Nextclade v3

[ivan-aksamentov]

This branch aggregates changes for the next major version of Nextclade

Preview: https://nextclade-git-v3-nextstrain.vercel.app/

Examples:

Existing datasets:

• sc2
• flu_h3n2_ha
• rsv_a
• rsv_b
• hMPXV_B1

New experimental datasets:

• sc2 "big"
• hbv
• hiv

(feel free to edit this message to add more)

Major features

• Better genome annotation handling #1073
• Tree builder #1187
• Alignment: improvements to seed matching #1190, #1221, #1220

Other features

• Make all inputs except ref sequence and query sequence optional
• Adjust software to the new dataset format
• Remove Nextalign and its data from repo; merge and simplify the code of Nextalign and Nextclade
• Optional automatic selection of a dataset according to seed index (handled separately)
• Group query sequences by ref sequence according to seed index (handled separately)
• Handle ambiguous nucs when decoding (#1204)
• Output trees in Newick format (#1205)
• Check consistency between ref seq and root node of the ref tree (#1211)

Notable bug fixes

• align gaps left when there was gap-placing ambiguity (#1206)
• codon position dependent gap-open-scores (fixed in 7dcc2ca)
• private amino acid mutations. (fixed in 05a7007 and 42ec126)

[vercel]

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Name	Status	Preview	Updated (UTC)
nextclade	✅ Ready (Inspect)	Visit Preview	Aug 30, 2023 2:36pm

[rneher]

this has happened to some times (this was on the tree builder branch, but I think it is independent of that): I doesn't find the default gene/cds to display. Might be some sort of race condition... it works on second try.

Error message: Error: Internal Error: Unable to find CDS 'S'. This is an internal issue, likely due to a programming mistake. Please report it to developers!

Nextclade version 2.14.1 (commit: 7d95263, branch: feat/greedy-tree-builder-2)

Memory available: unknown

User agent: Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:109.0) Gecko/20100101 Firefox/114.0

Browser details: {"browser":{"name":"Firefox","version":"114.0"},"os":{"name":"Linux"},"platform":{"type":"desktop"},"engine":{"name":"Gecko","version":"20100101"}}

Call stack:

c@https://nextclade-git-feat-greedy-tree-builder-2-nextstrain.vercel.app/_next/static/chunks/pages/_app-ff0b69f5615f5246.js:4:666403
86374/e<@https://nextclade-git-feat-greedy-tree-builder-2-nextstrain.vercel.app/_next/static/chunks/pages/_app-ff0b69f5615f5246.js:4:667201
d@https://nextclade-git-feat-greedy-tree-builder-2-nextstrain.vercel.app/_next/static/chunks/pages/_app-ff0b69f5615f5246.js:4:667643
70046/cv</a<@https://nextclade-git-feat-greedy-tree-builder-2-nextstrain.vercel.app/_next/static/chunks/pages/results-de705194f6b46b45.js:1:7267
useMemo@https://nextclade-git-feat-greedy-tree-builder-2-nextstrain.vercel.app/_next/static/chunks/framework-5774a691a4029c28.js:1:67799
81803/a.useMemo@https://nextclade-git-feat-greedy-tree-builder-2-nextstrain.vercel.app/_next/static/chunks/framework-5774a691a4029c28.js:1:135950
70046/cv<@https://nextclade-git-feat-greedy-tree-builder-2-nextstrain.vercel.app/_next/static/chunks/pages/results-de705194f6b46b45.js:1:7177
fW@https://nextclade-git-feat-greedy-tree-builder-2-nextstrain.vercel.app/_next/static/chunks/framework-5774a691a4029c28.js:1:61454
_@https://nextclade-git-feat-greedy-tree-builder-2-nextstrain.vercel.app/_next/static/chunks/framework-5774a691a4029c28.js:1:119698
h5@https://nextclade-git-feat-greedy-tree-builder-2-nextstrain.vercel.app/_next/static/chunks/framework-5774a691a4029c28.js:1:107755
h3@https://nextclade-git-feat-greedy-tree-builder-2-nextstrain.vercel.app/_next/static/chunks/framework-5774a691a4029c28.js:1:107684
h2@https://nextclade-git-feat-greedy-tree-builder-2-nextstrain.vercel.app/_next/static/chunks/framework-5774a691a4029c28.js:1:107535
hU@https://nextclade-git-feat-greedy-tree-builder-2-nextstrain.vercel.app/_next/static/chunks/framework-5774a691a4029c28.js:1:103898
hT@https://nextclade-git-feat-greedy-tree-builder-2-nextstrain.vercel.app/_next/static/chunks/framework-5774a691a4029c28.js:1:102863
A@https://nextclade-git-feat-greedy-tree-builder-2-nextstrain.vercel.app/_next/static/chunks/framework-5774a691a4029c28.js:1:137771
g@https://nextclade-git-feat-greedy-tree-builder-2-nextstrain.vercel.app/_next/static/chunks/framework-5774a691a4029c28.js:1:138302

[rneher]

getting this whenever I change datasets that have different default genes. Confirmed that it also happens on the main v3 branch.

[ivan-aksamentov]

I'll merge and continue work on master