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lonelyjoeparker / qmul-genome-convergence-pipeline

API and binaries for phylogenomic analyses, particularly comparison of input trees/alignments (CONTEXT) and detecting genomic convergence
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Training binary fails to call external libs #18

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Training binaries distributed with KQT-4.zip

BasicAlignmentStats and GeneralConvergenceRunnerXML (xml init) both run

But GeneralConvergenceRunnerXML (main job) fails on external call (nw_utils):

/pamlTest/training_KQT4/binaries/nw_prune 
/pamlTest/training_KQT4/input.short.tre  DASYPUS MONODELPHIS SOREX VICUGNA 

attempting command /pamlTest/training_KQT4/binaries/nw_prune 
/pamlTest/training_KQT4/input.short.tre  DASYPUS MONODELPHIS SOREX VICUGNA 
done with output
error:
e0 dyld: Library not loaded: /usr/local/lib/libnw.0.dylib
e1   Referenced from: /pamlTest/training_KQT4/binaries/nw_prune
e2   Reason: image not found
done
Exception in thread "main" java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 0
    at uk.ac.qmul.sbcs.evolution.convergence.NewickTreeRepresentation.<init>(NewickTreeRepresentation.java:106)
    at uk.ac.qmul.sbcs.evolution.convergence.handlers.NewickUtilitiesHandler.pruneTaxa(NewickUtilitiesHandler.java:51)
    at uk.ac.qmul.sbcs.evolution.convergence.analyses.SiteSpecificLikelihoodSupportAnalysis.pruneTaxa(SiteSpecificLikelihoodSupportAnalysis.java:981)
    at uk.ac.qmul.sbcs.evolution.convergence.analyses.SiteSpecificLikelihoodSupportAnalysis.pruneInputTrees(SiteSpecificLikelihoodSupportAnalysis.java:494)
    at uk.ac.qmul.sbcs.evolution.convergence.analyses.SiteSpecificLikelihoodSupportAnalysis.run(SiteSpecificLikelihoodSupportAnalysis.java:269)
    at uk.ac.qmul.sbcs.evolution.convergence.runners.GeneralCongruenceRunnerXML.main(GeneralCongruenceRunnerXML.java:100)
    ... 5 more

Original issue reported on code.google.com by seb...@me.com on 29 Aug 2013 at 4:02