# Error in rule tree

**URL:** <https://nextstrain.discourse.group/t/error-in-rule-tree/370>\
**Category:** Help and Getting Started\
**Created:** [February 25, 2021, 6:45pm UTC](https://nextstrain.discourse.group/t/error-in-rule-tree/370 "2021-02-25T18:45:23Z")\
**Posts on this page:** 1\
**Showing post:** 19

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**Author:** ![rneher](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/rneher/32/20_2.png) [@rneher](https://nextstrain.discourse.group/u/rneher)\
**Post date:** [March 22, 2021, 5:39pm UTC](https://nextstrain.discourse.group/t/error-in-rule-tree/370/19 "2021-03-22T17:39:54Z")

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I wrote a quick summary on how to switch to nextalign:

> [@Avoiding large memory requirements by switching to \`nextalign\`](https://nextstrain.discourse.group/t/avoiding-large-memory-requirements-by-switching-to-nextalign/447):
>
> By default, Nextstrain’s pipeline to analyze SARS-CoV-2 uses mafft with the options --addfragments --keeplength to align all input sequences to the reference genome. For large data sets (\>500k) this requires a lot of memory. To keep running the pipeline on the entire data set, we now use [nextalign](https://github.com/nextstrain/nextclade/tree/master/packages/nextalign_cli) instead of mafft. The reduces the memory requirements to a few Gb and is faster than mafft. To use nextalign in your own workflow with the [ncov](https://github.com/nextstrain/ncov) workflow, you need to set two variables in your paramet…

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_[View the full topic](https://nextstrain.discourse.group/t/error-in-rule-tree/370)._