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java -jar beastgen.jar to_fasta.template 1K_SARS-CoV-2.nexus 1K_SARS-CoV-2.fas
Mar 03, 2021 6:35:55 PM freemarker.log._JDK14LoggerFactory$JDK14Logger error
SEVERE: Error executing FreeMarker template
FreeMarker template error:
The following has evaluated to null or missing:
==> alignment [in template "to_fasta.template" at line 1, column 8]

Tip: If the failing expression is known to be legally null/missing, either specify a default value with myOptionalVar!myDefault, or use <#if myOptionalVar??>when-present<#else>when-missing</#if>. (These only cover the last step of the expression; to cover the whole expression, use parenthessis: (myOptionVar.foo)!myDefault, (myOptionVar.foo)??

The failing instruction (FTL stack trace):

==> #list alignment.sequences as sequence [in template "to_fasta.template" at line 1, column 1]

Java stack trace (for programmers):

freemarker.core.InvalidReferenceException: [... Exception message was already printed; see it above ...]
at freemarker.core.InvalidReferenceException.getInstance(InvalidReferenceException.java:98)
at freemarker.core.UnexpectedTypeException.newDesciptionBuilder(UnexpectedTypeException.java:41)
at freemarker.core.UnexpectedTypeException.(UnexpectedTypeException.java:24)
at freemarker.core.Dot._eval(Dot.java:81)
at freemarker.core.Expression.eval(Expression.java:111)
at freemarker.core.IteratorBlock.accept(IteratorBlock.java:94)
at freemarker.core.Environment.visit(Environment.java:265)
at freemarker.core.Environment.process(Environment.java:243)
at freemarker.template.Template.process(Template.java:277)
at dr.app.beastgen.BEASTGen.(Unknown Source)
at dr.app.beastgen.BEASTGen.main(Unknown Source)

Error processing template, to_fasta.template: The following has evaluated to null or missing:
==> alignment [in template "to_fasta.template" at line 1, column 8]

Tip: If the failing expression is known to be legally null/missing, either specify a default value with myOptionalVar!myDefault, or use <#if myOptionalVar??>when-present<#else>when-missing</#if>. (These only cover the last step of the expression; to cover the whole expression, use parenthessis: (myOptionVar.foo)!myDefault, (myOptionVar.foo)??

The failing instruction:
==> #list alignment.sequences as sequence [in template "to_fasta.template" at line 1, column 1]