bwa and bwa-mem2 relative indexing memory usage

[ImagoXV]

Hi there, there is something I find rather strange between bwa and bwa-mem2

bwa-mem2 is supposed to be faster and more memory efficient than bwa.

However, I cannot index SILVA 138.1 on my 32Gb 12cores with bwa-mem2 because of memory overusage. But I don't have any issue with bwa (expect, for sure, that it is really long).

I usually index on my cluster so memory is not that much of a problem. But for this particular application, I need it to be doable on a regular powerful laptop.

Maybe there is something I don't understand correctly, or maybe I'm not using bwa-mem2 index correctly

bwa-mem2 index -p SILVA_IDX SILVA_138.1_SSURef_tax_silva.fasta.gz

Kills my computer

bwa index -p SILVA_IDX SILVA_138.1_SSURef_tax_silva.fasta.gz

Runs smoothly.

Thanks for the discussion.

Arthur

[slw287r]

Peak memory ~72G building the index on our HPC:

bwa-mem2 index SILVA_138_SSURef_tax_silva.fasta.gz

[ImagoXV]

Yeah where bwa is max ~30Gb

Anyone know what are the discrepencies in indexing algorithm making so much difference ?