java.lang.NullPointerException

[mgandal]

I have been trying to run the MultipleAlignment module but continue to get an error.

Here is the call
java -jar ~/bin2/OMTools/OMTools.jar PairwiseAlignment --optmapin ALL_chr17q21.cmap --optresin ALL_chr17q21.oma --output test

Here is the error:
Reference: ALL_chr17q21 Exception in thread "main" java.lang.NullPointerException at aldenjava.opticalmapping.data.mappingresult.OptMapResultNode.getPotentiallyMappedRegion(OptMapResultNode.java:993) at aldenjava.opticalmapping.data.mappingresult.OptMapResultNode.getPotentiallyMappedRegion(OptMapResultNode.java:1004) at aldenjava.opticalmapping.mapper.Mapper.setParameters(Mapper.java:108) at aldenjava.opticalmapping.mapper.omblastmapper.OMBlastMapper.setParameters(OMBlastMapper.java:39) at aldenjava.opticalmapping.mapper.multithread.MultiThreadMapper.setParameters(MultiThreadMapper.java:78) at aldenjava.opticalmapping.mapper.PairwiseAlignment.main(PairwiseAlignment.java:58) at aldenjava.opticalmapping.OMTools.main(OMTools.java:201)

I can view everything fine with OMView and the alignment worked fine with OMBlastMapper. I get the same error with MultipleAlignment