TopHat did not find any junctions in GTF file

[mattanswers]

I can not figure out why I am getting the message, 'TopHat did not find any junctions in GTF file',
as well as the error, 'Couldn't build bowtie index with err = 1'.

When this file, TAIR10_GFF3_genes.gff, is used, eveything works fine.

Chr1	TAIR10	chromosome	1	30427671	.	.	.	ID=Chr1;Name=Chr1
Chr1	TAIR10	gene	3631	5899	.	+	.	ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
Chr1	TAIR10	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1
Chr1	TAIR10	protein	3760	5630	.	+	.	ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
Chr1	TAIR10	exon	3631	3913	.	+	.	Parent=AT1G01010.1

However, when this file, ath_miRBase_miRNA_Cap-Chr_V.gff3, is used, the error appears.

Chr1	TAIR10	chromosome	1	30427671	.	.	.	ID=Chr1;Name=Chr1
Chr1	TAIR10	miRNA_primary_transcript	28500	28706	.	+	.	ID=MI0005394_1;accession_number=MI0005394;Name=ath-MIR838
Chr1	TAIR10	miRNA	28635	28655	.	+	.	ID=MIMAT0004260_1;accession_number=MIMAT0004260;Name=ath-miR838;derives_from=MI0005394_1
Chr1	TAIR10	miRNA_primary_transcript	78927	79037	.	-	.	ID=MI0000199_1;accession_number=MI0000199;Name=ath-MIR165a

The command line is (the only difference being the file after the -G switch).

./tophat --library-type fr-unstranded
-o /A_ATCACG_set1_mRNA_TH-out
-G /ath_miRBase_miRNA_Cap-Chr_V.gff
/TAIR10_C_Bt2
/A_ATCACG_L008_R1.fastq

I have used bowtie2-inspect -n, and made sure the names are the same in the genome index, TAIR10_C_Bt2, and the gff3 file.
The formatting of the two gff files (the one that does work and the one that doesn't) seems exactly the same to me.