Error 1017

[githubgig]

Hello,

I used snapp_prep.rb to generate the .xml file, but I am getting the below error in BEAST (v2.6.3). I have already installed SNAPP, so I am not sure which other package is required:

Thanks

[mmatschiner]

Hi,

You’ll need a newer version of BEAST or an older version of this script.

Cheers, Michael

[githubgig]

Hi,

Thanks for the reply. I installed from Anaconda, so this is the newest version they have. Where can I find the older version of this script to work with v2.6.3?

[githubgig]

Hello again,

I managed to install the latest version of beast. I reran it with the xml generated using a starting tree, but I am getting an this error:

beast.base.evolution.tree.TreeParser$TreeParsingException: Label '#NEXUS' in Newick beast.tree could not be identified. Perhaps taxa or taxonset is not specified? at beast.base.evolution.tree.TreeParser$NewickASTVisitor.getLabelIndex(Unknown Source) at beast.base.evolution.tree.TreeParser$NewickASTVisitor.visitNode(Unknown Source) at beast.base.evolution.tree.TreeParser$NewickASTVisitor.visitNode(Unknown Source) at beast.base.evolution.tree.treeparser.NewickParser$NodeContext.accept(Unknown Source) at org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visit(AbstractParseTreeVisitor.java:18) at beast.base.evolution.tree.TreeParser$NewickASTVisitor.visitTree(Unknown Source) at beast.base.evolution.tree.TreeParser$NewickASTVisitor.visitTree(Unknown Source) at beast.base.evolution.tree.treeparser.NewickParser$TreeContext.accept(Unknown Source) at org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visit(AbstractParseTreeVisitor.java:18) at beast.base.evolution.tree.TreeParser.parseNewick(Unknown Source) at beast.base.evolution.tree.TreeParser.initAndValidate(Unknown Source) at beast.base.parser.XMLParser.initBEASTObjects(Unknown Source) at beast.base.parser.XMLParser.parse(Unknown Source) at beast.base.parser.XMLParser.parseFile(Unknown Source) at beastfx.app.beast.BeastMCMC.parseArgs(Unknown Source) at beastfx.app.beast.BeastMain.main(Unknown Source) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.base/java.lang.reflect.Method.invoke(Unknown Source) at beast.pkgmgmt.launcher.BeastLauncher.run(Unknown Source) at beast.pkgmgmt.launcher.BeastLauncher.main(Unknown Source)

Error 110 parsing the xml input file

validate and intialize error: Label '#NEXUS' 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' tate id='state'> stateNode id='tree' spec='beast.base.evolution.tree.TreeParser'

[mmatschiner]

Hi, the tree should be in Newick format, not in Nexus format. You can generate that if you open your tree file in FigTree (for example) and save again in Newick format.

I hope this helps!

[githubgig]

Hi Michael,

I converted to the tree to newick and reran, but I am now getting the below error. I am working with a RaxML tree generated from SNP data. My vcf file has sample names G1_G1 or G2_G2 etc. While generating the .xml, I specified the sample assignment to species. But .nwk tree file does not have this species assignment in the tree tip labels, it only has G1_G1 or G2_G2 as the labels. Is this why I am getting this error? Should I include both species and sample name for the tree tip labels? If not, how should I format the .nwk file?

Error 110 parsing the xml input file

validate and intialize error: Label 'G33_G33' 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'

[mmatschiner]

Hi, the tree should include exactly one tip per species and that tip should be named with the species ID, not any of the specimen IDs. In principle it should also be ultrametric with branch lengths that are in agreement with any age constraints that you may place on nodes. I agree that it can be tricky to prepare that tree. Can you run the analysis without providing a starting tree? How many species does your dataset include?