Angie Hinrichs

It's possible that our server is getting a little overloaded. I'll look into it.

About a week ago we had to impose some stricter limits on the total amount of memory used by all threads of the apache web server, because sometimes too many...

Sorry but with our new restrictions on total memory use, sending four requests in parallel might be a bit much... maybe back off to 2? If you need to run...

> We don't figure out what context samples we need, however, until we're actually in the functions building the relevant subtrees, long after we choose which metadata to load into...

Hi @liamxg, sorry but 1400 may be too many sequences for the web interface to handle all at the same time. If these sequences have already been in GISAID (or...

Sorry to hear that. Is there any way to subdivide those sequences? Are they your own sequences, or are they from a repository like GISAID / GenBank / GenBase? (If...

Sorry to hear that. Can you attach a file with the 500 IDs to this issue so I can try to reproduce the problem?

Sure, it is angie at soe dot ucsc dot edu (replace with proper punctuation).

Thanks Shay -- the first 3 are consequences of [branch-specific masking](https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml). The reversion A22995C is masked in BA.2.75, BA.5 and XBB because reversions on that base were too noisy. 241...

Hi @gp201, that is a great little test case. It appears that usher's Newick parsing does not handle quoting. So it appears to usher that there are two distinct sequences:...