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smirarab / ASTRAL

Accurate Species TRee ALgorithm
Apache License 2.0
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Error message regarding gene trees input file format #94

Open abcbot123 opened 4 months ago

abcbot123 commented 4 months ago

Hi, I'm using ASTRAL tool to get the species tree using gene trees. I have created the gene trees and the bootstrap gene trees using RAxML. This is the code I have used in ASTRAL. java -jar Astral/astral.5.7.1.jar -i genetree_combine -o astral_speciestree -b bootstrap_combine -r 100

This is the error I got, ================== ASTRAL =====================

This is ASTRAL version 5.7.1 Gene trees are treated as unrooted Exception in thread "main" java.lang.RuntimeException: Failed to Parse Tree number: 1 at phylonet.coalescent.CommandLine.readInputTrees(CommandLine.java:835) at phylonet.coalescent.CommandLine.readOptions(CommandLine.java:328) at phylonet.coalescent.CommandLine.main(CommandLine.java:513) 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:802) ... 2 more Is this error regarding my input file format? But I couldn't figure out any format errors in my input files. I have look for the test_data in the tool itself and seems my data is in the same Newick format. Could you please help me to figure out what's the formatting error in my input files.

Thanks so much!

biocyberman commented 4 months ago

I got the same error and figured out that it is because I have '/' characters in the identifiers of the entries in the newick tree files. After replacing them with _, it works. @smirarab

smirarab commented 4 months ago

It's hard for me to know what is going wrong without seeing the input. It may be an unsupported character, as @biocyberman mentioned. But it also could be the format of the bootstrap_combine files is wrong. Please see https://github.com/smirarab/ASTRAL/blob/master/astral-tutorial.md#multi-locus-bootstrapping Make sure you -b file inclues the path to newick files, as mentioned in the tutorial.