Hemant, The BWA index format was changed in 0.6.0 to integrate the BWT and reverse BWT into the same file. I would recommend using BWA 0.5.9 to generate the index, which does still create .bwt and .rbwt files. --Dave B. On 11/7/12 14:32:15.000, Kelkar, Hemant wrote:

We recently upgraded our local galaxy install and followed the procedure that now uses “bwa” from the galaxy toolshed. Since the upgrade “bwa” alignments are generating the following error (exact file paths redacted):

[bwt_restore_bwt] fail to open file '/path_to/bwa_path/mm9_all.fa.rbwt'. Abort!

/bin/sh: line 1: 14044 Aborted (core dumped) bwa aln -t 4 /path_to/bwa_path/mm9_all.fa /path_to/galaxy/002/dataset_2377.dat > /path_to/galaxy-prod/galaxy-dist/database/tmp/tmpxb3Bvr/tmpJeewN0

We are using indexes made by bwa (0.6.0 also tried 0.6.2) but I do not see the “*.rbwt” file mentioned above in the indexes we have. BWA was working prior to the upgrade with the indexes currently in place.

We are using “LSF” for job queuing on the cluster. All other tools appear to be working fine.

Thanks,

Hemant

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