I was wanting to try host removal with BBmap, as it’s a global aligner and I can set by percentage how close the read needs to map. But BBmap hits memory error using the standard Hg38 reference, same with Canine reference. Same issue on Usegalaxy.or as Usegalaxy.eu, is there something that can be done so BBmap can be utilized?? I know I can use it for small bacterial references, just not working for host removal.
Hi @Jon_Colman
If you want help reviewing what the exact problem might be, you are welcome to share back the history with the job failures. See the banner topic for how to generate the URL share link, and you can paste it back here in a reply.
Other than that, you could consider breaking up your query reads into smaller file chunks to see if that helps to get the data processed. This usually involves the tool Split File to Dataset Collection, followed by running the target tools, then collapsing or merging the results. We would need to see your current example to provide exact help.
Let’s start there, thanks! 
I ran it again so that I can show the issue. This should just be a standard mapping for human host removal.
Hi @Jon_Colman
Thanks for sharing the history.
The problem is likely this parameter
Specify behavior on ambiguously-mapped reads with multiple top-scoring mapping locations
What happens if you use the default for this instead? Anything with a weaker/suspect match you could run though in a separate mapping if you really need or want everything.
I will try that, thanks