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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--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___________________________________________________________
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
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/