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TravisWheelerLab / NINJA

Nearly Infinite Neighbor Joining Application
MIT License
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Error: java.lang.ArrayIndexOutOfBoundsException: 10000 #43

Closed J-Calvelo closed 1 year ago

J-Calvelo commented 1 year ago

Hello. I'm having issues running Ninja with some alignments with the following error:

error building tree
10000
java.lang.ArrayIndexOutOfBoundsException: 10000
        at com.traviswheeler.ninja.SequenceFileReader.<init>(SequenceFileReader.java:93)
        at com.traviswheeler.ninja.TreeBuilderManager.doJob(TreeBuilderManager.java:170)
        at com.traviswheeler.ninja.Ninja.main(Ninja.java:68)
Tree string not generated for some unknown reason. Aborting.

What is the source of it? I'm ataching one of the files. Thanks

N0.HOG0005632_work_cds.txt

traviswheeler commented 1 year ago

I suppose you must be using the Java version found at https://wheelerlab.org/software/ninja/. Sadly, that implementation had a limit on the length of the MSA: 10,000 characters long. We haven't fixed the problem in the Java version. (And this C-version captured in this repo is slightly buggy, awaiting a bit more care) sorry