BEAST 2.6.3 error in cluster using conda environment

[Maria Eleonora Rossi]

Hi, 

I am trying to run BEAST to build. a time calibrated tree. In my xml file I have both fossils and DNA sequences. Unfortunately I cannot manage to run it on my server. I have installed beast 2.6.3 and the beagle library through conda. 

When I start the run this is the message that I get 

"Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.evolution.sitemodel.SiteModel?

Perhaps a package required for this class is not installed?

Error detected about here:

  <beast>

      <run id='mcmc' spec='MCMC'>

          <distribution id='posterior' spec='util.CompoundDistribution'>

              <distribution id='prior' spec='util.CompoundDistribution'>

                  <distribution id='FBD.t:ALL_COI_Porifera_withfossils' spec='beast.evolution.speciation.SABirthDeathModel'>" 

I does not matter what version of BEAST or beagle library I use, the error is always the same. (I tried to run it also on CIPRES, but the results file are too big and it gives me Error)

Thank you very much for your help!

Eleonora

[Remco Bouckaert]

The SABirthDeathModel is in the SA package, but you mentioned installing BEAST and BEAGLE only. 

Installing the SA package should fix this problem.

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[andrea nino]

Hi Eleonora,  Im training run my beast analysis in a server where Beast2 is installed with conda environment. I have already my .xml file done with Beauti  but I have difficulties to fin the instruction of run the commands. I appreciate if you can guide me or recommend where find. 

Thank so much.

Andrea

[Maria Eleonora Rossi]

Hi,

I am trying to do that on a conda environment, so I installed BEAST with this command: conda install -c bioconda beast2 

How do I make sure that SA package is installed in a conda environment? 

Thanks for your help

[Maria Eleonora Rossi]

Hi andrea, 

this is normally what I do: I activate the conda environment with 

source activate beast_env

conda activate beast_env (this is another command that you can use to activate the environment)

and then I run this: beast Myfile.xml

My cluster has a queueing system, so I have to submit a specific script to that, but these are the command I generally use. 

Hope it helps!

Eleonora