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.
- How to capture that information → Troubleshooting resources for errors or unexpected results and How to get faster help with your question
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. 
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? ( 
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!
Hi @bethp
Update
Thanks for sending in the bug report. Yes, the tool was failing due to memory resources e.g. “too large” to process.
While the updated version of the tool is now available, it also fails with such a large query (3+ GB for each end of the pair) and target (mm39) combination. Indexing k-mers from the entire mouse genome is where the tool seems to have the immediate trouble.
I have ticketed the request for an increase in the memory allocation at UseGalaxy.org. Enhancement: allocate more memory for bbtools_bbduk 39.06+galaxy2 at ORG · Issue #750 · galaxyproject/usegalaxy-tools · GitHub
That will not be immediate. Meanwhile, I would suggest that you try at UseGalaxy.eu or UseGalaxy.org.au. You can easily move data between servers without a download step. See FAQ: Transfer entire histories from one Galaxy server to another
Thank you for the follow-up!