Unlinked codons and state reconstruction in BEAUTi

evolvedmicrobe / beast-mcmc

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Unlinked codons and state reconstruction in BEAUTi #636

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago

What steps will reproduce the problem?
1. Use BEAUTi to make an XML file with ancestral state reconstruction at all 
ancestors (for the nucleotide sequence) with two codon position partitions.
2. Run it in BEAST.

What is the expected output? What do you see instead?

The error is "Object with idref=CP1.treeLikelihood has not been previously 
declared." This is because the ancestralTreeLikelihood idrefs in the logTree 
block are to "CP1" and "CP2" when they should be "CP1+2" and "CP3", as far as I 
can see.

Original issue reported on code.google.com by mdhall272 on 19 Jun 2012 at 11:02

GoogleCodeExporter commented 9 years ago

Original comment by mdhall272 on 19 Jun 2012 at 11:03

Changed title: Unlinked codons and state reconstruction in BEAUTi

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 1 Aug 2012 at 1:55

Added labels: 1.7.2, BEAUti, Milestone-Release1.7.3

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 1 Aug 2012 at 4:16

Added labels: Milestone-Release1.7.4
Removed labels: Milestone-Release1.7.3

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 2 Aug 2012 at 2:17

Added labels: Milestone-Release1.7.3, Priority-High
Removed labels: Milestone-Release1.7.4, Priority-Low

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 3 Aug 2012 at 2:55

Changed state: Fixed