Question: Bwa Indexing Not Automatic?
0
gravatar for Joshua Orvis
4.3 years ago by
Joshua Orvis100
Joshua Orvis100 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 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?
bwa alignment • 827 views
ADD COMMENTlink modified 4.3 years ago by Jennifer Hillman Jackson23k • written 4.3 years ago by Joshua Orvis100
0
gravatar for Jennifer Hillman Jackson
4.3 years ago by
United States
Jennifer Hillman Jackson23k 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 -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD COMMENTlink written 4.3 years ago by Jennifer Hillman Jackson23k
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