Re: error in BEAST 1.7.5 run: Object with idref=tmrca(gene1.x) has not been previously declared
Andrew Rambaut
Hello!
I am trying to to run an analysis with 7 loci. In BEAST, I'm getting the following error message:
"Parsing error - poorly formed BEAST file, ND2-ND4-COI-tRNA-BFib-AK1-ODC_21-02-2013_35amostras_MB.xml:
Object with idref=tmrca(gene1.ALL) has not been previously declared."
Any help would very much be welcomed.--
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 http://groups.google.com/group/beast-users?hl=en.
For more options, visit https://groups.google.com/groups/opt_out.
Andrew Rambaut
Institute of Evolutionary Biology University of Edinburgh
Ashworth Laboratories Edinburgh EH9 3JT
EMAIL - a.ra...@ed.ac.uk TEL - +44 131 6508624
samuel...@utulsa.edu
I have been running into a similar problem with my dataset in the last few days and it seems to be related to using priors (for fossil calibrations). I have run into the same error when setting up xml files in BEAUTi and running with BEAST in both of the most recent versions (v. 1.7.5 and 1.8.0), and on two different computers (my laptop, a PC, and our lab computer, a Mac).
By iteratively setting up my analyses, adding more settings each
time, I’ve determined that the other settings aren’t an issue, and BEAST will
run the file. The problem only begins once I select anything besides “using
tree prior” on the priors tab for the taxon groups I’ve constructed (whether or
not monophyly is constrained doesn’t seem to matter). When I change the priors
to anything other than ‘tree prior only’ (e.g. lognormal, normal) and run the
resulting .xml file, BEAST will proceed for a bit and then return an error
message something like the following:
“Poorly formed BEAST file: object with idref=tmrca(cyp coi.fas.cyp
coi.fas.mylopharodon) has not been previously declared.”
The text in parentheses, referencing the tree model and taxon name, is variable
depending on other settings as I’m sure you’re aware, but I can’t seem to get
around this error. I can run an analysis using only rates for divergence dating
but without being able to select informative priors, I can’t apply fossil
calibrations to my dataset at all.
The settings I’m using (although again, the other settings
don’t seem to be an issue): I’m running an analysis with 17 genes (not *BEAST
coalescent analysis; the sparsely sampled supermatrix has too much missing data
and runs exhibit poor convergence) with unlinked clock and site models but
linked tree partitions. There are 3 groups with constrained monophyly (3
outgroup taxa, 297 ingroup taxa, and a sub-clade of the ingroup containing 285
taxa). There are 8 other groups without monophyly enforced, mostly monotypic
genera, which are included to place fossil constraints on. The different genes
have different substitution, heterogeneity, and partition models according to
jmodeltest (but all are HKY and GTR variants available in BEAST), lognormal
relaxed clocks with estimate rates selected (these seem to be automatically selected
once tmrca priors are selected), Yule process speciation tree prior, diffuse
gamma ucld.means (shape 0.001, scale 1000), CPs (relative rate parameters for
codon positions) are normal distributions with default prior settings. Finally,
as mentioned before, if I leave the tmrca parameters on the default setting (Using
Tree Prior), the resulting xml file will run fine in BEAST, but if I select any
other distribution (e.g. lognormal or lognormal) with priors left at defaults
or set according to the fossil calibrations I want to use, the xml file will
not run, instead giving me the error message mentioned earlier (idref=tmrca
hasn’t been declared).
As an aside, I’ve noticed that once I’ve selected anything besides ‘using tree
prior’ for the tmrca parameters, BEAUTi (versions 1.7.5 and 1.8.0) runs
extremely slowly on all the computers I’ve tested this data set on (it takes
about 20-30 minutes to set the priors because the program lags so much, so I
have to make sure all the other parameters are set properly before trying to
edit the tmrca parameters). Thanks for your time and hope to hear back!
Sam Martin
philli...@noaa.gov
Samuel Martin
--
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/6RlQ-4Qfc6M/unsubscribe.
To unsubscribe from this group and all its topics, send an email to beast-users...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.Visit this group at http://groups.google.com/group/beast-users.
PhD. Candidate
The University of Tulsa
Office: Oliphant Hall 311 N