BAM ID parsing error results in NPE

[aesteve@cn98 quantifications]$ flux-capacitor --threads 4 -a /project/devel/rna_pipeline/data/annotations/hg/gencode_v12.gtf -i ../bams/CF_11_TGACCA_L005_R1_001.bam -o CF_11_gencode_new.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 (00:00:18)
        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 (00:01:11)
[WARN] Skipped 724375 lines.
[INFO]  45013 loci, 183086 transcripts, 1188378 exons.
 OK (00:01:11)
        Scanning mapping file  OK (00:01:36)
[WARN] Skipped 132219 lines.
[INFO]  12434411 reads, 36942800 mappings: R-factor 2.9710133
[INFO]  36401674 entire, 541126 split mappings (0.14647672%)
[INFO]  Read descriptor seems OK
 OK (00:01:36)
[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_11_TGACCA_L005_R1_001.bam
[READ_DESCRIPTOR] {ID}/{MATE}[1,2]
[SORT_IN_RAM] false
[TMP_DIR] /scratch_tmp
[STDOUT_FILE] /project/devel/aesteve/capacitor-tests/quantifications/CF_11_gencode_new.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";
[WARN] Error in read ID: could not parse read identifier DD61XKN1:127:D1BY5ACXX:5:1314:5980:51033
[ERROR] Error while iterating loci:
java.lang.NullPointerException
        at barna.io.sam.SAMMappingSortedIterator.getMates(SAMMappingSortedIterator.java:163)
        at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.learn(FluxCapacitor.java:882)
        at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.run(FluxCapacitor.java:242)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.solve(FluxCapacitor.java:2152)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2684)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.getProfile(FluxCapacitor.java:2200)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1744)
        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:2737)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.getProfile(FluxCapacitor.java:2200)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1744)
        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.io.sam.SAMMappingSortedIterator.getMates(SAMMappingSortedIterator.java:163)
        at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.learn(FluxCapacitor.java:882)
        at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.run(FluxCapacitor.java:242)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.solve(FluxCapacitor.java:2152)
        at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2684)
        ... 4 more
[FATAL] Error occured during scanning
        java.lang.NullPointerException

[SOLVE] Deconvolving reads of overlapping transcripts.
        decomposing  [WARN] skipped line chr1   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 DD61XKN1:127:D1BY5ACXX:5:1205:4281:94301
[ERROR] Error while iterating loci:
java.lang.NullPointerException
        at barna.io.sam.SAMMappingSortedIterator.getMates(SAMMappingSortedIterator.java:163)
        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: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.NullPointerException

[aesteve@cn98 quantifications]$