Question: Bwa Indexing Not Automatic?
gravatar for Joshua Orvis
5.2 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 • 1.1k views
ADD COMMENTlink modified 5.2 years ago by Jennifer Hillman Jackson25k • written 5.2 years ago by Joshua Orvis100
gravatar for Jennifer Hillman Jackson
5.2 years ago by
United States
Jennifer Hillman Jackson25k 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 mailing list to reach the development community (drop from the to or cc). Thanks, Jen Galaxy team -- Jennifer Hillman-Jackson
ADD COMMENTlink written 5.2 years ago by Jennifer Hillman Jackson25k
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