I installed a new copy of galaxy today and then added the bwa_wrappers
tool.  After I upload my reference genome and left/right reads I get output
like this each time I try to run bwa for illumina:

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
/bin/sh: line 1: 11607 Aborted                 bwa aln -t 4 -I
> /tmp/tmpMuj4l2/tmpUIdxXT

If I manually do the 'bwa index' command on dataset_4.dat it works but
in the past this seemed to happen automatically.  Any clue what's
going on here?
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