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lonelyjoeparker / befi-bats-gui

Java software to analyse phylogeny-trait correlations in discrete traits, accounting for phylogenetic uncertainty via posterior sampling.
http://science.lonelyjoeparker.com
GNU General Public License v3.0
8 stars 3 forks source link

BaTS running Indefinitely #19

Open wbender1 opened 1 year ago

wbender1 commented 1 year ago

We are currently trying to use Single BaTS to produce a single treefile that is analyzing 2002 trees with 2 states. We have also tried an increased number of trees which has been unsuccessful. Our attempts were made using a linux based computer cluster to run the program and it has failed to run within our 15-day time limit. Additionally, our dataset is rather small and less than 200 sequences. The program has never quit out with any errors but simply never ends.

Any help or information would be greatly appreciated!

sky80830 commented 3 months ago

Was there any guidance for this issue?

lonelyjoeparker commented 3 months ago

Hi both @sky80830 @wbender1

Apologies, this project isn't really active at the moment so had notifications off. Have enabled them now.

Can you let me know:

It would also be ideal to attach the trees file in question if you're comfortable doing that. If it's too big to attach, that alone may be the problem so please include the header (states block and taxIDs) plus first 100 or so trees, as well as any screenshots or stack trace.

Also, this probably goes without saying but just to check - have you managed to successfully run the example files to completion?

lonelyjoeparker commented 3 months ago

For examples see https://github.com/lonelyjoeparker/befi-bats-gui/tree/master/examples and #16

sky80830 commented 2 months ago

@lonelyjoeparker JVM version is: openjdk 11.0.22 2024-01-16 OpenJDK Runtime Environment (build 11.0.22+7-post-Ubuntu-0ubuntu222.04.1) OpenJDK 64-Bit Server VM (build 11.0.22+7-post-Ubuntu-0ubuntu222.04.1, mixed mode, sharing)

OS: ubuntu linux running as WSL2 in Win11. (Home pc and some of the other programs have issue on java. Hence going with this)

32Gb of Ram installed; 16g assigned with: java -jar -Xmx16g BaTS_beta.jar single MCCRocahepevirus705_Bats2.trees 100 31 -v

I'm on an AMD Ryzen 9 3900X 12 core processor.

The file we try to run is too big to attach (210648 kB). If wanted we can arrange a file transfer somehow.