Unable to import alignment file into Beauti 2

[Antonio Galán Sánchez]

Hi there,

I am trying to import my Nexus file into Beauti 2 in order to create the xml file. The problem is that the file is never imported (65 MB, 554 terminals, UCE genomic data). The executable recognises the alignment and even asks what type of data it is, afterwards, it just remains open and does nothing. Could you give me any advice on this? Do you have ideas of what it could be? I am working from a laptop (16 GB RAM, 500 GB SSD).

Many thanks,

Antonio

[William Fernando Chaparro-Pico]

Hi Antonio,

I’m not an expert, but I’ve been using BEAST for a while. I encountered a similar issue during my initial attempts, and it turned out to be related to the file format. I recommend carefully reviewing the format of your file, particularly the beginning and the end.

This helped me because, in one of my files, the format wasn’t correct.

Hope this helps! Saludos 

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[Sydney Decker]

I am having this same issue (20 MB; 71 tips, RADseq data). I am not sure that it is a file formatting issue as it reads in fine to Beauti 1, just not Beauti 2, unless there are differences between the two that I'm unaware of when it comes to the nexus format. The program hangs on an attempt to load the data for several hours without throwing any errors. I have tried it on a mac OS (8 gb RAM), a windows machine (16 gb RAM), and hpc (192 gb RAM) and it never finishes importing the data. 

Sydney Decker

[Mamerto Brina]

Hi  Antonio!

I have also experienced this problem but mine is a FASTA file (118Mb). When I tried to import it to BEAUti, it recognized the alignment, but it didn't really open the file; it just loaded infinitely. What I did was allocate more memory to BEAUti using a command line. 

java -Xss1g -Xmx16g -cp "path\to\BEAST\lib\launcher.jar" beast.app.beauti.BeautiLauncher.

The Xss is the minimum allocation and the Xmx is the maximum allocation, implying that your device can allocate 1gb to 16gb of memory to BEAUti. If you prompt this in your command window, this will open BEAUti and then try importing your sequences. I hope this helps.

[Dan S]

Hi Mamerto,

I'm having the same issue as well and tried using your java line above but it didn't work for me. 

I have the correct path to the jar file but I'm stuck on the 'beast.app.beauti.BeautiLauncher' part. 

I get the return error "Could not find or load main class beast.app.beauti.BeautiLauncher"

Dan

[Mamerto Jr Brina]

Hi Dan, 

I have tried it again on my end and the command line works well for me. Is it possible to know the version you are using? And also in my post, there shouldn't be a dot "." 

java -Xss1g -Xmx16g -cp "path\to\BEAST\lib\launcher.jar" beast.app.beauti.BeautiLauncher

Best Ragards,

Mamerto

[Dan S]

Hi Mamerto,

I was able to borrow a colleague's 132g RAM Linux machine and bump up the Xmx to 120g and the program still throwing up error messages to either force quit or wait. My alignment file is 220Mb

Dan

[Mamerto Brina]

Hi Dan. 

Wow, that's a very big alignment file. So far, based on previous posts here, that command line I gave should work. I can't see where the problem is considering that you have already allocated 120gb. What are the errors you encounter? Is your alignment file a FASTA file?  Also, what BEAUti version are you using? 

Best regards,

Merto