Can't complete Skyline reconstruction using Tracer

[Matt Mitchell]

Hello,

Hopefully somebody can help me with this problem.  I'm trying to generate a Bayesian Skyline plot for my data, and I'm having difficulty getting Tracer to actually compute the reconstruction.  At first, I did a short sample run in BEAST using only 1 million replicates, and Tracer had no problem generating the Skyline plot once I loaded it in.  However, I decided to re-run my data through BEAST (this time using 10 million replicates) and when I load the log files into TRACER and clicked OK to generate the Skyline plot, TRACER just sits there with the status bar at 0%.  I've let it sit for days, to no avail.  Does anybody have any idea what the problem might be?

Thanks,
-Matt

[miguelal...@gmail.com]

Hi Matt,

It is an issue of computer memory (in fact, tracer is not running at all, so one could be waiting forever). I am currently experiencing the same problem, and according to some posts,  ways to fix it would be either to increase log parameters in MCMC tab (to reduce sampling, i believe) or re-sample after a beast run with logcombiner. I am trying the first option right now.

good luck

[pb&j]

Not sure what platform everyone is using but I am running Mac OS X 10.7.5 and could not get Tracer to complete the Skyline analyses when running Tracerv1.6 from the .dmg for a Mac.

However, finished in no time running the Java executable version.

http://tree.bio.ed.ac.uk/software/tracer/

Seems like it might have something to do with Lion…

[reynolds...@gmail.com]

Hi,

 

Im having the same problem as Matt and Im using the java executable version, same as the link given. Has anyone found a solution to the problem? is there a way to get the older version of Tracer?

 

Really frustrated.

[carlo pacioni]

Same here, Tracer 1.6 doesn't generate a BSP plot, but Tracer 1.5, with the same files and same computer (running W7), generates a plot in no time..

carlo

[Andrew Rambaut]

I will look into this but Tracer 1.5 is still available for download from this link:

http://tree.bio.ed.ac.uk/download.html?name=tracer&version=v1.5&id=88&num=2

where num=1 for Mac, 2 for Windows or 3 for Linux.

A.

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[Alexander Florez]

Dear Dr. Rambaut, 

I have the same problem mentioned by Matt, and when I am trying to download a previous version is not possible to connect to the server:

http://tree.bio.ed.ac.uk/download.html?name=tracer&version=v1.5&id=88&num=2 

Not Found

The requested URL /"".$redirectURL. was not found on this server.

====================================================

http://beast.bio.ed.ac.uk/Tracer

Forbidden

You don't have permission to access / on this server.

There is other way to download  a previous version of Tracer?

Best, 

Alex

[Irene Lobon]

Hi, 

I had the same problem but after reading the answers to this post I solved it. Indeed, v1.6 might have a bug because the same files loaded in v1.5 work perfectly. 

As Alexander pointed out, the official link doesn't work but I found v.1.5 here:

http://www.softpedia.com/get/Science-CAD/Tracer-AR.shtml

It doesn't have the dmg or tgz versions, only exe and jar (/lib/tracer.jar) so since I'm running Mac OS X 10.9.3 I used the jar version and I had the BSP graph in about 2 minutes. 

Hope this makes it easier!

Irene

[Alfonsina Trento]

Thanks!!!!...

[Simey]

I was having the same issues with Tracer 1.6, but increased memory from the default of 1024M to 16GB and it now works. I increased memory by following these instructions.

-Brian

[Oscar Huanel]

Hi Miguel,
Im having the same problem with plotting BSP in tracer. I think its correct to increase the log parameters in the MCMC in order to reduce the sampling. But how much should we increase the log parameter? Im running 50000000 MCMC with log parameter 5000 (this log sampling number is the mean number that i have found in the literature) with 3 replicates, that match in logcombiner v182. How much would you advise me to increase the log parameter?
regard!

[Francois Cholette]

[Francois Cholette]

Hello BEAST users,

I also experienced this problem with Tracer v1.6, however I have no problems with v1.5

Thanks,

Frank

On Monday, January 13, 2014 at 12:39:30 PM UTC-6, Matt Mitchell wrote:

[Yachen Hu]

It's a memory issue of Java. Increasing the maximum size of the Java memory allocation pool (-Xmx option) should work. 

在 2014年1月14日星期二 UTC+8上午2:39:30，Matt Mitchell写道：

[Raphael Sieber]

Thanks a lot for the instructions above! 

Increasing the memory worked for me (Mac book pro, OSX 10.12.6) following this tutorial: http://www.beast2.org/increasing-memory-usage/

On Monday, 13 January 2014 19:39:30 UTC+1, Matt Mitchell wrote: