I am encountering the same issue. From a different post it seems to be spacing or special characters creating issues. I can't seem to find any such issues in my xml, but it is possible I missed something. Did you manage to resolve your issue, if so what was the problem?
I am running on BEAST 2.4.0 on a GPU server. The xml was running prior to the inclusion of a backbone tree. As soon as I included the backbone errors arose. I should clarify that I was using the same backbone on the CIPRES portal, but as a starting tree. This analysis was running, but the backbone was not included in the xml file. i.e. CIPRES allows you to load a starting tree separately to your xml, CIPRES does not allow a backbone tree (unless it is included in the xml but I have not tried this). Because CIPRES does not allow a backbone constraint, it is difficult to decide if the backbone is creating the error, or if the text I used in the xml to define the backbone, is creating the issue.
In terms of resolving the issue, I am struggling to narrow down the areas I should be checking based on the error provide. Beast output is as follows:
bin/beast/bin/beast -threads 64 -overwrite RSA_all_calib_GPU_11Oct.xml
Checking out /home/genevieve/.beast/2.4/BEAST/lib
Loaded URL file:/home/genevieve/.beast/2.4/BEAST/lib/beast.jar
jardir = /home/genevieve/bin/beast/lib/launcher.jar
Loading package BEAST v2.4.0
Loading package BEAST v2.4.0
BEAST v2.4.0, 2002-2016
Bayesian Evolutionary Analysis Sampling Trees
Designed and developed by
Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard
Department of Computer Science
University of Auckland
re...@cs.auckland.ac.nz
ale...@cs.auckland.ac.nz
Institute of Evolutionary Biology
University of Edinburgh
a.ra...@ed.ac.uk
David Geffen School of Medicine
University of California, Los Angeles
msuc...@ucla.edu
Downloads, Help & Resources:
http://beast2.org/
Source code distributed under the GNU Lesser General Public License:
http://github.com/CompEvol/beast2
BEAST developers:
Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled,
Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li,
Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel,
Oliver Pybus, Chieh-Hsi Wu, Walter Xie
Thanks to:
Roald Forsberg, Beth Shapiro and Korbinian Strimmer
Random number seed: 1476773023537
File: RSA_all_calib_GPU_11Oct.xml seed: 1476773023537 threads: 64
Loading package BEAST v2.4.0
Loading package BEAST v2.4.0
[Fatal Error] RSA_all_calib_GPU_11Oct.xml:1:1: Content is not allowed in prolog.
- Strange characters in the internal node labels, I do not have such issues in my newick file.
- Defining the text in the xml for a constraint tree. I have referred to this blog, this has not resolved the issue although I am unsure if there are typos in one section of the text. My xml has the following setup for the backbone. I should mention that I did consider
<init id="NewickTree.t:tree" spec="beast.util.TreeParser" taxa="@Alignment10May15" IsLabelledNewick="true">
<input name="newick"> (Scabiosa,((((((((((Verbena,Acanthus),Lamium),((((Portulaca,Talinum),(Basella,Phytolacca)),((((((((Manilkara,Diospyros),(Impatiens,Curtisia)),Celosia),Beta),(Stellaria,Limeum)),Mollugo),((((Clethra,(Strychnos,Coffea)),((Catalpa,Sesamum),(Halleria,(Jasminum,Exacum)))),Galium),Maesa)),(Opuntia,Pereskia))),Gisekia)),Delosperma),((((((((Valeriana,Valerianella),Schefflera),Cussonia),((((Hydrocotyle,Anethum),Apium),Coriandrum),((((Daucus,Heteromorpha),(Sanicula,Arctopus)),Pittosporum),Gerbera))),(((Guizotia,Lactuca),Scaevola),Nymphoides)),((Villarsia,((Lobelia,Berzelia),Cyphia)),Brunia)),(Ilex,Sphenoclea)),(Montinia,(Ipomoea,((Nicotiana,Solanum),Ehretia))))),(Lampranthus,(Frankenia,Tamarix))),((((Myrtus,Olinia),(Bixa,Gossypium)),((Ribes,Choristylis),(((Leea,(Aphloia,Lythrum)),Terminalia),Eucalyptus))),(((((((((Plumbago,(((Limonium,(Polygonum,Fagopyrum)),((Drosera,Ximenia),Amborella)),Brasenia)),Nymphaea),((Dioscorea,Allium),Asparagus)),((Strelitzia,Zea),Oryza)),((Hordeum,Typha),(Chamaedorea,Smilax))),((Lemna,Potamogeton),Triglochin)),(((((Ceratophyllum,Gyrocarpus),Hernandia),Cryptocarya),(Annona,Cananga)),Aristolochia)),(((((Piper,Peperomia),(Ranunculus,Tinospora)),Buxus),Eschscholzia),((Myrothamnus,(Gunnera,Myriophyllum)),Kalanchoe))),Sedum))),(((Sterculia,Capparis),Brassica),(((Arabidopsis,Reseda),Schinus),((Geranium,Myrica),Melianthus)))),(((((((((Croton,(Acalypha,Dalechampia)),Hura),Suregada),((Euphorbia,Clutia),Drypetes)),((Lotus,Pisum),Medicago)),(((((((((((Glycine,Albizia),(Garcinia,Hypericum)),Phyllanthus),(((Polygala,Hugonia),(Linum,Ochna)),((Androstachys,Heywoodia),Lachnostylis))),Acridocarpus),(Rhizophora,Bruguiera)),((Bergia,Elatine),Dovyalis)),Flacourtia),(Salix,Casearia)),Paropsia),(((Cucumis,Begonia),Rhamnus),((Celtis,Cannabis),((Morus,Urtica),Prunus))))),Dichapetalum),Tapura),((Kiggelaria,Acharia),Hybanthus))),(((Viola,Rinorea),Elaeodendron),(Maytenus,Oxalis)))); /> </init>
- I should clarify there are monophyletic clades in the xml, that are linked to fossil dates. This setup was created in Beauti and the xml was running with all of the monophyletic clades and dates in place, without issue. I am now wondering if the monophyletic clades are contradicting the backbone tree (developed from the angio phylogeny). The vague error code does not allude to this though, so I am unsure on where to from here.
If anyone can provide some assistance it would be amazing! I have been 'arguing' with my xml for a number of days now. XML is attached.
