SPADes and MEGAHIT memory issues

[Martyn]

Hi, I am in the next step of my analysis and the jobs are just not completing for either of these. The error is an out of memory error. I have 5 samples.

Does anyone know what to do about this?

Best wishes

[jennaj]

Hi @Martyn

Below is the general path for troubleshooting memory issues during assembly.

@jennaj

Error message

This job was terminated because it used more memory than it was allocated.

If an assembly is running out of processing memory during execution, there are a few things you can do.

Use Case
The current work is running out of processing memory during job execution. This is different from the data storage available in your account.

What to try

• Run the reads through quality control to improve the content the tool is attempting to assemble.
• Set more input parameters to improve how the tool is attempting to assemble.
• Reduce the number of reads submitted with a tool like Sub-sample sequences. Some protocols involve pre-clustering with other strategies, too.
• Try at a different public server. Each hosts distinct resources.

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We also have some tutorials for metagenomic assembly. Find these linked from the bottom of the tool forms. Or, are you following one of these already but with your own data?

You are welcome to share your history for feedback. How to generate the link is in the banner of this forum, also here. → How to get faster help with your question

Hope this helps and we can follow up more!