BEAST 2.1.1 crashes without any log files.

[Rachel Arnold]

I'm trying to figure out why my .xml file keeps crashing (at the beginning) in BEAST 2.1.1 but Terminal closes before I have the chance to read any kind of fatal exceptions.  I went back and kept all the defaults in the starbeast template so I assume it has something to do with my taxa associations/names, but I can't figure it out and don't have any hints as to what might be going wrong.  Is there a way to get Terminal to stay open so I know what it's crashing on?

[Remco Bouckaert]

Hi Rachel,

By running BEAST from the command line error messages are printed on

If you are running Windows, open the Command Prompt window by clicking the Start button Picture of the Start button, clicking All Programs, clicking Accessories, and then clicking Command Prompt.

To run BEAST on MyBEASTFile.xml,  key in the following:

cd c:\BEAST
java -jar lib\beast.jar MyBEASTFile.xml

Note: running from the command line tends to make BEAST run faster on Windows, so that is another reason to use BEAST from the command line.

This assumes that BEAST is unzipped on drive C, so there is a directory C:\BEAST. If it is located in another place, you will need to replace "C:\BEAST" with wherever BEAST is located. Likewise, if your xml file MyBEASTFile.xml is located in another directory than C:\BEAST you should put that in front of the file name.

If you are running on a Max, to run BEAST on MyBEASTFile.xml, open a terminal and key in the following:

cd /Applications/BEAST 2.1.1
java -jar lib/beast.jar MyBEASTFile.xml

If that does not help, you can send me the XML file and I will have a look at what is going wrong.

Cheers,

Remco

[Rachel Arnold]

Thanks Remco--that did keep the window open.  My errors are:

SiteModel: Invalid category count (0) Setting category count to 1
CUDA error: "Driver not initialized" from file <GPUInterfaceCUDA.cpp>, line 131.

When looking at the .xml file generated from beauti, I noticed that the taxon sets have duplicated taxon ids; for instance, "D18_Glyt_B_idiomorpha" is defined as part of the taxon set, and the next item is "D18_Glyt_B_idiomorpha1".  This goes on for all my sequences, such that all of them have a duplicate with the "1" added at the end of the duplicated item.  I'm not sure if this is contributing to the errors above, is separate, or doesn't matter.

FYI, I'm running BEAST 2.1.1 on a mac with OS X 10.9.1.  I'd be happy to send you my .xml file if you'd like to take a look---can I send it to an email address or does it have to be posted openly here?

[Andrew Rambaut]

Dear Rachael,

The 'CUDA error' might suggest that something is wrong with BEAGLE. If you haven't already done so, there is an updated version

for Mac OS X here:

https://code.google.com/p/beagle-lib/

Get: BEAGLE v2.1.2 for Mac OS X 10.6 and later

A.

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[Remco Bouckaert]

This problem is due to a bug in the *BEAST template for BEAUti which prevented the file from initialising. Commenting out the topPopSize parameter and references to it in the XML fixed this problem for now, but this should be fixed in the next patch release -- available in a few weeks time.

Remco

[Rachel Arnold]

Thanks--actually I discovered that my new mac laptop comes with an intel graphics processor, rather than the nvidea card, so it appears I will not be able to use Beagle (I installed the cuda drivers before I realized this).  However, I did not click on the "use Beagle" if available option, so I'm not sure if beast should even be trying to use Beagle.

[Andrew Rambaut]

You can (and should) use BEAGLE even if you don't have an NVidia GPU. BEAGLE can significantly speed up BEAST on the CPU as well.

Andrew

On 28 Feb 2014, at 16:43, Rachel Arnold <frogf...@gmail.com> wrote:

Thanks--actually I discovered that my new mac laptop comes with an intel graphics processor, rather than the nvidea card, so it appears I will not be able to use Beagle (I installed the cuda drivers before I realized this).  However, I did not click on the "use Beagle" if available option, so I'm not sure if beast should even be trying to use Beagle.



On Wednesday, February 26, 2014 2:15:28 PM UTC-8, rambaut wrote:

Dear Rachael,

The 'CUDA error' might suggest that something is wrong with BEAGLE. If you haven't already done so, there is an updated version

for Mac OS X here:

https://code.google.com/p/beagle-lib/

Get: BEAGLE v2.1.2 for Mac OS X 10.6 and later

A.

On 26 Feb 2014, at 17:50, Rachel Arnold <frogf...@gmail.com> wrote:

Thanks Remco--that did keep the window open.  My errors are:

SiteModel: Invalid category count (0) Setting category count to 1
CUDA error: "Driver not initialized" from file <GPUInterfaceCUDA.cpp>, line 131.

When looking at the .xml file generated from beauti, I noticed that the taxon sets have duplicated taxon ids; for instance, "D18_Glyt_B_idiomorpha" is defined as part of the taxon set, and the next item is "D18_Glyt_B_idiomorpha1".  This goes on for all my sequences, such that all of them have a duplicate with the "1" added at the end of the duplicated item.  I'm not sure if this is contributing to the errors above, is separate, or doesn't matter.

FYI, I'm running BEAST 2.1.1 on a mac with OS X 10.9.1.  I'd be happy to send you my .xml file if you'd like to take a look---can I send it to an email address or does it have to be posted openly here?




On Tuesday, February 25, 2014 4:40:22 PM UTC-8, Remco Bouckaert wrote:

Hi Rachel,

By running BEAST from the command line error messages are printed on

If you are running Windows, open the Command Prompt window by clicking the Start button Picture of the Start button, clicking All Programs, clicking Accessories, and then clicking Command Prompt. 

To run BEAST on MyBEASTFile.xml,  key in the following:

cd c:\BEAST
java -jar lib\beast.jar MyBEASTFile.xml

Note: running from the command line tends to make BEAST run faster on Windows, so that is another reason to use BEAST from the command line.

This assumes that BEAST is unzipped on drive C, so there is a directory C:\BEAST. If it is located in another place, you will need to replace "C:\BEAST" with wherever BEAST is located. Likewise, if your xml file MyBEASTFile.xml is located in another directory thanC:\BEAST you should put that in front of the file name.

If you are running on a Max, to run BEAST on MyBEASTFile.xml, open a terminal and key in the following:

cd /Applications/BEAST 2.1.1
java -jar lib/beast.jar MyBEASTFile.xml

If that does not help, you can send me the XML file and I will have a look at what is going wrong.

Cheers,

Remco

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[christophe Lemaire]

Hello all
I am attempting to estimate intrahost dynamics for different populations
of HCV. For this purpose I would like to use the HPM framework as
described in Edo-Matas et al. 2010. However, it is not clear to me,
which parameters are to be linked and those are not in Beauti. Could
someone give me some little explanation?
Thank you in advance
Regards
Christophe

[Philippe Lemey]

Dear Christophe,
I am not sure if you got a reply on this one already, but it is up to user to decide which parameters to link in an HPM. In my opinion, this is generally a good strategy for substitution and clock parameters in different partitions or in different independent realisations of similar evolutionary processes such as intrahost viral evolution. An example from the Edo-Matas paper specified an HPM for the different GTR parameters, for the gamma distribution shape values, the mean rates in the relaxed clock models and also the population sizes in a constant-size demographic model. All these parameters are accessible in the prior panel in BEAuti, and if you select for example all the alpha shape parameters, you can link them in an HPM using the button in the lower left corner. I hope this helps.
Best,
Philippe