I am running 64-bit Ubuntu 14.04 and using java 1.7.0_79. I am running Haploview (v4.2) from the command line using the following;

java -jar /usr/bin/Haploview.jar -n -hapmapDownload -chromosome 17 -startpos 25545 -endpos 25588 -aggressiveTagging -panel CEU -release 27 -captureAlleles gene.captureAlleles

where gene.captureAlleles is a simple text file with one SNP per row. If I run this same command without the -captureAlleles gene.captureAlleles flag, all is well. I get the .TAGS and .TESTS files. However, if I run the full command (as above) I get the following error:

Downloading chromosome 17, analysis panel CEU, 25545..25588 from HapMap release 27.

Using capture alleles file: gene.captureAlleles
Starting tagging.
Exception in thread "Thread-0" java.lang.NullPointerException
    at edu.mit.wi.tagger.Tagger.peelBack(Tagger.java:422)
    at edu.mit.wi.tagger.Tagger.findTags(Tagger.java:311)
    at edu.mit.wi.haploview.tagger.TaggerController$TagThread.run(TaggerController.java:166)

I have checked that all of the SNPs included in the capture alleles file are present within these coordinates, and the are. It seems to be a thread issue - which is beyond my experience. Any help would be appreciated.