Haploview problem over heap space

Question

[Ripeapple]

Hi, All,

I am having problem with haploview that Java keeps output errors like "Exception in thread "main" java.lang.OutOfMemoryError: Java heap space" And "Fatal Error: Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded";

My command line is java -XX:+UseConcMarkSweepGC -Xmx40g -jar Haploview.jar -n -pedfile linkage.txt -info SNP_info.txt -dprime -blockoutput ALL (I tried allocate more memory still not working)

Can anyone help,

Very much appreciated!

[karl.stamm]

Well that means it ran out of memory. In particular, GC Overhead Limit implies it's doing a lot of work. Haploview was designed for SNP panels, are you trying to use NGS? Cut down the size of the input data and see if that helps. It might be requiring quadratic or exponential memory so removing a few snps or subjects will help a lot. I hope it's 64-bit Java.

[chrchang523]

What exactly do you need to compute? PLINK 1.9's --blocks and --r2 dprime commands are very memory-efficient, and cover a lot (though not all) of the uses of that Haploview command.