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?