diff --git a/pangolin/4.3.1-pdata-1.23/README.md b/pangolin/4.3.1-pdata-1.23/README.md index 647c7b131..2b1f5dd60 100644 --- a/pangolin/4.3.1-pdata-1.23/README.md +++ b/pangolin/4.3.1-pdata-1.23/README.md @@ -11,7 +11,7 @@ Additional tools: - [pangolin-data](https://github.com/cov-lineages/pangolin-data) 1.23 - [pangolin-assignment](https://github.com/cov-lineages/pangolin-assignment) 1.23 - [minimap2](https://github.com/lh3/minimap2) 2.26-r1175 -- [usher](https://github.com/yatisht/usher) 0.6.3 +- [usher](https://github.com/yatisht/usher) 0.6.2 - [faToVcf](https://github.com/yatisht/usher) 448 - [scorpio](https://github.com/cov-lineages/scorpio) 0.3.19 - [constellations](https://github.com/cov-lineages/constellations) 0.1.12 @@ -19,6 +19,14 @@ Additional tools: - [mafft](https://mafft.cbrc.jp/alignment/software/) 7.520 - python 3.8.18 +## Rare bug warning :warning: + +This docker image contains `usher` version 0.6.2. This version of usher has a bug that can cause some lineage A samples to be assigned to A.* sublineages or even B or B.* sublineages. + +If you are running `pangolin` on early 2020 sequences that may be lineage A, it is highly recommended to use the assignment cache (and upgrade to usher 0.6.3 when it is available) [See the pangolin-assignment v1.23 release page for more details](https://github.com/cov-lineages/pangolin-assignment/releases/tag/v1.23 + +We plan to upgrade `usher` to >=0.6.3 in the next release of this docker image. + ## pangoLEARN deprecation As of pangolin version 4.3, pangoLEARN mode has been deprecated. [More info can be found here on the v4.3 release page.](https://github.com/cov-lineages/pangolin/releases/tag/v4.3)