beauti2.2 crashes when importing alignment

[jssd...@gmail.com]

Hi folks,

I'm trying to import an alignment in Beauti2.2 that has a charset defined for only a subset of the data (e.g. for 5000 bp, only charset set=1-4500;). This import works fine in Beauti2.1.3, but Beauti2.2 crashes when I try to import the dataset. When partitions cover the entire range of characters in the dataset, Beauti2.2 opens it fine.

I have Java8, BEASTShell, Classic, and BEASTLabs installed.

Is there a workaround for the issue, or does Beauti2.2 just have more strict bookkeeping about partition definitions?

Thanks!

[jssd...@gmail.com]

The issue persists when I try to import separate nexus files without the charsets.

[Remco Bouckaert]

Hi John,

The partition-interpretation has not changed. 

Can you check that the file extension of the files you try to import is .nex or .nxs? It looks like Mac silently appends .txt a extension to files in some cases, and then the file is named xyz.nex.txt for example. BEAUti does not know how to deal with those. Removing the .txt extension from the file fixes this.

Cheers,

Remco

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[jssd...@gmail.com]

Hi Remco,

They are both .nex. I exported from Mesquite, and checked using get info for both of the files. Might there still be some hidden formatting issue?

~John

On Wednesday, February 4, 2015 at 11:17:55 AM UTC-5, jssd...@gmail.com wrote:

[Remco Bouckaert]

Hi John,

Could you send me a sample so I can check what is going wrong?

Cheers,

Remco

[jssd...@gmail.com]

Hi Remco,

I sent you the three nexus files.

[Remco Bouckaert]

Hi John,

I tried on OSX Mavericks with the package you have installed, and a few more, but could not replicate the problem. All files you sent imported without problem when I dragged them onto BEAUti and selected “Add alignment”. Can you do the following: open BEAUti, attempt to import an alignment, go to the menu Help/Messages and send the messages that are shown in the dialog that pops up.

Cheers,

Remco

On 5/02/2015, at 7:17 am, JS Denton <jssd...@gmail.com> wrote:

Hi Remco,

Here are the datasets. I have the latest versions of all the packages I have installed. I am running OSX Yosemite 10.10.2, with Java8.

Thanks for the quick reply.

~John

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<NEW_ALIGNMENT_autop.nex><mito.nex><nuclear.nex>

[Carlos Prada]

Hi,
I am having the same issue. I am running Beauti 2.2.0 on a OSX with mavericks. I tried the help/message and get "Error and warning messages are printed to stdout and stderr to show them here, start BEAUTI with the -capture argument".

Any help would be very welcome!
Thanks
Carlos

[Heather]

I'm also having this problem on Mavericks. As soon as I select the file to be imported, beauti2 quits. Anyone found a fix for this?

I have a similar issue with BEAST 1.8, where if I try to run an analysis with BEAGLE it quits. These two errors are probably unrelated though.

Cheers,

Heather

[Rafal Mostowy]

Hi all,

I can also report that this problem occurs on my laptop which has Mac 10.10, but it does *not* occur on my desktop which has Mac 10.9. I have installed Java8 on both.

Cheers,

Rafal

[Remco Bouckaert]

Hi Rafal,

Is it possible Java 6 or 7 is installed next to Java 8 on the Mac 10.10? If so, this might help:

https://groups.google.com/forum/#!searchin/beast-users/matzke$20java$20install/beast-users/tyq2fsZHhJQ/eHo8-OU2T64J

Cheers,

Remco

[Rafal Mostowy]

Hi Remco,

Thanks for the reply. Indeed, it was. However this cannot be the cause of the problem as:
1. I’ve just updated the JDK as you suggested and BEAUti still crashes
2. My Desktop (10.9) had the same java settings (only browser update) and BEAUti works like a charm.

Also, I’ve just noticed that BEAUti doesn’t crash when I open it using the binary file in the ‘bin’ directory, or at least it lets me load the alignment. I tried launching the original BEAUti.app from the terminal to record the output when it crashes but I don’t know how to do that.

