SNAPP XML Error 110: Could Not Identify Newick Tree Labels – Need Help

[EmaBerr]

Hi,

I am generating an XML file for SNAPP using the snapp_prep.rb script and following the tutorial: https://github.com/ForBioPhylogenomics/tutorials/tree/main/divergence_time_estimation_with_snp_data. The only difference from the tutorial is that I am using the -s option to specify a starting tree that I already have in .nwk format (generated with RAxML). Everything seems to work fine, and the XML file is generated without issues.

However, when I run it in beast, I keep getting the following error:

Error 110 parsing the xml input file validate and initialize error: Label 'CM-VM-01' in Newick beast.tree could not be identified. Perhaps taxa or taxonset is not specified? Error detected about here:
I have double-checked all the IDs, and they are all correct, so I believe the problem is with reading the tree itself. Unfortunately, I am not sure how to fix this, so I am asking for your help in trying to resolve the issue.

Thank you very much,
Emanuele

[mmatschiner]

Hi Emanuele, the tree should have species IDs as tips, not the IDs of individuals. Is that the case for your tree?

[EmaBerr]

Hi Michael, I believe the issue lies here: I have the sample ID rather than the species ID. Thank you very much! While I’m at it, I’d also like to ask, since the tips should carry the species ID, I assume they need to be represented one per species. In other words, I cannot have multiple tips with the same species ID, correct?

[mmatschiner]

Yes, you're correct about that.

[EmaBerr]

Perfect, Thank you so much for your help!