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chrismonit / SubRecon

SubRecon: Ancestral Reconstruction of Amino Acid Substitutions Along a Branch in a Phylogeny
Apache License 2.0
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java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: -1 after running #1

Open ghost opened 4 years ago

ghost commented 4 years ago

Good day. I am attempting to use SubRecon with a typical fasta file and a newick tree file. Upon running SubRecon with the following parameters

java -jar SubRecon.jar -s cluster_0.fasta -t rooted_tree_new.new -m jtt -k 4 -a 0.42 > out1.txt

the terminal gives

java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: -1 at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at subrecon.SubRecon.run(Unknown Source) at subrecon.SubRecon.main(Unknown Source) Caused by: java.lang.ArrayIndexOutOfBoundsException: -1 at pal.alignment.SimpleAlignment.getData(Unknown Source) at subrecon.molevo.AdvancedAlignmentAminoAcid.getStateBySequenceName(Unknown Source) at subrecon.recon.JointBranchReconstruction.downTreeMarginal(Unknown Source) at subrecon.recon.JointBranchReconstruction.downTreeMarginal(Unknown Source) at subrecon.recon.JointBranchReconstruction.downTreeMarginal(Unknown Source) at subrecon.recon.JointBranchReconstruction.recon(Unknown Source) at subrecon.recon.JointBranchReconstruction.call(Unknown Source) at subrecon.recon.JointBranchReconstruction.call(Unknown Source) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

My output file is also contains the following [HEADER] site ln[P(D|theta,alpha)] P(A=a,B=b|D,theta,alpha) ERROR: Site 1 ERROR: Site 2 ERROR: Site 3 ERROR: Site 4 ERROR: Site 5 ERROR: Site 6 ERROR: Site 7 ERROR: Site 8 ERROR: Site 9 ERROR: Site 10

chrismonit commented 4 years ago

Hi there, could you show/attach the alignment and tree files you are using? Without these it is difficult to work out the source of the problem

nagarnoopur commented 3 months ago

Hi I am facing the same issue with dataset. It would be really helpful if you can help in rectifying it.

The command/parameters given for the run are: java -jar SubRecon1.0.jar -s mcpSR3.fas -t mcpSR3_fin.raxml.bootstraps.tre -m wag -k 4 -a 0.5 > subrecon.out.txt

the output on terminal is:

java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 4
    at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
    at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
    at subrecon.SubRecon.run(Unknown Source)
    at subrecon.SubRecon.main(Unknown Source)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 4
    at subrecon.utils.Utils.getLnSumComponents(Unknown Source)
    at subrecon.recon.JointBranchReconstruction.recon(Unknown Source)
    at subrecon.recon.JointBranchReconstruction.call(Unknown Source)
    at subrecon.recon.JointBranchReconstruction.call(Unknown Source)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
    at java.base/java.lang.Thread.run(Thread.java:829)
java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 4
    at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
    at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
    at subrecon.SubRecon.run(Unknown Source)
    at subrecon.SubRecon.main(Unknown Source)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 4
    at subrecon.utils.Utils.getLnSumComponents(Unknown Source)
    at subrecon.recon.JointBranchReconstruction.recon(Unknown Source)
    at subrecon.recon.JointBranchReconstruction.call(Unknown Source)
    at subrecon.recon.JointBranchReconstruction.call(Unknown Source)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
    at java.base/java.lang.Thread.run(Thread.java:829)
java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 4
    at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
    at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
    at subrecon.SubRecon.run(Unknown Source)
    at subrecon.SubRecon.main(Unknown Source)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 4
    at subrecon.utils.Utils.getLnSumComponents(Unknown Source)
    at subrecon.recon.JointBranchReconstruction.recon(Unknown Source)
    at subrecon.recon.JointBranchReconstruction.call(Unknown Source)
    at subrecon.recon.JointBranchReconstruction.call(Unknown Source)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
    at java.base/java.lang.Thread.run(Thread.java:829)

The result and input files (zip file) are as follows: subrecon.out.txt mcp3SR_.zip