Please let me know if you have any ideas.

Thanks,
R

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[Remco Bouckaert]

Hi Rafal,

Would you mind trying the following: open a terminal and check the java version with

java -version

It should report something like ‘java version “1.8.0_45”’ if everything is fine. 

Next, start BEAUti from the terminal like so: change dir to BEAST

cd /Applications/BEAST\ 2.2.1/

then start BEAUti, like so:

java -cp lib/beast.jar beast.app.beauti.Beauti

Can you let me know what is printed on screen.

Thanks a lot,

Remco

[Liz Alter]

Hi Remco,

I am having the same issue with BEAUti and BEAST on OSX 10.10. Version of java when I check in terminal is 1.8.0_45. The error I am getting in terminal is:

CUDA error: "Driver not initialized" from file <GPUInterfaceCUDA.cpp>, line 169.

Thanks for any help!!

Liz

[Liz Alter]

Never mind -- fixed the issue by removing CUDA....

Thanks,

Liz

On Thursday, May 28, 2015 at 3:33:42 PM UTC-4, Remco Bouckaert wrote:

[Juan Diaz-Nieto]

Hi Remco,

Any updates on this topic? I ran into the same issue described above, BEAST/BEAUti crash every time I run the executable files, however they just run fine if I use the binary file (as described by Rafael). I can use the program just by going to the binary every time, but just wanted to know if there is a more permanent solution to that problem.

Thanks a lot,

juanf

[Gary Longo]

Hi Liz, 

Could you specify exactly what you removed to fix the issue? I got the exact same error. Sorry if this obvious and I'm just missing it.

Cheers,

Gary

[genevieve....@gmail.com]

Hi Gary,

You need to uninstall CUDA from your computer, I run mac and managed to solve it by deleting these files (there is no uninstall function):

/System/Library/Extensions/CUDA.kext
/Library/Frameworks/CUDA.framework
/Library/LaunchAgents/com.nvidia.CUDASoftwareUpdate.plist
/Library/PreferencePanes/CUDA/Preferences.prefPane
/System/Library/StartupItems/CUDA/

If you installed the tookits and samples, delete the following also:

/Developer/NVIDIA/CUDA-5.0
/usr/local/cuda

Hope it works!

Gen

[Gary Longo]

Hi Gen,

It worked perfectly, thanks so much!

Also apparently with the new Xcode, there is no longer a /Developer folder. At the least thats what the internets told me because I couldn't find it on my computer (I'm running El Capitan). 

Again, thank you!

Cheers,

Gary

[kbr...@berkeley.edu]

Hello, 

I am having a similar issue. I double-click on Beauti and the program opens fine. I click on file, then import, and when I select my .nex file Beauti quits immediately. I've tried everything above and nothing is working. 

I have a MacBook Pro 2015, running El Capitan. I just downloaded the BEAST/Beauti programs today. My Java is up to date (8). I did install CUDA and BEAGLE earlier today because I needed them for working in MrBayes. But when I went looking for the problematic CUDA files (like Gen mentions) they are nowhere to be found. 

Any help is appreciated. Thank you!!

Kinsey

[genevieve....@gmail.com]

Hi Kinsey,

I am unsure where you would have installed cuda? I found mine as an application under system preferences, directly next to the Java install. Check yours is installed, click on it and you should be able to locate the install files by navigating through the new window that opens. I can't give you exact instructions as I no longer run CUDA.

Maybe Gary can help, it looks like he also struggled to locate the files.

Good luck!

Gen

[Andrew Rambaut]

I just want to clarify: The BEAGLE installer doesn’t install CUDA (although it does give a link the the NVIDIA website for getting it). BEAGLE itself will detect if CUDA is installed and offer it as an option if it is. However, if CUDA is installed on a machine with no NVIDIA hardware then this might be an issue. One would have thought that CUDA would refuse to install on a machine without an NVIDIA GPU but when I just tested this (on a machine with no NVIDIA GPU) it happily let me install it. Running BEAST (beast -beagle_info) now gives the error:

CUDA error: "Driver not initialized" from file <GPUInterfaceCUDA.cpp>, line 169.

