Error "Introns cannot be less than zero" AssertionError: Introns cannot be less than zero

[martinmau1]

Hello,

I am mapping a transcriptome of the same species to its genome (both .fasta format). The transcriptome file holds the assembled transcripts (CDS only) in the following format:
'''

BA1G0000100:+
GGATCACCTAACCTCTTCTTTGATTCTCTTCAATCAAAT...
BA1G0000200:-
TTCTCTCTCTCTCCCCAAAAGTAAAACCCCGCAGCCATTGTTTCTCCTCCAC...
'''

when running gapmm2 with the following parameter:
'''
gapmm2 /datastore/SEED1/Martin/Apomixis_Breeding/Test_reference_genome/ES672_BA_G.028_chr.fasta ./BA_T.12.028.fasta -o ./ES672_T.12.028_annotated -f gff3 -t 4
'''

I am getting the error message ""Introns cannot be less than zero"
AssertionError: Introns cannot be less than zero".

I'd be glad if you can give me a hint how to resolve this issue.

Many thanks
Martin