QUAST ERROR. Can someone offer guidence?

[jennaj]

Hello @Martyn

Thanks for sharing all of these details!

Check your job logs in the Job Details view (using the i-info icon). Is the job failing for memory reasons? Like this topic below?

@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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For your use case, since you are already filtering for the contig length with this Quast parameter setting:

@Martyn

Minimum contig length = 500 bp

You could try pre-filtering the lengths first to reduce the size of the input data, and maybe avoid this error?

• Search the tool panel for: Filter sequences by length
• You can run this on the entire collection. If some of the samples are now empty, you might need to then run Filter empty datasets before running Quast.

If you want to share your history, we might be able to suggest more pre-steps or different Quast parameters to try. Thanks!

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