And here's my response to the user, which we could use as part of the description output by PF:
"What this means is that you have a single data block which has no A's C's or G's, but just T's (I think I got that right, in any case it has only a single base). Since it's not advisable to try and estimate the parameters for a GTR model from this kind of data, RAxML won't do it, and will exit. You could confirm this (if you wanted to!) by running the alignment b12c320a3c8cae07356dd884b5f54e3a.phy (in your subsets folder) in RAxML. You'll get the same error message.
The pragmatic solution here is to just merge that data block with another one (the most similar one you can think of a priori). Obviously this is not 100% ideal, but it's the only way to get RAxML to analyse this data, and so to get PartitionFinder to work on your data."
Sometimes, users have very small data blocks. They can end up with this error from RAxML:
Empirical base frequency for state number 1 is equal to zero in DNA data partition No Name Provided
However, although we do print out the output from RAxML, , because of our threading etc. it looks like something odd has gone on.
So, what we should do is catch this particular RAxML error and make PartitionFinder output a clear description of the problem.
Here's the thread on the google group:
https://groups.google.com/forum/?fromgroups#!topic/partitionfinder/KZU_lvQcekU
And here's my response to the user, which we could use as part of the description output by PF:
"What this means is that you have a single data block which has no A's C's or G's, but just T's (I think I got that right, in any case it has only a single base). Since it's not advisable to try and estimate the parameters for a GTR model from this kind of data, RAxML won't do it, and will exit. You could confirm this (if you wanted to!) by running the alignment b12c320a3c8cae07356dd884b5f54e3a.phy (in your subsets folder) in RAxML. You'll get the same error message.
The pragmatic solution here is to just merge that data block with another one (the most similar one you can think of a priori). Obviously this is not 100% ideal, but it's the only way to get RAxML to analyse this data, and so to get PartitionFinder to work on your data."
R