NullPointerException while iterating loci in BAM files

[ERROR] Error while iterating loci:
java.lang.NullPointerException
        at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.learn(FluxCapacitor.java:857)
        at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.run(FluxCapacitor.java:242)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.solve(FluxCapacitor.java:2175)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2707)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.getProfile(FluxCapacitor.java:2223)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1757)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:76)
        at barna.commons.launcher.Flux.main(Flux.java:197)
java.lang.RuntimeException: java.lang.NullPointerException
        at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2760)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.getProfile(FluxCapacitor.java:2223)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1757)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:76)
        at barna.commons.launcher.Flux.main(Flux.java:197)
Caused by: java.lang.NullPointerException
        at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.learn(FluxCapacitor.java:857)
        at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.run(FluxCapacitor.java:242)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.solve(FluxCapacitor.java:2175)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2707)
        ... 4 more
[FATAL] Error occured during scanning
        java.lang.NullPointerException

[COUNT] Counting reads to the following elements: splice junctions, all-intronic regions.

[SOLVE] Deconvolving reads of overlapping transcripts.
        decomposing  [WARN] skipped line 1      HAVANA  gene    317811  328455  .       +       .       transcript_id "ENSG00000240876.1"; havana_gene "OTTHUMG00000156972.1"; level "2"; transcript_name "RP4-669L17.11"; gene_name "RP4-669L17.11"; transcript_status "NOVEL"; gene_id "ENSG00000240876.1"; gene_type "processed_transcript"; transcript_type "processed_transcript"; gene_status "NOVEL";
[WARN] Error in read ID: could not parse read identifier D0KTLACXX120207:4:1301:12261:69282
[ERROR] Error while iterating loci:
java.lang.NullPointerException
        at barna.io.sam.SAMMappingIterator.getMates(SAMMappingIterator.java:101)
        at barna.flux.capacitor.graph.AnnotationMapper.map(AnnotationMapper.java:373)
        at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.run(FluxCapacitor.java:219)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.solve(FluxCapacitor.java:2175)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2709)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1763)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:76)
        at barna.commons.launcher.Flux.main(Flux.java:197)


[ERROR] java.lang.NullPointerException