I am trying to run Tophat on some Illumina data from an organism with no UCSC-supported genome.
I have taken my Illumina data and run it through the FASTQ groomer.
I input this data into tophat, and choose the built-in index option for the reference genome, using an uploaded GenBank FASTA genome.
I run this, but when I check the output by running NGS: SAM Tools > flagstat  on the bam output from tophat, I get 0% properly paired (see below for the exact output).
I have BLASTed the Illumina data just to double-check that I have not mixed files; it is in fact from the organism I am tophat-ing against.
I would greatly appreciate input on what I may be doing wrong?  Is the "built-in index" supposed to be just the genome sequence in FASTA format or is it something more complex?

6667700 in total
0 QC failure
0 duplicates
6667700 mapped (100.00%)
0 paired in sequencing
0 read1
0 read2
0 properly paired (-nan%)
0 with itself and mate mapped
0 singletons (-nan%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)