Re: [galaxy-dev] BWA installation

[Ross]

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 .  wrote:

> 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 
>
>> 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 .  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=UCUuEM4J
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Re: [galaxy-dev] BWA installation

[מירב .]

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 

> 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 .  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
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
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Re: [galaxy-dev] BWA installation

[Carl Eberhard]

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 .  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
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
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[galaxy-dev] BWA installation

[מירב .]

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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