NullPointerException in BiasProfiler while iterating loci

This is the script I ran:

flux-capacitor -a gencode.v15.annotation.exon.gtf -o flux/262.txt -i 262.bam --count-elements SPLICE_JUNCTIONS --profile-output flux/262.profile --stats-file flux/262.stats --threads 5

The following is the output from the program:

Flux-Capacitor v1.4 (Flux Library: 1.24)

[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 *[WARN] Unsorted in line 29 - cannot perform gene clustering: chr1 - ENST00000541675.1 @ 24734 after ENST00000438504.2 @ 29321
[INFO] Sorting /home/hcho06/data/ref/annot/gencode.v15.annotation.exon.gtf
sorting GTF file ^@ OK (00:02:06)
scanning ^@ OK (00:00:51)
[INFO] 46708 loci, 195433 transcripts, 1201574 exons.
OK (00:00:51)
Scanning mapping file ^@@
[INFO] The Flux Capacitor is not using the SAM flags for counting the number of reads in the mapping file.
[WARN] This process can be long for big files!
OK (00:03:56)
[INFO] 13575924 mapped reads, 13577061 mappings: R-factor 1.0000838
[INFO] 7404434 entire, 6172627 split mappings (45.463646%)
[INFO] Read descriptor seems OK
OK (00:03:56)
[INFO] Annotation and mapping input checked
[HEHO] We are set, so let's go!
[ANNOTATION_FILE] /home/hcho06/data/ref/annot/gencode.v15.annotation.exon.gtf
[MAPPING_FILE] /mnt/iscsi/data/hcho06/bam/gsnap/262.bam
[READ_DESCRIPTOR]

/

[1,2]
[SORT_IN_RAM] true
[TMP_DIR] /tmp
[STDOUT_FILE] /mnt/iscsi/data/hcho06/bam/gsnap/flux/262.txt
[INFO] mate pairing information considered
[PROFILE] Loading profile

[PROFILE] Scanning the input and getting the attributes.
profiling [ERROR] Error while iterating loci:
java.lang.NullPointerException
at barna.flux.capacitor.profile.BiasProfiler.learn(BiasProfiler.java:293)
at barna.flux.capacitor.profile.BiasProfiler.profile(BiasProfiler.java:207)
at barna.flux.capacitor.profile.BiasProfiler.call(BiasProfiler.java:101)
at barna.flux.capacitor.reconstruction.FluxCapacitor.getProfile(FluxCapacitor.java:2196)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1878)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:74)
at barna.commons.launcher.Flux.main(Flux.java:197)
java.lang.RuntimeException: java.lang.NullPointerException
at barna.flux.capacitor.profile.BiasProfiler.profile(BiasProfiler.java:252)
at barna.flux.capacitor.profile.BiasProfiler.call(BiasProfiler.java:101)
at barna.flux.capacitor.reconstruction.FluxCapacitor.getProfile(FluxCapacitor.java:2196)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1878)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:74)
at barna.commons.launcher.Flux.main(Flux.java:197)
Caused by: java.lang.NullPointerException
at barna.flux.capacitor.profile.BiasProfiler.learn(BiasProfiler.java:293)
at barna.flux.capacitor.profile.BiasProfiler.profile(BiasProfiler.java:207)
... 5 more
[FATAL] Error occured during scanning
java.lang.NullPointerException
first round finished .. took 0 sec.

0 single transcript loci
13577061 mappings in file
0 mappings fall in single transcript loci
0 mappings in annotation-mapped pairs
0,0 min/max read length

[COUNT] Counting reads to the following elements: splice junctions.

[SOLVE] Deconvolving reads of overlapping transcripts.
decomposing [WARN] Error in read ID: could not parse read identifier M00659:32:000000000-A1U0F:1:1101:10474:27971
[ERROR] Error while iterating loci:
java.lang.NullPointerException
at barna.flux.capacitor.graph.AnnotationMapper.map(AnnotationMapper.java:366)
at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.call(FluxCapacitor.java:1071)
at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2630)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1886)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:74)
at barna.commons.launcher.Flux.main(Flux.java:197)

[ERROR] java.lang.NullPointerException
java.lang.RuntimeException: java.lang.NullPointerException
at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2680)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1886)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:74)
at barna.commons.launcher.Flux.main(Flux.java:197)
Caused by: java.lang.NullPointerException
at barna.flux.capacitor.graph.AnnotationMapper.map(AnnotationMapper.java:366)
at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.call(FluxCapacitor.java:1071)
at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2630)
... 3 more

Any help would be greatly appreciated!