caitiecollins

Dear @tseemann, I am unfortunately running into a similar error. I'm trying to run snippy-multi on a set of assembled genomes. I did this with no issues when using my...

Hey Conrad, I'm afraid I'm not entirely sure what's causing this problem for you. You're correct that the warning message should be there, as you have single-individual clusters and xval...

Unfortunately, this sounds like you’re running into an error rather than a slow process. I wouldn’t expect a single run of xvalDapc on a dataset of your size to take...

Hi, Could you please confirm by running this line on your tree and phen: `all(tree$tip.label %in% names(phen))` Does it return `TRUE`? If you are able to share your tree and...

Hi Daisy, I just pushed a change that should resolve the current issue you're facing. So if you re-download and install the treeWAS package (with dependencies=TRUE) from GitHub, it should...

Hi Daisy, That sounds like far longer per chunk than I would expect. It sounds like you may be bumping up against some memory constraints still, which could be slowing...

Hi, If either of you could send me your input data, I'm happy to try to figure out what the issue is. Would you be able to email your snps,...

My email is [email protected]

If there are privacy concerns, you could also send me a re-named subset of your data, or anything that has similar contents and reproduces the error. Best, Caitlin.

treeWAS actually uses phytools' fastAnc function internally to produce the ML reconstructions for continuous phenotypic variables ;)