noah10 • written 9 months ago by liorglic340

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.

ADD REPLYlink modified 7 months ago • written 7 months ago by Jim Robinson290

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

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by liushaorui0

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

ADD REPLYlink written 6 weeks ago by _r_am32k
1
gravatar for Noah
13 days ago by
Noah10
Noah10 wrote:

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.

ADD COMMENTlink written 13 days ago by Noah10
0
gravatar for Pierre Lindenbaum
9 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k wrote:

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.

ADD COMMENTlink modified 6 weeks ago by _r_am32k • written 9 months ago by Pierre Lindenbaum133k

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.

ADD REPLYlink written 9 months ago by liorglic340

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.

ADD REPLYlink written 8 months ago by phenomata10

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

ADD REPLYlink written 8 months ago by liorglic340

Thanks for the reply lior. Hope for the best!

ADD REPLYlink written 8 months ago by phenomata10

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.

ADD REPLYlink written 13 days ago by Noah10
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