bbtools:bbduk memory issue

I am trying to use bbtools:bbduk to remove host (mouse) contaminants from my metagenomics data but am running into an issue regarding memory needed for Galaxy to run this, and the job will not complete. Is there a way to adjust the memory? Or any other solutions? Thanks!

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Hi @bethp

I’m curious about what server you are working at, what the error looks like, what the data looks like, and which exact tool parameters + version you are using.

Meaning, is this an “out of quota space” problem, or a data/parameter problem, or a true “job running out of memory resources” type of problem. The first is solved by purging old data. The second can probably be solved here or the tool might need more computing resources to handle the job, which we can sometimes help with here, or at least provide some guidance.

Let’s start there. I’ll watch for your reply with the extra details. :slight_smile:

Hi @jennaj

The error is referring to needing to increase the -Xmx flag because the job ran out of memory, so I was thinking it was due to the computing resources needed. Thoughts? Thanks!

Hi @bethp

It looks like you are running this at UseGalaxy.org.

Would you please submit a bug report? ( :beetle: icon inside the red dataset)

In the comments section of the bug form, please paste in a link to this forum topic so I can link the two. If you already sent one, it is Ok to send in another this way.

Thanks!