I just installed a new instance of Galaxy and bwa_wrappers from the main toolshed. I then uploaded a reference genome along with two FASTQ files in order to run "Map with BWA for Illumina". When I run it, I get this error:

The alignment failed.

Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2

[bwa_aln] 38bp reads: max_diff = 3

[bwa_aln] 64bp reads: max_diff = 4

[bwa_aln] 93bp reads: max_diff = 5

[bwa_aln] 124bp reads: max_diff = 6

[bwa_aln] 157bp reads: max_diff = 7

[bwa_aln] 190bp reads: max_diff = 8

[bwa_aln] 225bp reads: max_diff = 9

[bwt_restore_bwt] fail to open file '/export/galaxy-dist/database/files/000/dataset_1.dat.bwt'. Abort!

Aborted

I've used the same tool on other Galaxy instances and it always auto-indexes the reference genome here before continuing. What's going wrong? (I made sure bwa was in the user's PATH that is running run.sh)