Error 110 - validate and intialize error - SNAPP

[Angelica Cuevas]

Hello,

I'm trying to run SNAPP but after generating the *.xml file using snapp_prep.rb script, from the tutorial, beast gives me the following error:

Error 110 parsing the xml input file

validate and intialize error: Label 'T.lon.lon.AU_F289_UNL_174002_P003_WA11_i5-512_i7-107_S2550' in Newick beast.tree could not be identified. Perhaps taxa or taxonset is not specified?

Error detected about here:

  <beast>

      <run id='mcmc' spec='MCMC'>

          <state id='state'>

              <stateNode id='tree' spec='beast.base.evolution.tree.TreeParser'>

I have checked whether the issue is just different names for the taxon in tree and taxon id or whether I have extra " or ' in all specificated taxon names, but I can't find any name problem in the snapp.xml file. 

I noticed that this taxon id 'T.lon.lon.AU_F289_UNL_174002_P003_WA11_i5-512_i7-107_S2550' is the first taxon specified in the tree, and that if I just swap it with another taxon, without changing the structure of the tree, the error message now will point me to the newly fist taxon on the tree. So I don't think this is an issue with any labeling or the newick tree.

I get the same error using snapper.

I'll highly appreciate any help you guys can give me.

I'm attaching the snapp.xml and snapper.xml files

best regards,

Angelica

[Emanuele Berrilli]

Hi Angelica,

I hava the same problem, do you manage to resolve at the end?

Thanks,

Emanuele

[Angelica Pulido]

Hi Emanuele,

Unfortunately not, I haven't been able to solve this issue. I saw in other discussion that the error 110 is quite common.
In this discussion Timothy Vaughan mentioned that "This error ("110 parsing the xml input file") is actually extremely general: a variety of problems beast 2 encounters while processing the XML will produce this same error."

So I'm not sure now whether there is any issue regarding the naming of the samples.

Any chance you have gotten more clarity on this? unfortunately there hasn't been any answer on this discussion so I still don't know how to solve it.

Best,

Angelica

This error ("110 parsing the xml input file") is actually extremely general: a variety of problems beast 2 encounters while processing the XML will produce this same error.  So it's unlikely that the problem you're seeing is directly related to those earlier in the thread.

[Emanuele Berrilli]

Dear Angelica,

I already replied in the other conversation, but I’ll answer here as well. It turns out that the problem is related to the tree tips, which need to be labeled with the species ID rather than the voucher/sample ID. I’ll re-run the analysis accordingly, and hopefully this will resolve the issue.

Best,
Ema

[Angelica Pulido]

Hi Emanuele,

Many thanks for finding a solution to this issue. I hadn't get back to my SNAPP analyses since, got busy with other things, but will do so now that you found out how to solve it!

Cheers,

Angelica