Error in read ID: could not parse read identifier in indexed bam generated by GEMtools

Hi,

I am running into a problem with the capacitor, where it doesn't seem to like my read descriptors. Input is a samtools indexed bam of paired end sequencing, generated by GEMtools. Settings are default. Below the log-dump of the crash.

Thanks
Martijn

[INFO] Annotation and mapping input checked
[HEHO] We are set, so let's go!
[ANNOTATION_FILE] ../gencode.v12.annotation.gtf
[MAPPING_FILE] ../test_run/results/WTCHG_45272_215_combi_sequence_mapping_filtered.bam
[READ_DESCRIPTOR]

/

[1,2]
[SORT_IN_RAM] false
[TMP_DIR] ../tmp
[STDOUT_FILE] ../test_flux/output
[INFO] mate pairing information considered
[INFO] writing insert sizes to ../test_flux/inserts

[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 WTCHG_45272_215:2:1105:11500:148871#CTATTGTG
[ERROR] Error while iterating loci:
java.lang.NullPointerException
at barna.io.sam.SAMMappingIterator.getMates(SAMMappingIterator.java:95)
at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.learn(FluxCapacitor.java
:880)
at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.run(FluxCapacitor.java:2
42)
at barna.flux.capacitor.reconstruction.FluxCapacitor.solve(FluxCapacitor.java:2129)
at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2661)
at barna.flux.capacitor.reconstruction.FluxCapacitor.getProfile(FluxCapacitor.java:2177)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1720)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:76)
at barna.commons.launcher.Flux.main(Flux.java:212)
java.lang.RuntimeException: java.lang.NullPointerException
at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2713)
at barna.flux.capacitor.reconstruction.FluxCapacitor.getProfile(FluxCapacitor.java:2177)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1720)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:76)
at barna.commons.launcher.Flux.main(Flux.java:212)
Caused by: java.lang.NullPointerException
at barna.io.sam.SAMMappingIterator.getMates(SAMMappingIterator.java:95)
at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.learn(FluxCapacitor.java
:880)
at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.run(FluxCapacitor.java:2
42)
at barna.flux.capacitor.reconstruction.FluxCapacitor.solve(FluxCapacitor.java:2129)
at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2661)
... 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 WTCHG_45272_215:2:1105:11500:148871#CTATTGTG
[ERROR] Error while iterating loci:
java.lang.NullPointerException
at barna.io.sam.SAMMappingIterator.getMates(SAMMappingIterator.java:95)
at barna.flux.capacitor.graph.AnnotationMapper.map(AnnotationMapper.java:353)
at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.run(FluxCapacitor.java:2
19)
at barna.flux.capacitor.reconstruction.FluxCapacitor.solve(FluxCapacitor.java:2129)
at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2663)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1726)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:76)
at barna.commons.launcher.Flux.main(Flux.java:212)
[ERROR] java.lang.NullPointerException