Re: [Bio-bwa-help] BWA sampe aborted

[Tom S. <ts...@sa...>]

Hi Yaowu,

The first two lines you list are console messages, normally written to 
the stderr output. The rest looks like .sai data, which is normally 
written to stdout and redirected to a file with >. You've apparently got 
stderr and stdout going to the same file. Are you doing something like 
"bwa aln ... > file.sai 2>&1"?
The 2>&1 (or similar redirection operation, depending on which shell 
you're uising) would send stdout messages to the .sai file, as you are 
seeing.

It's not clear that this is the cause of your original problem, but the 
.sai file you describe isn't right.

--TS

Keith Bettinger wrote:
> Hi Yaowu,
>
> .sai files are binary (human-unreadable), so if your .sai files 
> contain the readable text "[bwa_aln_core] calculate SA coordinate... 
> 61.71 sec", there is something wrong.  Try deleting that .sai file and 
> rerunning your aln and see if things work better for you.
>
> -----
>    _.--'"`'--._     _.--'"`'--._    _      Keith Bettinger
> '-:`.'|`|"':-.  '--:`.'|`|"':-.  '.` : '.  Software Developer, Research
>   '.  | |  | |'.   '.  | |  | |'.  '.:   ' Stanford Center for 
> Genomics and
> '.  '.| |  | |  '..  '.| |  | |  '.  '.  :          Personalized Medicine
>   '.  `.:_ | :_.'  '.  `.:_ | :_.' '.  `.'
>      `-..,..-'        `-..,..-'       `    bet...@st... 
> <mailto:bet...@st...>
>
> On Sep 29, 2010, at 10:30 AM, Yaowu Yuan wrote:
>
>> Hi Keith, 
>>
>> Thanks for your information. The .sai files (a pair of files) look 
>> normal in terms of file size. The genome size is about 400MB, and the 
>> .sai files are about 520 MB. The first few lines of the .sai file is 
>> pasted below. Does a normal .sai file look like this?
>>
>> [bwa_aln_core] calculate SA coordinate... 61.71 sec
>> [bwa_aln_core] write to the disk... 
>> ^C^@^@^@^K^@^@^@^D^@^@^@^C^@^@^@^E^@^@^@^P^@^@^@<80><84>^^^@^@^@<80>?^C^@^@^@^A^@^@^@^F^@^@^@^B^@^@^@ 
>> ^@^@^@
>> ......
>> .......
>>
>>
>> Thanks again. 
>>
>> Yaowu
>>
>> On Sep 29, 2010, at 1:02 PM, Keith Bettinger wrote:
>>
>>> My guess is that "aln" actually did fail, and your .sai file is 
>>> empty.  Take a look.
>>>
>>> -----
>>>    _.--'"`'--._     _.--'"`'--._    _      Keith Bettinger
>>> '-:`.'|`|"':-.  '--:`.'|`|"':-.  '.` : '.  Software Developer, Research
>>>   '.  | |  | |'.   '.  | |  | |'.  '.:   ' Stanford Center for 
>>> Genomics and
>>> '.  '.| |  | |  '..  '.| |  | |  '.  '.  :          Personalized 
>>> Medicine
>>>   '.  `.:_ | :_.'  '.  `.:_ | :_.' '.  `.'
>>>      `-..,..-'        `-..,..-'       `    bet...@st... 
>>> <mailto:bet...@st...>
>>>
>>> On Sep 29, 2010, at 7:20 AM, Yaowu Yuan wrote:
>>>
>>>> Hi there,
>>>>
>>>> I was trying to run BWA to map some PE illumina reads (ca. 60  
>>>> milliion). The "index" and "aln" steps went fine, but the "sampe"  
>>>> couldn't run at all, with a error message "[bns_restore_core] fail to  
>>>> open file 'IRGSP_B5.fa.nt.ann'. Abort!"
>>>>
>>>> I then checked the index results, there were 8 files:
>>>> IRGSP_B5.fa.amb
>>>> IRGSP_B5.fa.ann
>>>> IRGSP_B5.fa.bwt
>>>> IRGSP_B5.fa.pac
>>>> IRGSP_B5.fa.rbwt
>>>> IRGSP_B5.fa.rpac
>>>> IRGSP_B5.fa.rsa
>>>> IRGSP_B5.fa.sa
>>>>
>>>> I didn't see there was any ".nt.ann" file. I tried both "is" and  
>>>> "bwtsw" for the "index" step, got the same 8 files. The same problem  
>>>> occurs to both bwa-0.5.8a and bwa-0.5.7 (I didn't try even earilier  
>>>> versions). Does anyone have a clue what might be the problem?
>>>>
>>>> Thanks for any insights.
>>>>
>>>> Yaowu
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Start uncovering the many advantages of virtual appliances
>>>> and start using them to simplify application deployment and
>>>> accelerate your shift to cloud computing.
>>>> http://p.sf.net/sfu/novell-sfdev2dev
>>>> _______________________________________________
>>>> Bio-bwa-help mailing list
>>>> Bio...@li... 
>>>> <mailto:Bio...@li...>
>>>> https://lists.sourceforge.net/lists/listinfo/bio-bwa-help
>>>
>>
>> Yaowu Yuan
>> 4505 Miller Plant Sciences Building
>> Department of Plant Biology
>> University of Georgia
>> Athens, GA, 30602
>>
>>
>>
>>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> ------------------------------------------------------------------------
>
> _______________________________________________
> Bio-bwa-help mailing list
> Bio...@li...
> https://lists.sourceforge.net/lists/listinfo/bio-bwa-help
>   



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.