Using maskFileDir in Scripture

[riccardo.aiesecigliano]

Hello,
I am trying to use Scripture to analyse RNAseq data from Arabidopsis. My idea is to first run Scripture on the Arabidopsis gtf file to obtain the expression values of the already annotated transcripts. Then I would lunch Scripture again providing the Arabidopsis genome as "mask" to identify only new splicing variants or new transcripts.
While the first step works well, I am having problems to provide the masked file to Scripture. I created a new directory where I put the gtf file. I have tried to put the gtf of the whole genome and to split it into different chromosomes but each time I have the following message error:

Using Version VPaperR3
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1
at broad.pda.annotation.BEDFileParser.loadAlignmentData(BEDFileParser.java:1077)
at broad.pda.annotation.BEDFileParser.loadAlignmentData(BEDFileParser.java:1352)
at broad.pda.seq.segmentation.ContinuousDataAlignmentModel.parseMaskFiles(ContinuousDataAlignmentModel.java:261)
at broad.pda.seq.segmentation.ContinuousDataAlignmentModel.main(ContinuousDataAlignmentModel.java:2254)

I have also tried other files than gtf (gff, bed) but it did not work.
Can anybody help me?
The other possibility would be to use Scripture in its default mode, however in this case I don't know how to match the transcripts with the already annotated ones. Any suggestions?

Thank you
Riccardo