Scripture-v3.1 error: Java exception

[cnash2]

Hi all,

I'm trying to run the latest version of scripture. I used the following command,

java -jar ~/programs/Scripture-v3.1.jar -task reconstruct -alignment VMP-sorted.bam -genome rn6_dna.fa -out VMP-scripture

This in order to use Scripture on the whole genome. However, I get the following error part way through the run.

Intron intention Filter: 0.95
Premature Assembly Filter: 0.2
Splice junction Filter :
Number of spliced reads : 3.0
Percentage of total spliced reads: 0.05
Alpha for single exon assemblies : 0.01
INFO [2016-09-30 15:16:54,499] [BuildScriptureCoordinateSpace.java:233] [main] Reference name: 1
INFO [2016-09-30 15:16:54,499] [JCSAlignmentModel.java:249] [main] Computing global stats for bam file /Users/clairenash/Documents/Temp-4-algos/VMP-sorted.bam.PairedEnd.bam...
Exception in thread "main" java.lang.NullPointerException
at nextgen.core.annotation.BasicAnnotation.overlaps(BasicAnnotation.java:399)
at nextgen.core.annotation.AbstractAnnotation.overlaps(AbstractAnnotation.java:155)
at nextgen.core.annotation.AbstractAnnotation.overlaps(AbstractAnnotation.java:151)
at nextgen.core.model.JCSAlignmentModel.overlapsWindow(JCSAlignmentModel.java:594)
at nextgen.core.model.JCSAlignmentModel.access$0(JCSAlignmentModel.java:588)
at nextgen.core.model.JCSAlignmentModel$FilteredIterator.getNext(JCSAlignmentModel.java:841)
at nextgen.core.model.JCSAlignmentModel$FilteredIterator.hasNext(JCSAlignmentModel.java:817)
at nextgen.core.model.JCSAlignmentModel$FilteredIterator.<init>(JCSAlignmentModel.java:783)
at broad.core.datastructures.JCSCache.query(JCSCache.java:267)
at nextgen.core.model.JCSAlignmentModel.getOverlappingReadCounts(JCSAlignmentModel.java:525)
at nextgen.core.model.JCSAlignmentModel.getReferenceSequenceCount(JCSAlignmentModel.java:1194)
at nextgen.core.model.JCSAlignmentModel.getReferenceSequenceCounts(JCSAlignmentModel.java:1186)
at nextgen.core.model.JCSAlignmentModel.computeGlobalStats(JCSAlignmentModel.java:251)
at nextgen.core.model.JCSAlignmentModel.getRefSequenceLambda(JCSAlignmentModel.java:1174)
at nextgen.core.scripture.BuildScriptureCoordinateSpace.assemble(BuildScriptureCoordinateSpace.java:234)
at nextgen.core.scripture.BuildScriptureCoordinateSpace.<init>(BuildScriptureCoordinateSpace.java:131)
at nextgen.core.scripture.BuildScriptureCoordinateSpace.main(BuildScriptureCoordinateSpace.java:2685)

I tried searching for this problem on this forum and others and although others have had something similar, it's not exactly the same error I'm getting. Does anyone have any ideas on what the problem is?

Thanks in advance!