Issue with loading MCC tree from BEAST v 1.10.4

[taylorpaisie]

I am having an issue when loading and trying to plot one of my MCC trees from a BEASTv1.10.4 run. Here is the link to my R code: https://gist.github.com/taylorpaisie/0c8b07d81003419d94426bfe814ea4ff

Here is the link to the tree I am trying to load and plot: https://gist.github.com/taylorpaisie/bc8b55df56a1730abeda49eb82d6bf1e

The warning message I receive when reading the BEAST tree with 'read.beast()' is:

Warning message: In matrix(x, ncol = 2, byrow = TRUE) : data length [163] is not a sub-multiple or multiple of the number of rows [82]

Then when I use the 'ggtree' command in my script, my R session aborts completely. Any idea what could be causing this error?

[GuangchuangYu]

There should be something wrong with your file.

ape::read.nexus() will parse the file with only tree structure by ignoring annotation.

It throws the same issue and can't draw the tree.

[brj1]

There is a space in one of the taxon labels of the nexus file, which is causing read.nexus to not read the labels correctly. Changing line 51 of your nexus from 'MF574563.1 _COL_2015' to 'MF574563.1_COL_2015' and line 137 from 46 'MF574563.1 _COL_2015', to 46 'MF574563.1_COL_2015', should make the file readable.

I'm not sure if spaces in labels is allowed by the nexus format. If so, this is a bug in ape::read.nexus.

[GuangchuangYu]

As the labels are single-quoted, they should be supported IMO. Maybe we should include @emmanuelparadis to the discussion of this issue.

[xiangpin]

I think this issue should be fixed by this request, the problem is like @brj1 said, I had submitted the request to solve the problem, so the development version of ape should work.