Error message running GeMoMa

I am trying to run GeMoMa for gene annotation using RNA-seq evidence.

java -jar -Xms25G -Xmx50G GeMoMa-1.6.1.jar CLI GeMoMaPipeline t=target.fasta s=own a=ref-annotation.gff  g=ref.fa outdir=test r=MAPPED ERE.s=FR_UNSTRANDED ERE.m=target-accepted_hits.bam  ERE.v=SILENT ERE.c=true tblastn=true Extractor.p=true Extractor.r=true Extractor.s=true Extractor.f=true AnnotationFinalizer.u=YES AnnotationFinalizer.r=NO p=true pc=true pgr=true

However, I am getting this error message:

> starting extractor for species 0

> java.lang.StringIndexOutOfBoundsException: String index out of range:
> -1    at java.lang.String.charAt(String.java:658)     at projects.gemoma.Extractor.transcript(Extractor.java:835)     at
> projects.gemoma.Extractor.extract(Extractor.java:667)     at
> projects.gemoma.Extractor.run(Extractor.java:142)     at
> projects.gemoma.GeMoMaPipeline$JExtractorAndSplit.doJob(GeMoMaPipeline.java:1166)
>   at
> projects.gemoma.GeMoMaPipeline$FlaggedRunnable.run(GeMoMaPipeline.java:937)
>   at
> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
>   at java.util.concurrent.FutureTask.run(FutureTask.java:266)     at
> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
>   at java.util.concurrent.FutureTask.run(FutureTask.java:266)     at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>   at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>   at java.lang.Thread.run(Thread.java:748)
> 
> 
> Statistics: Job   WAITING RUNNING INTERRUPTED FAILED  SUCCEEDED
> --------------------------------------------------------- MakeBlastDB 0   0   0   0   1 EREAndFill    1   0   0   0   0
> 
> ExtractorAndSplit 0   0   0   1   0
> 
> 2 jobs did not finish as expected. Please check the output carefully.
> Did not delete temporary files allowing to debug.
> 
> Elapsed time: 15 seconds  (0h 0m 15s) Exception in thread "main"
> java.lang.RuntimeException: Did not finish as intended. String index
> out of range: -1  at java.lang.String.charAt(String.java:658)     at
> projects.gemoma.Extractor.transcript(Extractor.java:835)  at
> projects.gemoma.Extractor.extract(Extractor.java:667)     at
> projects.gemoma.Extractor.run(Extractor.java:142)     at
> projects.gemoma.GeMoMaPipeline$JExtractorAndSplit.doJob(GeMoMaPipeline.java:1166)
>   at projects.gemoma.GeMoMaPipeline$FlaggedRunnable.run(GeMoMaPipeline.java:937)
>   at
> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
>   at java.util.concurrent.FutureTask.run(FutureTask.java:266)     at
> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
>   at java.util.concurrent.FutureTask.run(FutureTask.java:266)     at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>   at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>   at java.lang.Thread.run(Thread.java:748)

I think I’ve tried everything I know. Does anyone could please help me?