Error 110 parsing the xml input file

[Francis Nge]

Hi there,

I'm trying to constraint my starting tree to try and see if that can get the BEAST run to converge faster, and there seems to be this error:

Error 110 parsing the xml input file

validate and intialize error: Index 535 out of bounds for length 359

Error detected about here:
  <beast>
      <run id='mcmc' spec='MCMC'>
          <init id='NewickTree.t:2607A-top30' spec='beast.util.TreeParser'>

I checked the forum here and other sites which suggest that this may be due to a mismatch between my alignment labels and the starting tree tip labels. But I can confirm that they are all matching.

Any help would be appreciated.

Cheers

Francis

[Artem B]

Hello Francis,

Do you add a starting tree via beauti or directly by xml editing? And what's version of the BEAST do you use?
As for me, the simplest way is adding a tree in beauti, especially in beast 1.

Best,
Artem

суббота, 6 августа 2022 г. в 02:57:21 UTC+8, franci...@gmail.com:

[Francis Nge]

Hi Artem yes, I did include a starting tree via Beauti (in BEAST v2). Turns out it needs to be re-configured to a newick tree file again. I had pruned the newick tree and for some reason, beast doesn't like that. So I re-configured the pruned tree into a newick tree file again just to make sure. And it works

Thanks