Beauti 2.2.1 won't load alignment

[Weston Testo]

Hi - 

I am working with a relatively large dataset (~3400 taxa, 7400 sites, Nexus file 34.5MB) and am having difficulty loading my data into Beauti. I am using v. 2.2.1 on a Mac (OS X, 2.7GHz, 4GB memory). The problem is when I attempt to import the alignment - the program looks to get hung up and fail to load (blue loading symbol hangs there indefinitely). Checking the activity monitor on the computer, it looks that when the allocated memory gets to ca. 1.2GB, the program crashes. Allocating more memory to Java (I am using v. 8) does not resolve this issue, which makes me wonder if this is limited to the program itself.

I have attempted to load this alignment on several computers - all seem to have this problem. I am able to load the alignment using the same computer using Beauti 1.8.2, but the interface freezes when I attempt to set node calibration priors (once one is set, the program inevitably freezes). 

Is this a hard limit on Beauti's end? Or is it more likely on my computer's end? 

Let me know if I can provide any more information that is needed.

Thank you.

Wes

[Andrey Yurchenko]

The same problem with 13 taxa

четверг, 30 апреля 2015 г., 18:48:10 UTC+4 пользователь Weston Testo написал:

[Remco Bouckaert]

Hi Andrey,

There is no explicit limit on what you can load, if memory is available. I tried loading a large nexus file from freebase (M22169 which is just over 20MB) and it loads in seconds.

Perhaps there is partition information in the file that causes BEAUti to create a lot of partitions, which may take a bit of time. To test this, you could remove the partition information and see whether it loads.

Cheers,

Remco

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