[BUG] tree missing some obvious merges

[babarlelephant]

Hi, in the european lineage today there are two edges with the same mutation and very similar sequences inside http://www.paris8.free.fr/bug_nextstrain.png

https://nextstrain.org/ncov?c=gt-nuc_15324&label=clade:A2a @lmoncla

2 April at 3h GMT+1 there wasn't such a problem, at 14h the problem was there so I think it appeared in thisone

[emmahodcroft]

To Nextstrain people: see on live tree here, at top of this part (can't zoom further in URL): https://nextstrain.org/ncov?branchLabel=clade&c=gt-nuc_15324&label=clade:A2a

[babarlelephant]

Now solved. Someone did anything special ?

For me it is easy to notice those kind of bugs because I'm copying then modifying the tree to make some more epidemiological clades (every country I mention have > 1000 deaths, not all the clades are perfectly reliable so I need to check if the new sequences fit with it or not)

[lmoncla]

I didn't end up doing anything to fix this, but I'm glad it got sorted

[emmahodcroft]

Thanks for pointing this out @acx01b . I don't know what caused this, and it apparently fixed itself during one of our builds. If you spot it again please do let us know and we can take another look!

[babarlelephant]

@lmoncla The bug is back :-) at the same place

It doesn't seem to appear elsewhere in the tree at least not in a such obvious form.

No idea if it is related but I found that every sequence with travel history, and only them, don't have any "branch_attrs" field in the JSON file.

[babarlelephant]

There are now two appeareances of the bug, both in the European lineage @jameshadfield

https://nextstrain.org/ncov?c=gt-nuc_15324&label=clade:A2a https://nextstrain.org/ncov?c=gt-nuc_20268&label=clade:A2a

[jameshadfield]

We should inspect the IQTREE tree (i.e. before refine) to see if this structure is there. I suspect it is, but I don't have an obvious reason why they're not monophyletic.

No idea if it is related but I found that every sequence with travel history, and only them, don't have any "branch_attrs" field in the JSON file.

Unrelated -- but this should also be improved. For travel history isolates we split the branch in 2 to improve the DTA but we can't duplicate the mutations etc (branch_attrs) without causing double counting in the entropy panel.

[babarlelephant]

There is clearly a problem see https://nextstrain.org/ncov/?c=gt-nuc_26144,14805,17247&m=div where the iranian cluster became a subtree of a lineage having 3 unrelated mutations, I'm quite sure the divergence tree would be cleaner with a basic minimum spanning tree algorithm

[babarlelephant]

At least in my basic script the bug seems gone, probably related with that many identical sequences (from australia,uk,usa,iceland,netherlands..) have been removed.

[emmahodcroft]

Ok, if it pops up again, please do shout and I'll tag someone else in who might have a better idea. But I don't want to call him in if we don't have an example :) As a tip, you can link to a dated tree by putting the date: https://nextstrain.org/ncov/global/2020-04-08 (or sub 'global' with one of the regions) which means that it'll hopefully persist even after the current live build has moved on. However, we do update multiple times a day, so this works best at the end of the US day...

[babarlelephant]

Tks there is one https://nextstrain.org/ncov/2020-04-02?c=gt-nuc_15324,20268&label=clade:A2a&m=div half-resolved two days later https://nextstrain.org/ncov/2020-04-04?c=gt-nuc_15324,20268&label=clade:A2a&m=div but the worst one (for one day the Iranian cluster became a subtree of a seemingly unrelated one) is not archived.

[emmahodcroft]

Thank you for the great examples! Yes, unfortunately if a build is updated multiple times in the day, the earlier ones aren't archived.

@rneher Would you have insight into why this is happening? Is this a known problem, or something new we should make an issue about? Thanks!

[trvrb]

Closing this issue as no longer relevant.