Trinity "OutOfMemoryError: GC overhead limit exceeded"

Question: Trinity "OutOfMemoryError: GC overhead limit exceeded"

13 months ago by

Hello,

I am trying to use Galaxy Trinity to assemble a set of stranded paired-end reads (two 1.4GB FASTQ files). I keep getting this error:

succeeded(38798) 62.3471% completed.
succeeded(38799) 62.3487% completed.
succeeded(38800) 62.3503% completed.
succeeded(38801) 62.352% completed. succeeded(38802) 62.3536% completed.

We are sorry, commands in file: [failed_butterfly_commands.15715.txt] failed. :-(

Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded at java.util.HashMap.newNode(HashMap.java:1734) at java.util.HashMap.putVal(HashMap.java:630) at java.util.HashMap.put(HashMap.java:611) at java.util.HashSet.add(HashSet.java:219) at PairPath._cache_path_nodes(PairPath.java:70) at PairPath.<init>(PairPath.java:31) at TransAssembly_allProbPaths.update_PairPaths_using_overlapDAG_refined_paths(TransAssembly_allProbPaths.java:1837) at TransAssembly_allProbPaths.create_DAG_from_OverlapLayout(TransAssembly_allProbPaths.java:1590) at TransAssembly_allProbPaths.main(TransAssembly_allProbPaths.java:918) Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Trinity run failed. Must investigate error above.

I understand that this is because the job ran out of RAM? Is there any way to circumvent this?

Thank you very much!

trinity • 725 views

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modified 13 months ago by Jennifer Hillman Jackson ♦ 25k • written 13 months ago by nancydong20 • 0

13 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This looks like an input sequence quality problem (that said, the resources/setting/tool version available at PCS Bridges that executes Trinity from https://usegalaxy.org may simply not be enough to handle your particular data as discussed here).

Did you run FastQC on the data yet? That can give some clues about what QA/QC could to be done before running through an assembly tool. Sometimes that can help, if input quality is a factor (hard to tell, the errors given by tool at failure are not always specific to the actual root cause of problems).

Note that QC will not solve all problems. An inherently low-quality sequence dataset cannot be fixed after the fact. Some tools are more sensitive to quality than others (and certainly assembly tools). The tools can get "stuck" at certain steps and then fail (exceeding memory or with other errors). The lab that created the data could be contacted. But if public data, that won't be possible and you might want to use different, higher quality data. You also might want to consider setting up your own Galaxy server with more resources/modified tool run parameters to see if these will actually solve your problems as they did for some of those involved in the linked ticket above).

Resources:

Help for interpreting FastQC results is in the tool's help or you can review the documentation here: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Tutorials here cover performing QA/QC within Galaxy: https://galaxyproject.org/learn/
Job error troubleshooting FAQs: https://galaxyproject.org/support/#troubleshooting
Ways to use Galaxy: https://galaxyproject.org/choices/

Thanks! Jen, Galaxy team

ADD COMMENT • link modified 13 months ago • written 13 months ago by Jennifer Hillman Jackson ♦ 25k

I see, thank you very much!

ADD REPLY • link written 13 months ago by nancydong20 • 0

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