Hi everyone,
I successfully ran Minimap2 on Galaxy using my viral reference genome and FASTQ.gz reads without any issues. However, when I try to run it with hg38 or T2T as the reference genome using the same FASTQ.gz input, I get an error saying that I don’t have enough memory.
I find this strange because I’ve only used 5% of the 250GB available, so there should be plenty of memory left. Has anyone else encountered this issue? Is there a way to optimise Minimap2 settings?
Thanks for any help!
Welcome @jagoda_33
This is how to interpret this error. It is unrelated to how much storage space is in your account.
For your case, there could be a few reasons:
Not enough QA done on the reads, and the tool was able to handle the data anyway with smaller genomes, but larger genomes lead to problems.
The current parameters are not working well for the human genomes, or the human T2T assembly in particular. More about why that could be is in here. → Reference genomes at public Galaxy servers: GRCh38/hg38 example
Are you trying to screen out the host genome? You could try using a tool like BLASTN instead to see what happens.
Then, if you are still getting an error, is there a GTN tutorial that walks through those steps you could use as an example? If you share the types of reads and what you are trying to do, we can help to point you to the right place.
Tutorials are linked from tool form, too, if you want to search that way. Scroll all the way down into the Help section to find these.
We also have QA tutorials. Some are included in with the primary tutorials since sometimes the analysis domain has specific considerations, but this one has a good overview to start with.
Let’s start there and we can follow up! A shared history is best when reviewing an error. How to share is in the banner topic of this forum, also here.
Thanks! 