Continuous errors with classifier subcommands - problem in tax file?

[anniebtp]

Hi there

We have been struggling a while with errors when running taxa-sim and loot as subcommands in classifier with our own created database and tax file (using the methods of [https://github.com/iimog/meta-barcoding-dual-indexing]).

The most recent error we are getting is:

Exception in thread "main" java.lang.IllegalArgumentException:
The taxID for ancestor 'f__undef__27' of sequence '27526738' at depth '5' with parent id '272' is not found!
at edu.msu.cme.rdp.classifier.train.validation.TreeFactory.getTaxonomy(TreeFactory.java:213)
at edu.msu.cme.rdp.classifier.train.validation.TreeFactory.addSequence(TreeFactory.java:167)
at edu.msu.cme.rdp.classifier.train.validation.TreeFactory.addSequence(TreeFactory.java:149)
at edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain.createTree(LeaveOneOutTesterMain.java:109)
at edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain.(LeaveOneOutTesterMain.java:79)
at edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain.main(LeaveOneOutTesterMain.java:186)
at edu.msu.cme.rdp.classifier.cli.ClassifierMain.main(ClassifierMain.java:75)

There are no weird characters like "*" or anything in the file (saw it was a problem with someone else), everything seems fine at first glance. I am not a bioinformaticist though and our senior bioinformaticist is swamped. What could this error be indicating?

Will it be helpful to share a shortened version of the sequence file and the tax file? Or the full files?
Any help will be greatly appreciated, we are at wits' end.

Thanks a lot,
Annie