Re: [Samtools-help] bwa error: SA-BWT inconsistency: seq_len is not the same.

[Ivan G. <iva...@gm...>]

I see now. Let me say it explicitly for posterity:

1) Alignment via bwa aln involves two steps.
These steps are bwa aln plus either bwa samse or bwa sampe.

2) Alignment via bwa bwasw involves only one step.
This step is, obviously, bwa bwasw.

Thank you Heng and Joe.

Ivan


Ivan Gregoretti, PhD



On Sat, Apr 28, 2012 at 2:53 PM, Heng Li <lh...@sa...> wrote:
> bwasw output sam
>
> On Apr 28, 2012, at 2:11 PM, Ivan Gregoretti wrote:
>
>> Hello Joe,
>>
>> It seems that you were right, or partially right at least.
>>
>> I deleted all the mouse.mm9.fasta.* files, indexed with bwa 0.6.1 and
>> re run bwa bwasw. This time it worked but, alas! a new error arose
>> later:
>>
>> bwa samse mouse.mm9.fasta myfile.sai myfile.fq.gz
>> [bns_restore_core] fail to open file 'mouse.mm9.fasta.nt.ann'. Abort!
>> Aborted (core dumped)
>>
>> Well, the error is true, bwa indexing generated mouse.mm9.fasta.ann,
>> not mouse.mm9.fasta.nt.ann. So, mouse.mm9.fasta.nt.ann does not exist.
>>
>> I tried renaming mouse.mm9.fasta.nt.ann to mouse.mm9.fasta.ann
>> followed by bwa samse but it only ends in segmentation fault.
>>
>> Any thoughts?
>>
>> Thank you,
>>
>> Ivan
>>
>>
>> Ivan Gregoretti, PhD
>>
>>
>>
>> On Fri, Apr 27, 2012 at 3:17 PM, Joseph Fass <jos...@gm...> wrote:
>>> That can't be the meaning of that error message - bwasw has no requirement
>>> about uniform read lengths. It looks more like there's an issue with the
>>> indexing of the reference, and there was indeed a major change in the
>>> reference indexing between the 0.5 and 0.6 versions. I'm guessing that you
>>> indexed the reference with 0.5.9, since the alignment is working with that
>>> version. Try moving or removing all the mouse.mm9.fasta.* files,
>>> re-indexing, and re-trying the command.
>>> HTH,
>>> ~Joe
>>>
>>>
>>>
>>> On Fri, Apr 27, 2012 at 11:23 AM, Ivan Gregoretti <iva...@gm...>
>>> wrote:
>>>>
>>>> Hello everybody,
>>>>
>>>> BWA seems to have introduced a bug in version 0.6.1
>>>>
>>>> This is how I get it shown:
>>>>
>>>> /bwa-0.6.1/bwa bwasw -t 4 mouse.mm9.fasta myfile.fq.gz > myfile.sai
>>>> [bwt_restore_sa] SA-BWT inconsistency: seq_len is not the same. Abort!
>>>> Aborted
>>>>
>>>> I am currently running successfully the exact same command with version
>>>> 0.5.9.
>>>>
>>>> I interpret the error message as saying that the input sequences have
>>>> different lengths. I checked, all sequences are 76 nucleotides long.
>>>>
>>>> Am I the only one seeing this?
>>>>
>>>> Thank you,
>>>>
>>>> Ivan
>>>>
>>>>
>>>> Ivan Gregoretti, PhD
>>>>
>>>>
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>>>
>>>
>>>
>>> --
>>> Joseph Fass
>>> Lead Data Analyst
>>> UC Davis Bioinformatics Core
>>> http://bioinformatics.ucdavis.edu/
>>> joseph.fass -at- gmail.com
>>> 530.752.2698 (w)
>>>
>>
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>> _______________________________________________
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