Hi Joshua,

Just to double check, you are running the latest stable distribution?

There are a few different BWA wrappers in the tool shed, maybe you are using a different one than previously? Using a custom reference genome from the history with bwa is possible with the wrapper with the owner "devteam" (assuming Galaxy is installed where there are suitable resources - same as command line bwa).

If you want to try again and report back any ongoing issues, please use the galaxy-...@bx.psu.edu mailing list to reach the development community (drop galaxy-u...@bx.psu.edu from the to or cc).

Thanks,
Jen
Galaxy team


On 9/27/13 7:37 PM, Joshua Orvis wrote:
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 
'/seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat.bwt'.
 Abort!
/bin/sh: line 1: 11607 Aborted                 bwa aln -t 4 -I 
/seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat 
/seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_2.dat 
> /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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