Annoyingly, neither the NVIDIA Package Installer nor the System Preference panel give a way to uninstall CUDA. At the moment the only solution to this is to manually remove all the components from the various locations as described by Gen, below:

/System/Library/Extensions/CUDA.kext 
/Library/Frameworks/CUDA.framework 
/Library/LaunchAgents/com.nvidia.CUDASoftwareUpdate.plist 
/Library/PreferencePanes/CUDA/Preferences.prefPane 
/System/Library/StartupItems/CUDA/ 

*** The key thing here is not to install CUDA unless you have an NVIDIA GPU installed. *** 

We will add it as an issue to BEAGLE that it could handle this better (i.e., catch the error above and report the issue more informatively) but essentially the solution is to remove CUDA drivers.

Andrew

On the Mac, as Gen says, the CUDA driver settings are in the System Preferences (with, I believe an option to uninstall).

Visit this group at https://groups.google.com/group/beast-users.

[Jayden Cordes]

Hi everyone,

I'm having the same kind of problem. Beauti opens fine, but when I select the nexus file it closes instantly. What's more curious is that other nexus files import just fine, so it's a problem specific to a certain nexus file rather than problem with the program itself or java (I checked the Java version and opened Beauti from the terminal in the manner described above anyway, and all seemed okay).

The one thing which is unique to my problematic nexus file is that it contains categorical variables which use letters as well as numbers as character symbols (I ran out of numbers so I started using letters, so variables can be any number from 1-9 and letters from a-h. It works for Mesquite which lets you have up to 55 possible states using any numbers, capital and lowercase letters). The nexus file which works fine just contains simple binary variables.

Could this be the source of the trouble or might something else be going wrong?

Cheers,
Jayden.

[Remco Bouckaert]

Hi Jayden,

If you are using BEAUti v2.2, you may consider upgrading to the latest version v2.4.3, which has quite a few problems fixed.

If that does not help, could you send me the file that causes this problem so I can investigate?

Cheers,

Remco

[Jayden Cordes]

Thanks so much Remco. I was using v2.4.0. I've upgraded to 2.4.3 now but the problem is the same.

I'll send you the files in a pm.

Cheers,

Jayden.

[Remco Bouckaert]

Hi Jayden,

Thanks for the file — as you suspected, currently, the standard datatype only accepts digits, but the alignment in the file you sent contained non-digit data, which causes the crash. I cannot think of a quick workaround. If you plan to use one of the MK models (in the morph-models package), it does not matter which characters you use in the alignment, since sites with the same number of states will be grouped together. So, replacing the letters for a site with one of the numbers not yet used for that site will give the same result.

Cheers,

Remco

[Todd Knutson]

Hi all, 

I just wanted to mention that I was having a similar problem: Beauti crashing when trying to import a nexus file. I did not immediately realize that my nexus file had the wrong datatype listed in the file header. Mine listed "datatype=DNA", when I was providing amino acid sequences. Thus, simply editing the nexus file to "datatype=protein" solved my Beauti crash problem. This now seems obvious, but I just wanted to post here in case anyone else had similar issue.

Thanks,

Todd

[JP]

Similar to Todd's post...

I was configuring 14 different files in BEAUTi (12 individual genes, one concatenated dataset, one *BEAST species tree). Only one file (one of the 12 individual genes) was causing the problem of crashing BEAUTi when loaded. I had been using .fasta format for my alignments and after multiple attempts, I switched that one alignment to a .nexus file and it loaded fine.

This seems like an obvious thing to try, but like above felt I should post it here, especially since I didn't see anyone mention using a .fasta file above. I generally prefer .fasta for programs like this because it does not require syntax at the top (ergo, fewer mistakes for me to make).

Cheers,

-John