Just to double check, you are running the latest stable
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 firstname.lastname@example.org mailing list to reach the development
community (drop email@example.com from the to or cc).
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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