Memory usage exceeding 350 GB about quast HOT 3 CLOSED

Interestingly enough, both --scaffold-gap-max-size 100000 (100 kbp) and --scaffold-gap-max-size 1000000 (1 Mbp) completed, but 10 kbp exceeded available memory.

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Hmm, --scaffold-gap-max-size should not affect memory usage (at least significantly). Maybe the memory consumption was at the border line (around 350 Gb) and a little bit exceeded it with 10 kbp threshold while succeeded with higher thresholds.

Anyway, we committed few changes in genome analyzer module, so it should become much less memory consuming than before. Our test on several human assemblies showed max RAM consumption of 130 Gb.

I'll try reducing the number of threads.

Yes, this should always work :) Also note that we have --memory-efficient option which is even more RAM effective (and slow!) than --threads 1.

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I increased the memory limit to the max available (380 GB), and it succeeded. It looks like it was right on the cusp. Thanks for the improvements!

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