BEAUTi: wrong alignment blocks for multi-gene when choosing "create empty alignment"

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ok, solved. In case others come across the same problem: when several
genes are imported in different nex files, different taxa, beauty 152
does not builds properly the alignment blocks. it gave me just one,
corresponding to the taxa and bp of the first gene.
I had to replicate them and also replicate the site patterns block.
now it runs!
sara

-------------------------------

Hi!

I am trying to run beast without data to check on my priors influence,
and I thought that could be done only by pressing the "generate empty
alignment".. but no. I have a 5 genes dataset and beauty (152) just
creates me one collumn with one N, what makes then that the program
doesn't run.... I get the error:
"
Creating site model.
Creating site model.
Using Java nucleotide likelihood core java.lang.UnsatisfiedLinkError:
no NucleotideLikelihoodCore in java.library.path
TreeLikelihood using Java nucleotide likelihood core
  Ignoring ambiguities in tree likelihood.
  With 1 unique site patterns.
Branch rate model used: strictClockBranchRates
Parsing error - poorly formed BEAST file, msey_ebsp3p.xml:
Object with idref=alignment2 has not been previously declared.
Exception in thread "main" java.lang.RuntimeException: ErrorLog:
Maximum number of errors reached. Terminating BEAST
        "

am I doing something wrong here? do I have to modify the xml file?
thanks!

Original issue reported on code.google.com by dong.w.xie@gmail.com on 19 Nov 2009 at 4:00

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Original comment by dong.w.xie@gmail.com on 19 Nov 2009 at 4:01

• Changed title: BEAUTi: wrong alignment blocks for multi-gene when choosing "create empty alignment"
• Changed state: Started

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Original comment by dong.w.xie@gmail.com on 19 Nov 2009 at 9:41

• Changed state: Fixed