error index out of bounds fluxcapacitator

I found this error: [ERROR] java.lang.ArrayIndexOutOfBoundsException: -1

The command line is as follows:

flux-capacitor --threads 4 -a /project/devel/rna_pipeline/data/annotations/hg/gencode_v12.gtf -i ../bams/CF_10_CGATGT_L005_R1_001.bam -r -o CF_10_gencode.gtf

Flux-Capacitor v1.2.2-SNAPSHOT (Flux Library: 1.19-SNAPSHOT)

[PRE-CHECK] I am checking availability of the required lpsolve JNI libs.
[PRE-CHECK] * successfully loaded lpsolve JNI (version 5.5,release 0,build 14)

Scanning annotation file Checking GTF ********** OK (00:00:14)
scanning [WARN] skipped line chr1 HAVANA gene 11869 14412 . + . transcript_id "ENSG00000223972.4"; havana_gene "OTTHUMG00000000961.2"; level "2"; transcript_name "DDX11L1"; gene_name "DDX11L1"; transcript_status "KNOWN"; gene_id "ENSG00000223972.4"; gene_type "pseudogene"; transcript_type "pseudogene"; gene_status "KNOWN";
OK (00:01:12)
[WARN] Skipped 724375 lines.
[INFO] 45013 loci, 183086 transcripts, 1188378 exons.
OK (00:01:12)
Scanning mapping file OK (00:02:42)
[WARN] Skipped 148178 lines.
[INFO] 21330986 reads, 63678600 mappings: R-factor 2.9852629
[INFO] 62707765 entire, 970835 split mappings (0.1524586%)
[INFO] Read descriptor seems OK
OK (00:02:42)
[INFO] Annotation and mapping input checked
[HEHO] We are set, so let's go!
[ANNOTATION_FILE] /project/devel/rna_pipeline/data/annotations/hg/gencode_v12.gtf
[MAPPING_FILE] /project/devel/aesteve/capacitor-tests/quantifications/../bams/CF_10_CGATGT_L005_R1_001.bam
[READ_DESCRIPTOR]

/

[1,2]
[SORT_IN_RAM] true
[TMP_DIR] /scratch_tmp
[STDOUT_FILE] /project/devel/aesteve/capacitor-tests/quantifications/CF_10_gencode.gtf
[INFO] mate pairing information considered

[LEARN] Scanning the input and getting the attributes.
profiling [WARN] skipped line chr1 HAVANA gene 11869 14412 . + . transcript_id "ENSG00000223972.4"; havana_gene "OTTHUMG00000000961.2"; level "2"; transcript_name "DDX11L1"; gene_name "DDX11L1"; transcript_status "KNOWN"; gene_id "ENSG00000223972.4"; gene_type "pseudogene"; transcript_type "pseudogene"; gene_status "KNOWN";
OK (00:03:55)
first round finished .. took 235 sec.

24662 single transcript loci
63678600 mappings in file
20112686 mappings fall in single transcript loci
16493180 mappings in annotation-mapped pairs
65,121 min/max read length

[SOLVE] Deconvolving reads of overlapping transcripts.
decomposing [WARN] skipped line chr1 HAVANA gene 11869 14412 . + . transcript_id "ENSG00000223972.4"; havana_gene "OTTHUMG00000000961.2"; level "2"; transcript_name "DDX11L1"; gene_name "DDX11L1"; transcript_status "KNOWN"; gene_id "ENSG00000223972.4"; gene_type "pseudogene"; transcript_type "pseudogene"; gene_status "KNOWN";
[ERROR] Error while iterating loci:
java.lang.ArrayIndexOutOfBoundsException: -1
at barna.flux.capacitor.graph.AnnotationMapper.getEdge2(AnnotationMapper.java:612)
at barna.flux.capacitor.graph.AnnotationMapper.map(AnnotationMapper.java:383)
at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.run(FluxCapacitor.java:219)
at barna.flux.capacitor.reconstruction.FluxCapacitor.solve(FluxCapacitor.java:2152)
at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2686)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1750)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:76)
at barna.commons.launcher.Flux.main(Flux.java:197)

[ERROR] java.lang.ArrayIndexOutOfBoundsException: -1