BEAUti 2.1 Import Alignment problem

[andrew...@gmail.com]

Hello,

I have a large dataset (hundreds of genes, >1 million total bp) which I have been attempting to analyze with *BEAST (yes, I know it might be too large, but there's no way to know for sure without exploring the possibility).

In BEAUti v1.8 I had no issues dealing with this dataset. I could import the dataset as a single .nex file with a block at the bottom listing the coordinates of each gene, or I could import hundreds of individual .nex files, all within a matter of seconds. I have been able to create XML files for exploratory *BEAST analyses without issue (running the analyses is another matter entirely).

However, it was suggested to me that BEAST 2 would have major advantages as I attempt my analyses, so I downloaded and installed the BEAST 2.1.0 package yesterday. Unfortunately, I am stuck at the first step.

I can not import all of my gene alignments into BEAUti 2.1.0., at least in any reasonable time frame. I don't get any errors as others have reported here (mostly for previous versions of BEAUti), I just get a spinning wheel of frustration and 80-100% CPU usage (dual-core Windows 7) for up to 2 hours, which is the most patience I have had so far.

This happens if I try to import either my single file .nex alignment with the gene coordinate block at the bottom or if I try to import individual alignments.

Well, I should back up and say that if I select only 1 or 2 individual gene alignments, they import into BEAUti without issue, although it still takes several minutes. If I select another 1 or 2 alignments, they will also import after several minutes. If I attempt to select 10-20 .nex files they will show up after 30+ minutes. However, I need to import hundreds of alignments, so this is clearly problematic.

I have attempted to re-download and re-install the software with no change in behavior. I also downloaded the BEAST 2.1.0 for Mac and installed it on an iMac. In that case, I was able to import all alignments (still took several minutes rather than several seconds on v1.8.0), but BEAUti locked up repeatedly while I was trying to proceed through the steps of setting up my XML file.

Are these known issues (especially the issue I'm having on my Windows machine)? Is there some sort of memory restriction/leak in BEAUti 2.1.0.? Again, these exact same .nex files will import into BEAUti 1.8 on the same computer in a matter of seconds.

Is anyone using BEAUti 2.1.0 without issue, for large numbers of genes?

Thanks,
Andy

[Alexei Drummond]

Dear Andy,

We would be happy to look at how to fix this if you can send us some example data. Probably half of what you are running will be enough to demonstrate the problem. I can then profile the program and see where all the time is being wasted.

Cheers

Alexei

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[andrew...@gmail.com]

Thanks Alexei,

I have been in communication with Joseph Heled regarding the issue and he has passed along my dataset to Remco, so I think we're making progress.

Thanks,
Andy

[Remco Bouckaert]

These problems should now be fixed in version 2.1.1, available from http://www.beast2.org/.

Best,

Remco