Thanks fo your answer, But when I am tring to use the bwa and to do "Map
with BWA for
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
Aborted (core dumped)
It seems like the ".rbwt" file is missing and cause the error?!
2013/5/30 Carl Eberhard <carlfeberh...@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 . <mer...@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
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