NullPointerException with crossvalidate

[iimog]

I'm trying to crossvalidate my training set with the latest classifier version from github (2014-11-24) on 64 bit Ubuntu 14.04 with java version "1.7.0_65" (OpenJDK). Unfortunately I get a NullPointerException each time I try:

java -Xmx1g -jar ~/software/RDPTools/classifier.jar crossvalidate -o minimal.txt -s minimal.fa -t minimal.tax
164458368
298507601
298507603
164458369
298507604
Exception in thread "main" java.lang.NullPointerException
    at edu.msu.cme.rdp.classifier.train.validation.HierarchyTree.getWordOccurrence(HierarchyTree.java:289)
    at edu.msu.cme.rdp.classifier.train.validation.NBClassifier.calculateProb(NBClassifier.java:107)
    at edu.msu.cme.rdp.classifier.train.validation.NBClassifier.assignClass(NBClassifier.java:68)
    at edu.msu.cme.rdp.classifier.train.validation.DecisionMaker.getBestClasspath(DecisionMaker.java:42)
    at edu.msu.cme.rdp.classifier.train.validation.crossvalidate.CrossValidate.runTest(CrossValidate.java:117)
    at edu.msu.cme.rdp.classifier.train.validation.crossvalidate.CrossValidateMain.main(CrossValidateMain.java:121)
    at edu.msu.cme.rdp.classifier.cli.ClassifierMain.main(ClassifierMain.java:77)

For testing purpose I attach my minimal.fa and minimal.tax below. They work fine with loot, taxa-sim and train.
minimal.fa: https://gist.github.com/iimog/aa2ce23ab6f4d63cfa2b
minimal.tax: https://gist.github.com/iimog/4ea791d8be7f51073c46

Any help would be highly regarded.

Thanks in advance,
Markus Ankenbrand

[rdpstaffmsu]

Hello, we are sorry for the late reply there have been some issues on our notifications! We are currently working on troubleshooting this and will hopefully have an answer for you soon.

[rdpstaffmsu]

Hello, we have updated our classifier to resolve the problem you were having, if you could please update your version and try it again. Let us know if you have any other issues!

[iimog]

Thank you very much for solving the problem. Crossvalidate works now also on my full dataset. However if I set --rdmRank to species, family, order, class, phylum, kingdom or rootrank I get only NaN in the output. And for "--rdmRank genus" I get another NullPointerException:

java -Xmx1g -jar ~/software/RDPTools/classifier.jar crossvalidate -o minimal.genus.txt -s minimal.fa -t minimal.tax -r genus
Exception in thread "main" java.lang.NullPointerException
    at java.util.AbstractCollection.addAll(AbstractCollection.java:341)
    at edu.msu.cme.rdp.classifier.train.validation.crossvalidate.RdmSelectTaxon.randomSelectTaxon(RdmSelectTaxon.java:92)
    at edu.msu.cme.rdp.classifier.train.validation.crossvalidate.CrossValidate.runTest(CrossValidate.java:65)
    at edu.msu.cme.rdp.classifier.train.validation.crossvalidate.CrossValidateMain.main(CrossValidateMain.java:121)
    at edu.msu.cme.rdp.classifier.cli.ClassifierMain.main(ClassifierMain.java:77)

This applies to my full data set as well as the minimal example provided above.
Thank you very much for solving the first problem.

Best wishes,
Markus