annotator: Error Parsing Input Tree

[Lisa]

Hello

I am having an error in tree annotator that I am unable to resolve. I am using BEAST 2/TreeAnnotator v/2.5.1. Annotator is unable to read the tree file formed by logcombiner. The error I am receiving is: 

Processing 12802 trees from file after ignoring first 20% = 3200 trees.

Ignoring translation:[88, Eigenmannia_vicentespelaea, 11649]

java.io.IOException: Around line 422

null

at beast.util.NexusParser.parseFile(Unknown Source)

at beast.util.NexusParser.parseFile(Unknown Source)

at beast.app.treeannotator.TreeAnnotator$FastTreeSet.<init>(Unknown Source)

at beast.app.treeannotator.TreeAnnotator.<init>(Unknown Source)

at beast.app.treeannotator.TreeAnnotator.main(Unknown Source)

Error Parsing Input Tree: Around line 422

null

In the combined tree file, line 422 is around here: 

   417                         Tinca_tinca

    418                         Vaillantella_maassi

    419                         ;

    420 End;

    421 Begin trees;

    422         Translate

    423                    1 Adontosternarchus_balaenops_2612,

    424                    2 Adontosternarchus_cf_clarkae_8673,

    425                    3 Adontosternarchus_cf_nebulosus_8679,

From what I see this is proper NEXUS formatting? Has anyone encountered this type of error before? 

Thanks kindly!

Lisa

[Tim Vaughan]

Hi Lisa,

It'd be great if you could try this with beast 2.5.2 and let us know if this fixes things.  (There are a number of nexus parsing issues that have been recently resolved.)  If this doesn't work, if you could perhaps email me a minimal example of a combined file that breaks things I could have a shot at figuring out what's going wrong in this instance.

Tim

--
You received this message because you are subscribed to the Google Groups "beast-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to beast-users...@googlegroups.com.
To post to this group, send email to beast...@googlegroups.com.
Visit this group at https://groups.google.com/group/beast-users.
For more options, visit https://groups.google.com/d/optout.

[Lisa Byrne]

Hi Tim,

Thanks for the reply. I installed the newer version and I am still having the same problem. 

I have attached the combined tree file- I have shortened it to the first 1000 lines, if that is helpful.

Thanks,

Lisa

You received this message because you are subscribed to a topic in the Google Groups "beast-users" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/beast-users/_HRaz-zfzQ8/unsubscribe.
To unsubscribe from this group and all its topics, send an email to beast-users...@googlegroups.com.

To post to this group, send email to beast...@googlegroups.com.
Visit this group at https://groups.google.com/group/beast-users.
For more options, visit https://groups.google.com/d/optout.

--

*Lisa Byrne, M.Sc*
*University of Toronto*
*Department of Ecology and Evolutionary Biology*

[Remco Bouckaert]

Hi Lisa,

It looks like there are two species with spaces in their names, which are confusing TreeAnnotator: "Eigenmannia_vicentespelaea 11649” and “T Brachyhypopomus_sp_PALE_8783”. If you edit the file and replace the space with underscores (lines 510 and 712), TreeAnnotator runs on the file you posted.

Cheers,

Remco

<FJ_gymnotiformes_combined.trees>

[Lisa Byrne]

Thanks so much for taking a look. I checked my original xml file and there are no spaces there, so I have no idea where they got lost in the chain of events!

Sincerely,

Lisa