Problem with constrain File

[Gavin Martin]

Dear IQ team, 

I am having issues running a contrain file with the -g option,

The error I get is ERROR: A taxon has no name.

I'm not sure what this error means, as during a previous iteration, I received a different error telling me of a taxon not being present in my alignment file. 

See attached log file. 

[Heiko Schmidt]

Dear Gavin,

> I am having issues running a contrain file with the -g option,
> The error I get is ERROR: A taxon has no name.

More complete the message is: “ERROR: A taxon has no name. (line 1 column 55)”

Could you please check whether the tree file has an error at position 55 in line 1?
I guess the error points out that there is an extra comma (‘,’) or else there is a sequence name missing where there should be one. Maybe when constructing the constraint tree either a comma was left in when removing some sequence names or an additional one sneaked in.

It’s hard to tell without having the tree file.

> I'm not sure what this error means, as during a previous iteration, I received a different error telling me of a taxon not being present in my alignment file.
> See attached log file.

See above. Without the treefile we can only guess.

Best wishes,
Heiko


-----------------------------------------------------------------------------
Heiko Schmidt
Center for Integrative Bioinformatics Vienna (CIBIV)
University of Vienna / Max F. Perutz Laboratories (MFPL)
http://www.cibiv.at/
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[Gavin Martin]

Heiko, 

Thank you for your reply. That actually should help as I was not sure what IQtree was referring to as columns. But at site 55, there is a comma and parenthesis, so I can start checking there for what may be the issue. 

[Heiko Schmidt]

Hi Gavin,

Is the parenthesis you mention a closing one?
If that looks like this “…(…,)…", then IQ-TREE is right.
There cannot be a comma that is not followed either by a sequence-name or an opening bracket (which contains another subtree).

If the above is the case, you have to delete the comma.
Subsequently, you should check, that after deletion there are still (at least) two entities (i.e. sequence names and/or subtree in a pair of brackets) remain within the bracket after deletion.

So if the bracket looks like this “…((…))…” or “…(sequence-name)…” you have to delete a pair of brackets as well.
If there is something like “:0.134” after the bracket - this is the branch length attached and has to be deleted as well. If the constraint tree was obtained from a tree reconstruction it may contain branch lengths.

I hope that helps.

Cheers,
Heiko

[Gavin Martin]

Thank you, it looks like the problem was that I had single entities within their own brackets. All seems to be working now. 

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Gavin Martin

PhD Student

Bybee Lab

Brigham Young University