aidenlab/3d-dna

.Exception in thread "main" java.lang.OutOfMemoryError: Java heap space and GC overhead limit exceeded

zhangna123-ux opened this issue · 0 comments

When I deal with a huge merged_nodups.txt file about 511G with run-asm-pipeline.sh. There is an issue like '.Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded'. It happened at the visualize stage when generating the .hic file. What would be a suitable value should I set for the parameter -Xmx in juicer_tool.sh and how to request more memory when resolving this issue. Here is the memory status of my server (Linux):
4491704805441_ pic

Thanks in advance!