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

na zhang

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Jan 10, 2024, 9:11:18 AM1/10/24

to 3D Genomics

Hi All,

Thank you for developing the 3d-dna genome assembly software, which is very useful. However, 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 -Xms in juicer_tool.sh and how to request more memory when resolving this issue. I also hope that changing the value of -Xms parameter will not affect the normal functioning of my server. Here is the memory status of my server (Linux):

Thanks in advance!

Olga Dudchenko

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Jan 12, 2024, 2:37:13 PM1/12/24

to 3D Genomics

The parameter you want to increase is in the 3d-dna/visualize/juicer_tools.sh in 3d-dna. Best, -Olga

nn

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Jan 14, 2024, 5:55:29 PM1/14/24

to 3d-genomics

Hi, 3d-genomics

Thank you very much for your prompt reply. I increased the default memory by 5 times, i.e. set it to: java -Xms245760m -Xmx245760m. The issue regarding OutOfMemoryError has been resolved, but a new error has emerged (Screenshot of the error messages in log file show in Figure 1):

:| Warning: depletion region size 41666 and bin size 8333 parameters are incompatible (41666 % 8333 != 0). Changing depletion region size to 41665.

...Dumping 8333 resolution matrix

HiC file version: 8

Unable to dump

java.io.IOException: Normalization missing for: assembly_assembly_BP_8333

at juicebox.data.DatasetReaderV2.readNormalizedBlock(DatasetReaderV2.java:719)

at juicebox.data.MatrixZoomData.dump(MatrixZoomData.java:675)

at juicebox.tools.clt.old.Dump.dumpMatrix(Dump.java:282)

at juicebox.tools.clt.old.Dump.run(Dump.java:505)

at juicebox.tools.HiCTools.main(HiCTools.java:86)

Figure 1:

I loaded the obtained 0.hic file onto Juicebox and appear many gaps show in Figure 2. Figure 3 shows the result after loading the 0.assembly file.

Figure 2: