Jennifer -
Yes, I installed Galaxy that same day with:
1 http://wiki.galaxyproject.org/Admin/Get%20Galaxy#CA-6e8244969be36356bce6775f270761066e912e0d_1 % hg clone https://bitbucket.org/galaxy/galaxy-dist/ 2 http://wiki.galaxyproject.org/Admin/Get%20Galaxy#CA-6e8244969be36356bce6775f270761066e912e0d_2 % cd galaxy-dist 3 http://wiki.galaxyproject.org/Admin/Get%20Galaxy#CA-6e8244969be36356bce6775f270761066e912e0d_3 % hg update stable
Then I searched for bwa_wrappers in the toolshed (there were only two matches) and chose the devteam one.
What steps should I go through or log files should I submit to help track the problem down?
Thanks -
Joshua
On Mon, Sep 30, 2013 at 9:36 PM, Jennifer Jackson jen@bx.psu.edu wrote:
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-dev@bx.psu.edu mailing list to reach the development community (drop galaxy-user@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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