Cannot run SNAPP, package not displayed in AppLauncher

[Annabel Smith]

Hello,

Mac 10.12.3, Beast 2.5.0, Java 1.8.0_181

I want to run SNAPP but it has only installed the SNAPP tree set analyser, not the main SNAPP package.

I installed SNAPP in the Beauti Package Manager but the application is not listed in the AppLauncher, only the tree set analyser (see applauncher_image.jpeg).

I tried running it from the command line (java -jar beast.jar filt3.xml) but get the error pasted below.

I specifically installed JDK 8 based on recommendations from this group (from here http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html).

I tried installing Beast with and without (from here http://www.beast2.org/) Java and I have the same problem.

The SNAPP folder appears in the package directory: /Users/name/Library/Application Support/BEAST/2.5/SNAPP, but the version file only lists the tree set analyser (see below).

So it seems like SNAPP has not actually installed. Does anyone know how I can fix this problem?

Many thanks,

Annabel

# Error when running in the command line:

Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.math.distributions.Beta?

Error detected about here:
  <beast>
      <run id='mcmc' spec='MCMC'>
          <state id='state'>
              <stateNode id='Tree.nexus_filt3' spec='beast.util.ClusterTree'>
                  <taxa id='snap.nexus_filt3' spec='snap.Data'>

# Contents of: /Users/name/Library/Application Support/BEAST/2.5/SNAPP/version.xml

<package name='SNAPP' version='1.4.1'>
    <depends on='beast2' atleast='2.5.0'/>
    <packageapp description="SNAPP tree set analyser"
        class="snap.app.analysis.TreeSetAnalyser"
        args="-window -working -options"
        icon="snap/app/analysis/tsa.png"
    />
</package>

[Remco Bouckaert]

Hi Annabel,

SNAPP is a package to BEAST that when installed will show up in BEAUti as a template under the File/Templates menu. Choosing that template allows you to set up a SNAPP analysis that you can run with BEAST — this is not something you need AppLauncher for.

BEAST v2.5.0 does not pick up packages when run with “java -jar beast.jar …” but should be started from the beast script, which is in /Applications/BEAST\ 2.5.0/bin/beast on OS X, so

/Applications/BEAST\ 2.5.0/bin/beast filt3.xml

should run. (See http://www.beast2.org/2018/04/10/what-is-new-in-v2.5.0.html if you still want to use beast.jar directly)

Cheers,

Remco

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<applauncher_image.jpeg>

[Annabel Smith]

Hi Remco,

Thanks for the explanation - it makes sense and Beast is running now.

I got confused because I was following the SNAPP tutorial (https://github.com/BEAST2-Dev/SNAPP/releases/download/v1.2.0/SNAPP.pdf), which suggests that SNAPP has a separate GUI  - with a picture of a prawn!

Thanks again,

Annabel

[vanina v]

Hello, I am trying to run SNAPP in a server where they installed  beast new version. I used to do it perfectly but using the same xml that before was working ok, now I have the following error message:

Error 1017 parsing the xml input file

I tried to change the way I run SNAPP according to the solutions of this forum but Still it is not working. I attach my xml and the commands that I am using to run it  in case you can see what am I doing wrong.

Thanks!!!

Vanina

[Remco Bouckaert]

Hi Vanina,

It appears that the SNAPP package is not installed properly on the server, since the class path in the screen output you posted does not contain snap.addon.jar though for some reason it does contain mtj.jar and junit-4.8.2.jar, which should not be in the class path. These last two libraries should not be in the SNAPP/lib directory.

You can try to install SNAPP locally using the package manager, by using from a terminal:

/path/to/beast/bin/packagemanager -add SNAPP

where “/path/to” the path to where BEAST is installed, and see whether the local install is picked up. If not, you can ask the system administrator to at least remove the mtj.jar and junit-4-8-2.jar files and reset the class path by removing the beauti.properties file 

rm ~/.beast/beauti.properties

Next time you start BEAST, a new beauti.properties file appears with the new class path, which should contain snap.addon.jar.

Hope this helps,

Remco

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<c85d5m20p10_2_2000.xml><SNAPP_run4.sh><Snapp_uhag.out>

[vanina v]

HI Remco, 

thank you for your help, now SNAPP is running in my server!!!

Evidently, SNAPP was not properly installed. 

Thanks!

Vanina

[Krzysztof Kozak]

Hello,

I have experienced the same Error 1017 on two different CentOS servers. In both cases, I have installed BEAST 2.5 and tried to add Mascot: first with packagemenager, which didn't lead to a working installation, and then manually. According to packagemanager -list, I have Mascot 1.2.1 installed (the latest version from T Vaughan's github).

I have only one version of BEAST in /.beast and I have reset the beauti.properties (attached). The xml I am using was generated and runs correctly on a mac.

Still, I get this. It happens both when using the beast script and the command java -Dbeast.load.jars=true -jar beast.jar.

Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.evolution.tree.coalescent.TreeIntervals?

Error detected about here:

  <beast>

      <run id='mcmc' spec='MCMC'>

          <state id='state'>

              <stateNode id='Tree.t:erato41' spec='beast.app.mascot.beauti.TreeWithTrait'>

java.lang.UNIXProcess$ProcessPipeInputStream@27973e9b

[

Not sure where to take it from here!

Best,

[nicola.fel...@gmail.com]

Dear Krzysztof,

I had a wrong url in the package manager list, which caused the package to not actually be downloaded while being displayed as installed. The error is corrected and re-installing Mascot should fix the issue.

Best,

Nicola

[Krzysztof Kozak]

Dear Nicola,

Thanks! That's not it, the problem is also when I perform a manual install from a directly downloaded zip.

I tried with packagemanager just now and it gets interesting. Mascot installed, but then I get 

         Sample      posterior ESS(posterior)     likelihood          prior

-- org.jblas ERROR Couldn't load copied link file: java.lang.UnsatisfiedLinkError: /tmp/jblas8225694584675432367libjblas_arch_flavor.so: /tmp/jblas8225694584675432367libjblas_arch_flavor.so: failed to map segment from shared object: Operation not permitted.

On Linux 64bit, you need additional support libraries.

You need to install libgfortran3.

However, libgfortran3 is installed! OK, so I run as sudo and get:

Error 1018 parsing the xml input file

Class beast.app.mascot.beauti.TreeWithTrait could not be found.

This XML requires the following package that is not installed: Mascot v0.0.5

We're investigating with the admin, I'll report if we get to the bottom of this.

best,