When trying to import a Newick file (from MEGA) to construct a molecular clock, I kept getting the following error message:

Node names should begin with a letter, a number, or an underscore. Had:(((((((((EO5A:0.04386799,gabonin-?2:0.00931429)0.78:0.02439405,gab Current BL Command:Build Tree givenTree from string treeString Current Task has been terminated. Would you like to see the remaining error messages, if there are any?


Any ideas?

Dear sam,

In HyPhy, all taxon (and tree leaf) names must be valid programming identifiers, i.e. consist only of letters, numbers and the underscore character. Looks like you tree had 'gabonin-2' as a taxon name and HyPhy complained about the '-' character. If you replace '-' with the underscore in the tree string (and also in the alignment file), the error should disappear.

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Cheers,
Sergei

Thanks for the tip, Sergei, but I guess there is still another problem.

I tried replacing the '-' character with an underscore in both the tree and alignment files, and now got this error message:

Node names should begin with a letter, a number, or an underscore. Had:.04386799,gabonin_2:0.00931429)0.?80:0.02439405,gabonin_1:0.030896 Current BL Command:Build Tree givenTree from string treeString Current Task has been terminated. Would you like to see the remaining error messages, if there are any?

Any suggestions?

Dear sam,

'.' is also invalid (0.80 in your case). If you look at the placement of the '?' in the error message, it will be immediately FOLLOWING the offending character.

Cheers,
Sergei

Thanks, Sergei.  I kept going through and removing the offending '.' characters that were reported on each error message.

Now I am getting the following:

givenTree.049 is already being used - please rename one of the two variables.
Current BL Command:Build Tree givenTree from string treeString Current Task has been terminated. Would you like to see the remaining error messages, if there are any?

What do you think?  (Maybe just deleting the offending characters wasn't the best approach)?

Thanks for your help, Sergei.

Dear sam,

It looks like your original tree used a shorthand notation for bootstrap support (e.g. 0.78) and branch lengths at once. E.g. as in the following
((((((((EO5A:0.04386799,gabonin_2:0.00931429)0.78:0.02439405).

HyPhy (as per the Newick format) will interpret 0.78 (or 078 with the edited '.') in the above as a taxon name. Now assume that two internal branches have 0.78 bootstrap support - this will lead to two internal branches having the same name. HyPhy complains about that because each branch needs to have a unique name so that we can refer to the branch if needed.

Try deleting these numerical values before feeding the tree into HyPhy.

Aren't the lack of format standards and ad-hoc extensions which only one or two packages understand great?

Cheers,
Sergei

Thanks for the suggestion, Sergei.

I tried deleting all of the numbers in the tree that were of the same format as that bolded below:

((((((((EO5A:0.04386799,gabonin_2:0.00931429)0.78:0.02439405).

Maybe I didn't understand your recommendation correctly, or maybe I didn't execute it correctly, because I now have the the following error message:

The number of tree tips in givenTree (65) is not equal to the number of species in the data filter associated with the tree (82). Current BL Command:Construct the following likelihood function:filtedData; givenTree; Current Task has been terminated. Would you like to see the remaining error messages, if there are any?

Lol, yes I can see how difficult formatting can be.

Any thoughts on what went wrong?

Dear sam,

Either there are too few leaves in the tree, or you may have inadvertently deleted something in the tree string to shorten it. If you are using a GUI version of HyPhy, you can go to Windows->Object Inspector (or on Windows, to File->Object Inspector), select the Trees option from the menu and double click on the tree name to show a graphical view of the tree HyPhy read.

I would check your tree string for premature ')' and missing ','. You can also go back to MEGA and try to save the tree without the bootstrap support info. Finally, you can use HyPhy to build a NJ tree (the kind MEGA does) in the vanilla Newick format.

Cheers,
Sergei

Thanks, Sergei, it looks like I was finally able to get my data in an acceptable format, and it looked like the molecular clock analysis was running.  But, now I got the following error message:

Constrained optimization failed, since starting point within the domain specified for the variables couldn't be found. Set it by hand, or check your constraints for compatibility. Failed constraint:clockTree.CV.mu=clockTree.jerd.m Current Task has been terminated. Would you like to see the remaining error messages, if there are any?

Any suggestions?

Dear sam,

Which model options did you select? This error is a bit unusual - it probably suggests that the data may be very non-clock like, so much so, that the program fails to find a feasible solution. Make sure the tree is rooted correctly. If all else fails, send me the data (spond at ucsd edu), so that I can duplicate the error and diagnose the source.

Cheers,
Sergei

Thanks, Sergei.

The options I selected were:  MolecularClock.bf>TRN>Global

I tried selecting several other options, though, and got either the same error or the same kind of error (very similar error).

I ended up going back to MEGA and recreating my tree without the bootstrap values.  How can I be absolutely certain that my tree is rooted correctly?

Thanks for all your help, Sergei.

Dear sam,

Something strange is going on - this error is very rare; I am afraid I can't give you meaningful advice unless I can see your data and recreate the problem. I'd like to get to the bottom of this.

Sorry you are having so many difficulties... it must be frustrating.

Cheers,
Sergei

Thanks, Sergei.  No problem.    ;)

I really appreciate your help.

Dear sam,

Thanks to you, I discovered that I introduced a bug in HyPhy (in the last 1.5 months) which led to unwarranted error messages under certain conditions (like those found in MolecularClock.bf).

I fixed the problem in today's build (Apr 12th 2007); please download the latest version (if you are using an Intel Mac, do not use the universal binary - I will update that later today - get the older OS X version instead) and run the analyses using it.

Thanks so very much for helping me discover and eliminate this potentially serious bug!

Cheers,
Sergei

Thank you so much, Sergei!  I was finally able to run my analyses!   :D

For some reason, though, I can't seem to save HYPHY batch files.  They don't seem to save with an extension.  When I tried inserting ".gb" in the file name, that didn't seem to help either.

Any suggestons?

Dear Sam,

Not sure what you mean. Could you be more specific (e.g. what OS are you running, what exactly are you trying to save, etc)?

Cheers,
Sergei