Flux capacitor outputs very high incorrect RPKM values

Hi,

I am using the flux capacitor to quantify expression in my samples using the gtf for gencode v17. Most of the time this goes well, but for some reason for two samples the RPKM values seem completely off. I will rerun to see whether this will resolve the issue, but, given normal read counts, it seems strange the program returns these RPKMs.

Here are some random examples for transcripts from one genes (I can supply more if required):

15 HAVANA transcript 45004157 45008757 . + . transcript_id "ENST00000560681.1"; locus_id "15:45003675-45011075W"; gene_id "ENSG00000166710.12"; reads 106.075058; length 572; RPKM 185445904.000000
15 HAVANA transcript 45007698 45010343 . + . transcript_id "ENST00000561139.1"; locus_id "15:45003675-45011075W"; gene_id "ENSG00000166710.12"; reads 5366.204102; length 717; RPKM 7484245504.000000
15 HAVANA transcript 45003707 45011049 . + . transcript_id "ENST00000561424.1"; locus_id "15:45003675-45011075W"; gene_id "ENSG00000166710.12"; reads 44011.839844; length 604; RPKM 72867282944.000000

Thanks,
Martijn