Thanks fo your answer, But when I am tring to use the bwa and to do "Map with BWA for Illumina"

I'm getting this error:

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 '/home/user/extra_galaxy_project/bwa/data/hg18full/hg18full.fa.rbwt'. Abort!
Aborted (core dumped)

It seems like the ".rbwt" file is missing and cause the error?! 

2013/5/30 Carl Eberhard <carlfeberhard@gmail.com>

Hello, מירב

It looks like the indexing system/format in 'bwa index' has changed

and we haven't updated the wiki to reflect the changes. 

The reverse index (which includes the .r* files) are now part of the forward index. You

should be fine to proceed.

I'll update the wiki to reflect this.

From https://github.com/lh3/bwa/blob/master/NEWS :

Release 0.5.10 and 0.6.0 (12 November, 2011)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The 0.6.0 release comes with two major changes. Firstly, the index data structure has been changed to support genomes longer than 4GB. The forward and reverse backward genome is now integrated in one index.

On Thu, May 30, 2013 at 8:03 AM, מירב . <mermam@gmail.com> wrote:

Hello all,

I am trying to install BWA , I used the command:
 " bwa index -a bwtsw /global_data/hg18full.fa " and I got only 5 files insted of 8

The missing files are

• rbwt
• rpac
• .rsa

I didn't recieve any error message while running.

thanks for your help

merav

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