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AfZheng126 / MORA

MetagenOmic read Re-Assigner and abundance quantifier
MIT License
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Limit RAM usage #3

Open sternp opened 1 year ago

sternp commented 1 year ago

Hi again,

Is there a way to limit or reduce the amount of RAM MORA uses?

MORA gets killed when it exceeds the available RAM. This becomes an issue because some of my BAM files are quite large (30GB which can use 600GB+ of RAM).

Thanks

bluenote-1577 commented 1 year ago

Hi @sternp,

I talked to @AfZheng126 about this issue. Currently, it's not easy to limit the amount of RAM MORA uses, because during the read reassignment step, we need all of the ram.

It is very likely that we can lower the RAM usage of MORA through some engineering. We're focusing on getting the paper submitted and revised right now, so we will take a deeper look later on.

As a temporary suggestion, you can split up the BAM files, perform reassignment, and then collect the assigned reads. This won't give identical results, but as it should be reasonable as long as most of the species' coverages are not too low.

@AfZheng126 We can leave this issue up for now and hopefully get around to it later on.

Thanks,

Jim