Error during construction of splicing graph

I just run Flux Capacitor

using parameter.txt:

ANNOTATION_FILE HoSa_build37.2_Genes_genes.gtf
COUNT_ELEMENTS [SPLICE_JUNCTIONS, INTRONS]
ANNOTATION_MAPPING AUTO

./flux-capacitor -p parameter.txt -i control.sorted.bam -o control.fluxcapacitor.gtf &

My outputfile contains only 303 lines, and then I got the following error (after about half an hour):

[WARN] Further collapsed transcripts are sent at debug verbosity level.
[ERROR] Error while iterating loci:
java.lang.ArrayIndexOutOfBoundsException: 0
at barna.model.splicegraph.SplicingGraph.constructGraph(SplicingGraph.java:1241)
at barna.flux.capacitor.graph.AnnotationMapper.<init>(AnnotationMapper.java:141)
at barna.flux.capacitor.graph.AnnotationMapper.<init>(AnnotationMapper.java:131)
at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.call(FluxCapacitor.java:1041)
at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2541)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1782)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:73)
at barna.commons.launcher.Flux.main(Flux.java:197)

[ERROR] java.lang.ArrayIndexOutOfBoundsException: 0
java.lang.RuntimeException: java.lang.ArrayIndexOutOfBoundsException: 0
at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2591)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1782)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:73)
at barna.commons.launcher.Flux.main(Flux.java:197)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 0
at barna.model.splicegraph.SplicingGraph.constructGraph(SplicingGraph.java:1241)
at barna.flux.capacitor.graph.AnnotationMapper.<init>(AnnotationMapper.java:141)
at barna.flux.capacitor.graph.AnnotationMapper.<init>(AnnotationMapper.java:131)
at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.call(FluxCapacitor.java:1041)
at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2541)
... 3 more