Hi, מירב

Sounds like you might want to try reindexing and make sure you have plenty
of disk space - I have a .rbwt file from the last time I indexed using BWA
version: 0.6.2-r126 and it works fine for me.



On Sun, Jun 2, 2013 at 4:02 PM, מירב . <mer...@gmail.com> wrote:

> Thanks fo your answer, But when I am tring to use the bwa and to do "Map
> with BWA for 
> Illumina<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3>
> "
>
>
> 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 <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
>>
>>
>> merav
>>
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>
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-- 
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
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