Trouble running SNAPP on Linux Cluster

[Jim McGuire]

Hi All,

I've been attempting to get SNAPP to run on our Linux cluster. The xml file was generated using the latest version of BEAST2 and runs using the Mac executable version of BEAST with SNAPP implemented. However, when I attempt to run the program using the Linux version on our cluster I receive the error message appended below. I have been concerned that perhaps the linux version does not have SNAPP activated. When I opened Beauti from the cluster console and attempted to use the Manage Packages feature, the window did not show any of the packages that must be manually activated in the Mac version. Indeed, nothing at all appeared in the Manage Packages window.

I'm no expert with Linux, so this may be something simple. Hopefully, someone with more Linux know-how can help me out.

Cheers,

Jim

Random number seed: 1410471774497

File: 10X_all_SNPS_CUT.xml seed: 1410471774497 threads: 1

Beta => beast.math.distributions.Beta

Exponential => beast.math.distributions.Exponential

InverseGamma => beast.math.distributions.InverseGamma

LogNormal => beast.math.distributions.LogNormalDistributionModel

Gamma => beast.math.distributions.Gamma

Uniform => beast.math.distributions.Uniform

prior => beast.math.distributions.Prior

LaplaceDistribution => beast.math.distributions.LaplaceDistribution

OneOnX => beast.math.distributions.OneOnX

Normal => beast.math.distributions.Normal

java.lang.Exception: Class could not be found. Did you mean beast.math.distributions.Beta?

at beast.util.XMLParser.createObject(Unknown Source)

at beast.util.XMLParser.parseInputs(Unknown Source)

at beast.util.XMLParser.createObject(Unknown Source)

at beast.util.XMLParser.parseInputs(Unknown Source)

at beast.util.XMLParser.createObject(Unknown Source)

at beast.util.XMLParser.parseInputs(Unknown Source)

at beast.util.XMLParser.createObject(Unknown Source)

at beast.util.XMLParser.parseRunElement(Unknown Source)

at beast.util.XMLParser.parse(Unknown Source)

at beast.util.XMLParser.parseFile(Unknown Source)

at beast.app.BeastMCMC.parseArgs(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

Error 122 parsing the xml input file

Cannot create class: snap.Data. 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.10X_all_SNPS_CUT' spec='beast.util.ClusterTree'>

                  <taxa id='snap.10X_all_SNPS_CUT' spec='snap.Data'>

[Remco Bouckaert]

Hi Jim,

The error message indicates that the snap.Dat class cannot be found. Can you check that the SNAPP package is installed? From a terminal, use

/path/to/BEAST/bin/addonmanager -list

to list all packages and whether they are installed or not. If it is not installed, you can use

/path/to/BEAST/bin/addonmanager -add SNAPP

to install the package.

Cheers,

Remco

[石勇]

Dear Remco,

       Would mind give me some advices? 

       Sorry to post it here. This problem keeps troubling me for a few days.

        After adjusting my parameters, I got pretty fine ESS value of posterior and likelihood. However, the ESS of prior distribution is pretty low. 

       I used GTR model for some of the markers. If I change all the site models to HKY, I got even lower ESS value of posterior, prior and likelihood distribution. 

       Strangely, according to this post (http://goo.gl/j9fYSE), I found changing the "Jeffrey's" prior (birthRate.t and popMean) back to "lognormal" prior could not improve the ESS of prior  in my case.

      Any comment would be appreciated.

Best wishes,

Sandy

在 2014年9月12日星期五UTC+8下午2时46分43秒，Remco Bouckaert写道：

[Masse T.]

Hi Remco,

I have installed packages model selection and snapp as subdirectories of dir beast, still when running beast, I receive this error:

Random number seed: 1580895428614

File: m20-run1.xml seed: 1580895428614 threads: 1

Loading package MODEL_SELECTION v1.5.2

Loading package BEASTLabs v1.9.1

Loading package SNAPP v1.5.0

Loading package BEAST v2.6.0

Loading package BEAST v2.6.0

Error 1017 parsing the xml input file

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

Perhaps a package required for this class is not installed?

Error detected about here:

 <beast>

     <run spec='beast.inference.PathSampler'>

         <mcmc id='mcmc' spec='MCMC'>

             <state id='state' spec='State'>

                 <stateNode id='Tree.m20' spec='beast.util.ClusterTree'>

                     <taxa id='snap.m20' spec='snap.Data'>

what should I do?

[Shuang Xu]

Hi,  Masse.  I've come into the same error. Did you solve it?
Would you please give me some advice if you've finished successfully?

Xu