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[BUG]An error related with State number

See original GitHub issue

Current Behavior
When we tried to build the tree with TreeTime, we encountered with an error saying that “180 or more distinct discrete states found. TreeTime is currently not set up to handle that many states”. All the process before this one was finished.

Expected behavior
The evolution tree should be generated after the tree.nwk file was obtained.

How to reproduce
WechatIMG2475

Your environment: if browsing Nextstrain online

Operating system:
Browser:

Your environment: if running Nextstrain locally

Operating system: centos 7
Browser: Chrome
Version (e.g. auspice 2.7.0): nextstrain 1.14.0a

Additional context
We are not sure if some strains in the dataset led to this error. Since we are not only using the strains from GISAID but there are 10 more strains from other source in our dataset. But they have been in our dataset for a while but this error never shown up before.

Issue Analytics

State:
Created 3 years ago
Comments:9 (5 by maintainers)

Top GitHub Comments

1reaction

brianpardycommented, Apr 5, 2020

Hi @JosephLee815, I believe you need to upgrade the release of augur that you are running and likely also the version of treetime, please see https://github.com/nextstrain/augur/pull/495 for more details.

0reactions

jameshadfieldcommented, Apr 9, 2020

Hi @JosephLee815 – this may be a problem on our side (too many missing values in weights.tsv). In the meantime, you should be able to add in those missing demes to the TSV file yourself & give them a weight of 1.0 to proceed.

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