Exception in thread "main" java.lang.RuntimeException: Failed to Parse Tree number: 1

[Xiaojun928]

Hi,

Thanks for developing the fancy DiscoVista. I tested the example of frequency analysis and it generated results as expected (like relativeFreq.pdf and tree.pdf), which may suggest that DiscoVista was installed successfully.

Next, I tried to do the frequency analysis using my data (the species tree was constructed using iqtree based on concatenated alignment, and the gene tree each was constructed using iqtree based on individual gene alignment). The command is below: python2 $WS_HOME/DiscoVista/src/utils/discoVista.py -a annotation.txt -m 5 -p /share/home-user/xjwang/ILS/230501_diverse_samples/03_incongruence_vis/ -o /share/home-user/xjwang/ILS/230501_diverse_samples/03_incongruence_vis/DiscoVista_result -g C7

However, I cannot get the plots for my dataset. No useful information was found in the error.log (attached). I got error report in astral-job.log, which states

This is ASTRAL version 5.6.1
Gene trees are treated as unrooted
2116 trees read from estimated_gene_trees.tree
Scoring /share/home-user/xjwang/ILS/230501_diverse_samples/03_incongruence_vis/DiscoVista_result/main-hypo.tre
Scoring: 1 trees
Exception in thread "main" java.lang.RuntimeException: Failed to Parse Tree number: 1
        at phylonet.coalescent.CommandLine.readInputTrees(CommandLine.java:815)
        at phylonet.coalescent.CommandLine.runScore(CommandLine.java:551)
        at phylonet.coalescent.CommandLine.main(CommandLine.java:524)
Caused by: phylonet.tree.io.ParseException: ')' expected
        at phylonet.tree.io.NewickReader.readNode(NewickReader.java:405)
        at phylonet.tree.io.NewickReader.readNode(NewickReader.java:399)
        at phylonet.tree.io.NewickReader.readNode(NewickReader.java:399)
        at phylonet.tree.io.NewickReader.readNode(NewickReader.java:399)
        at phylonet.tree.io.NewickReader.readNode(NewickReader.java:399)
        at phylonet.tree.io.NewickReader.readNode(NewickReader.java:399)
        at phylonet.tree.io.NewickReader.readNode(NewickReader.java:399)
        at phylonet.tree.io.NewickReader.readTree(NewickReader.java:374)
        at phylonet.tree.io.NewickReader.readTree(NewickReader.java:95)
        at phylonet.coalescent.CommandLine.readInputTrees(CommandLine.java:782)
        ... 2 more

I compared the main-hypo.tre in the example and that of mine (attached), the difference is that all branch length of main-hypo.tre in the example is 1.0, while my branch length varies. Maybe this is not the cause. The file main-uncollapsed.tre in my case is empty. I am not sure how to deal with this exception, could you please give me some suggestions?

Best, Xiaojun

main-hypo.tre.txt

error.log