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 'fundef27' 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.
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 'fundef27' 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