Comments (1)
Hi @pre-mRNA,
No solution that would yield identical results. Reducing the number of cores seems like the best option.
Another alternative is to use the parameter --use_NAM_seeds
(based on strobemer seeds), which has a fixed peak memory roughly equivalent to using uLTRA with 18 cores (at least on human genome) - and this option is also faster. Then you should be able to specify --t 48
.
However, this parameter does not guarantee identical alignments. I observed that uLTRA's alignments with --use_NAM_seeds
were a tiny bit worse than default on the datasets I tried with. The --use_NAM_seeds
uses StrobeMap instead of slaMEM to find matches. StrobeMap
is automatically installed if you installed uLTRA through conda. For details about --use_NAM_seeds
, see section "New since v0.0.4" in the readme.
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