Question: Bwa Indexing Not Automatic?
0
Joshua Orvis • 100 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?
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modified 5.2 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
5.2 years ago by
Joshua Orvis • 100
