AU test: A taxon has no name

[Connor French]

Hello,

I am trying to run an AU test in iq-tree, but I get an error: Tree 1ERROR: A taxon has no name. (line 6 column 45). I checked other resolved issues with the same error, but my tree file doesn't seem to suffer from the same problem as other users. The tree file loads into figtree fine, so I don't know what may be going on. I've also run the program on individual topologies from the input topology set separately, and they get the same error, but at a different column number. I have a feeling the problem may be due to too many parentheses, but any attempt at reducing them results in an incorrect topology. 

I've attached a log file, along with one of the topologies that triggers an error.

Thank you for the help!

[Bui Quang Minh]

Hi Connor,

I believe this was discussed in the forum before. Please search it. The problem is due to an outer-most parentheses pair. Removing it will resolve the problem.

Cheers,

Minh

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<top.tre><mafft-nexus-clean-75p_10.phylip.log>

[Connor French]

Hello Minh,

I have tried removing the outermost parentheses pair, but the tree topology changes and I get a new error "Tree file must be ended with a semi-colon ';' (line 1 column 49)". My outgroup contains two taxa, so the outer parentheses pair is necessary to enclose the entire tree. If I root the tree to where one of my outgroup taxa is the outgroup "(out1,(out2,(....)))" I still get the same error. 

Thanks for your help!

Connor

On Sat, Jan 27, 2018 at 6:43 AM, Bui Quang Minh <minh...@univie.ac.at> wrote:

Hi Connor,

I believe this was discussed in the forum before. Please search it. The problem is due to an outer-most parentheses pair. Removing it will resolve the problem.

Cheers,

Minh

On 27 Jan 2018, at 4:43 am, Connor French <confr...@gmail.com> wrote:

Hello,

I am trying to run an AU test in iq-tree, but I get an error: Tree 1ERROR: A taxon has no name. (line 6 column 45). I checked other resolved issues with the same error, but my tree file doesn't seem to suffer from the same problem as other users. The tree file loads into figtree fine, so I don't know what may be going on. I've also run the program on individual topologies from the input topology set separately, and they get the same error, but at a different column number. I have a feeling the problem may be due to too many parentheses, but any attempt at reducing them results in an incorrect topology. 

I've attached a log file, along with one of the topologies that triggers an error.

Thank you for the help!

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To unsubscribe from this group and stop receiving emails from it, send an email to iqtree+unsubscribe@googlegroups.com.

[Bui Quang Minh]

Hi Connor,

I had a look at your tree file again. There is indeed a double-brackets “((…))” for the subtree ending at the reported position, which is not the outer-most bracket. So the error message:

ERROR: A taxon has no name. (line 6 column 45)

should have been something like

ERROR: Redundant double-bracket ‘((…))’ with closing bracket ending at line 6 column 45

We will change this for the next release to make error message more informative. Please find the corrected tree file attached.

Cheers,

Minh

[Connor French]

Hello Minh,

Thank you very much for working through this with me! No problems after the correction.

Best,

Connor