Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded

[Damianyangyang]

java -jar omixer-rpm-1.1.jar -a 2 -d /home/bioinfo/sunyy/work/CRC/java_GMMs/omixer-rpm-1.1/GMMs/GMMs.v1.07.txt -i /home/bioinfo/sunyy/work/CRC/java_GMMs/temp/test.tsv -o /home/bioinfo/sunyy/work/CRC/java_GMMs/gmm_output/ Hi， Theses error occurs when I use the above command. What is the reason? Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded at java.util.LinkedList.addAll(LinkedList.java:424) at java.util.LinkedList.addAll(LinkedList.java:387) at java.util.LinkedList.(LinkedList.java:119) at org.omixer.rpm.model.Module.makeAllPaths(Module.java:286) at org.omixer.rpm.service.impl.ModuleManagerImpl.optimizeModule(ModuleManagerImpl.java:298) at org.omixer.rpm.service.impl.ModuleManagerImpl.inferModulesCore(ModuleManagerImpl.java:228) at org.omixer.rpm.service.impl.ModuleManagerImpl.inferModules(ModuleManagerImpl.java:106) at org.omixer.rpm.service.impl.ModuleManagerImpl.lambda$inferModules$3(ModuleManagerImpl.java:190) at org.omixer.rpm.service.impl.ModuleManagerImpl$$Lambda$1/1305193908.accept(Unknown Source) at java.util.HashMap$EntrySpliterator.forEachRemaining(HashMap.java:1699) at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:647) at org.omixer.rpm.service.impl.ModuleManagerImpl.inferModules(ModuleManagerImpl.java:183) at org.omixer.rpm.core.InferenceApp.main(InferenceApp.java:252)

[omixer]

Hello,

As written in the error log, Java ran out of memory!

Could you please try running the command as follows?

java -Xmx4G -jar omixer-rpm.jar....

You can increase the amount of given memory if the process still fails!

Please let me know if the above solution doesn't fix your issue!

Best regards, Youssef

[Damianyangyang]

Your solution successfully solved my error! Thanks!