Hello Joshua,

It may be that the local instance is running out of memory and the custom reference genome approach is the wrong one for your configuration. Instead, try installing the reference database as a built-in index.


Instructions are here:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

If you need follow-up help, you will want to post a brand new question as a brand new thread on the galaxy-...@bx.psu.edu mailing list. That list is for local install questions and will get you the most feedback from the development community.
http://wiki.galaxyproject.org/MailingLists

Take care,

Jen
Galaxy team

On 6/14/13 12:16 PM, Joshua Orvis wrote:
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)


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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
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local Galaxy instances and the Galaxy source code, please
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