Downloading OBAMA on a Linux server

[Corné van der Linden]

Hi all,

I am a first-time BEAST2 user and new to the group, but the posts here have already helped me along quite a bit. However, now I have run into a problem which I cannot seem to fix.

I would like to run BEAST2.6 on a Linux cluster and so far it's installation has been successful. However, when attempting to run my xml file (created in BEAUTi on a laptop, not the cluster where I would like to run BEAST) I receive the following error:

Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.math.distributions.Prior?
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='OBAMA_PropInvariablePrior.s:mtART' spec='beast.math.distributions.BMTPrior'>

Correct me if I am wrong, but I seem to gather that the package OBAMA may be causing the problem and not allowing me to run the analysis. When checking for the package "OBAMA", I turn up empty handed. It is not listed when I run:

~/Dating/BEAST2$ ~/Programs/beast/bin/packagemanager -list

 So I tried to download it using:

~/Dating/BEAST2$ ~/Programs/beast/bin/packagemanager -add OBAMA
Could not find package 'OBAMA' (typo perhaps?)

The issue that I cannot seem to figure out is how to properly install OBAMA on the Linux command line. I can download the package, but then don't know how to go about letting BEAST know where it is. Or perhaps I need to do something entirely different problem? Perhaps I need to get the amino acid models from OBAMA somewhere else?

Any help would be much appreciated!

Thanks in advance,

Corné

[Remco Bouckaert]

Hi Corné,

The OBAMA package was only available when the package-extra.xml repository was added to the package manager. However, since it is peer reviewed now, I moved it to the the default package repository, and it should be available now. If you can try

> ~/Programs/beast/bin/packagemanager -add OBAMA

again, it should install the package. Let me know if you into any trouble.

Cheers,

Remco

[Corné van der Linden]

Hi Remco,

Thank you for moving OBAMA. I have tried your suggestion:

~/Programs/beast/bin/packagemanager -add OBAMA

~/Programs/beast/bin/packagemanager -list

And OBAMA was downloaded and visible in the list. So that works.

However, my initial error has not been fixed. When I run my xml file, I again receive the following:

Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.math.distributions.Prior?
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='OBAMA_PropInvariablePrior.s:mtART' spec='beast.math.distributions.BMTPrior'>

Would you be able to point me in the right direction to fix this?

Thanks for your help so far!

Greetings from Corné

Op donderdag 20 januari 2022 om 00:31:38 UTC+1 schreef higg...@gmail.com:

[Corné van der Linden]

Dear all,

I have since managed to fix this problem. Running

~/Programs/beast/bin/packagemanager -add OBAMA

indicated that OBAMA was installed, package was not “activated” at the start of the run. So eventually I removed the faulty installation and re-ran:

~/Programs/beast/bin/packagemanager -add OBAMA

Which properly installed it. Showing this at the start of the run:

Loading package BEAST v2.6.6

Loading package BEAST_CLASSIC v1.5.0

Loading package MODEL_SELECTION v1.5.3

Loading package BEASTLabs v1.9.7

Loading package OBAMA v0.2.0

This never popped up before. After this happened I was able to run analyses using OBAMA.

Hope this helps other users!

Greetings from Corné

Op donderdag 20 januari 2022 om 18:50:35 UTC+1 schreef Corné van der Linden: