Katherine Eaton

I noticed you have the error about 0 variants being called in your snps.log: ``` Converted 0 SNPs to TAB format. ``` And there also seems to be some error...

**Update**: I just got a similar error when using a bam file as input. For me, this was caused because the name of the bam (```SAMN02442721.bam```) did not match the...

Hi @Rathanin-github, I also got this issue with a recent re-install of snippy v4.6.0 within the last 2 weeks. For me, the variants disappear right at this point: ``` bcftools...

I think I might be having a similar error (if not I can open a new issue). When estimating date confidences using the marginal likelihood, some nodes will sporadically have...

I was thinking numerical accuracy too. This is a large phylogeny with many small branches (1e-8). Would there be any value in rescaling the branch lengths before (ex. multiply them...

Thanks for your reply! The variation I notice has been node dates (both joint and marginal). I'll play around with the parameters and see if I figure out anything more.

I've found a workaround for this issue that I wanted to share. Briefly, the steps are: 1. Screenshot the map to pdf, using the [pyppeteer](https://github.com/pyppeteer/pyppeteer) API. 2. Import the pdf...

Thanks for the idea, that makes sense so I'll try to reproduce this analysis.

Interestingly, I get the same results using the public tree and the web browser (https://genome.ucsc.edu/cgi-bin/hgPhyloPlace). Identical node placement ([link](https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_fe52_1c5180.json?c=pango_lineage_usher&label=nuc%20mutations:T17410C)):  But different lineage assignments:  The "true" assignment should be...

> That is really strange @ktmeaton! Was the auspice JSON for your first image generated using matUtils? After using usher to add the Canadian sequences to the public tree? Yup,...