Entering edit mode
7.7 years ago
Lars
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1.1k
Hi all, I am working with Human amplicon data and have been using bwa mem (0.7.15) up to now. Unfortunately, on some datasets the memory consumption exceeds the 8GB RAM I have at spare.
Can someone tell me why this is the case?
I have already tried to modify the parameter (-c or -t) but none of them made it able to run it. Could it be caused by parts of the data aligning to repeat regions/low complexity regions?
If I cannot find a solution to it, I will switch to an alternative aligner that does not need that really high amount of RAM.
8 GB is not really high amount of RAM. Don't most bottom of the line laptops ship with 8 GB these days? Hell, my phone has 6 GB RAM..
Thank you for this information about your phone with 6GB RAM. I cannot see any use in this comment.
I have a HPC with 2 TB RAM and 32 cores. But this amplicon project has to run on a laptop with exact 8GB RAM. It looks like bwa-mem is the wrong tool then. Thank you anyway.
Phone having 6 GB RAM goes to show how exhausting 8 GB of RAM is not "incredible high memory consumption" as in the original title of your post..
I already changed it. Wanted to attract people. ;)
You should specify what you are aligning against. If it is not human genome then you could take a look at BBMap.
I align against the human genome.
Then you have to consider aligning against a subset of the human genome. Perhaps just the regions you are amplifying.
That is not an option. It has to be the complete human genome and on exactly this laptop. My question: Is it possible with bwa-mem, by using some specific parameters?
Did you see Heng Li's (author of bwa) answer that I had linked below?
Yes, I know this comment of Heng Li and I tried it, but it didn't work.
If you are using human genome to align against then ~6 G is minimally required by bwa for one thread. Other aligners actually will need more than 8 G.
Invest in your future and get a better machine.