XML fails to run
Closed this issue · 4 comments
ArtPoon commented
Attempting YFV FASTA file with tip dates and UCLN clock.
Read alignment: alignment
Sequences = 71
Sites = 654
Datatype = nucleotide
Site patterns 'patterns' created from positions 1-654 of alignment 'alignment'
unique pattern count = 280
Mar 29, 2021 11:30:52 PM dr.app.beast.BeastMain <init>
SEVERE: Parsing error - poorly formed BEAST file, test.xml:
Object with idref=taxa must not have other content or attributes (or perhaps it was not intended to be a reference?).
Error thrown at: dr.xml.XMLParser.convert(Unknown Source)
ArtPoon commented
Same exception thrown with no modifications to analysis options (JC, strict clock..)
ArtPoon commented
I think this is the problem:
<coalescentSimulator id="startingTree">
<taxa xmlns="http://www.w3.org/1999/xhtml" idref="taxa"></taxa>
<constantSize idref="constant"/>
</coalescentSimulator>
ArtPoon commented
Manually edited the XML file. The problem is this bit: xmlns="http://www.w3.org/1999/xhtml"
ArtPoon commented
Changing this from createElement
fixed the problem:
taxa = document.createElementNS("", "taxa"),