Hi,
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
what is going wrong??
Thanx
Hanneke
1 Comment
Micha Sammeth
Dear Hanneke,
I created an issue ticket from your observation:
http://sammeth.net/jira/browse/BARNA-365
The error occurs when the splicing graph is constructed from the annotation, so I guess that something in the annotation file is not as expected. If possible, could you point us where to find the annotation that provokes the behavior, and please also provide us with the flux version you are using.
Thanks
Micha