Found BUG in BEAST?!

Thijmen B

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Dec 29, 2015, 12:12:46 PM12/29/15

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Hi,

I've found something strange in BEAST and I have no idea if it is a bug or my fault, can someone help?

I'm still trying to run BEAST with a starting tree (on CIPRES)

I'm using one calibrate node and the "prior" looks like this in the xml:

"<distribution id="CHEI-ONTH.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="true" tree="@NewickTree.t:p14">

<taxon id="668687_Onth_rhin_1" spec="Taxon"/>"

At least the start of it.. So all taxa end with an "1", this is added by BEAUTI not by me.

running it on cipres results in an error: "Cannot find taxon 668666_Onth_long_1 in data" But I can open it in BEAUTI!

So I created a second xml file where I removed all "1's" by hand, as follows:

"<distribution id="CHEI-ONTH.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="true" tree="@NewickTree.t:p14">

<taxon id="679441_2Onth_gir_" spec="Taxon"/>"

Running it on cipres results in an error: Cannot open file... And indeed I cannot open this xml in BEAUTI, trying results in the following error:

Error 104

"IDs should be unique. Duplicate ID '668666_Onth_long_' found"

Error detected about here: ...

What is wrong?

Thanks and happy new year in advance!

Thijmen

Remco Bouckaert

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Jan 5, 2016, 3:59:33 PM1/5/16

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Hi Thijmen,

This is indeed a bug in BEAUti and I logged an issue for it (#478). For now, fix this in the XML, replace

with

for every taxon that was specified before, for example, because it was already used in another calibration. Taxa with the same ID should only be specified once, so if you want to use them a second time you should refer to the first one through the “idref” (removing the spec attribute is optional, but will produce warning which you can safely ignore in this case).

Cheers,

Remco

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Jeremy Jensen

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Mar 15, 2026, 2:47:28 PM (yesterday) Mar 15

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I know that I'm replying to a very old post but I am experiencing this same issue and was wondering if there's been a solution reached that is better than my current solution. I'm very new to BEAST so I might be missing something very basic

Within all my priors Beauti adds a 1 after my specimen IDs (ie Fedtschenkia_anthracina_BLX40661 instead of Fedtschenkia_anthracina_BLX4066). If I try to run as is I get an error that BEAST can not locate the taxon "Cannot find taxon Fedtschenkia_anthracina_BLX40661 in data".

I then remove the 1 and again if I run this I get an error of duplication " Ds should be unique. Duplicate id 'Fedtschenkia_anthracina_BLX4066' found"

This is when I found this post. I was able to go in remove all 1's added to my priors and change "<taxon id=" to "<taxon idref=" but this takes a long time to fix. Is there a fix for this or change I need to make to my ID's to avoid this issue?