Re: [Bio-bwa-help] mysterious sampe errors

[Carrie W. <ca...@du...>]

Sure, 

bwa-0.6.2/bwa index TrinityBarb.fasta

bwa-0.6.2/bwa aln -t 16 TrinityBarb.fasta s_1.fastq > neom-barb-fwd.sai

bwa-0.6.2/bwa aln -t 16 TrinityBarb.fasta s_2.fastq > neom-barb-rev.sai

bwa-0.6.2/bwa sampe TrinityBarb.fasta neom-barb-fwd.sai neom-barb-rev.sai s_1.fastq s_2.fastq > neom-barb.sam



Thanks!

I'm retrying using the -6 command just in case that miraculously solves the problem.


On Aug 22, 2012, at 3:15 PM, Matt Edwards wrote:

> Hmm... not sure what the diagnosis is then.  Can you post the commands
> you're using for each of the three steps?
> 
> Matt
> 
> On Wed, Aug 22, 2012 at 3:07 PM, Carrie Wessinger <ca...@du...> wrote:
>> Thanks so much for your response!
>> 
>> Actually, I have been running all three steps separately each time I try a new version, so I don't think that is my problem.
>> 
>> Thanks,
>> Carrie
>> 
>> On Aug 22, 2012, at 3:05 PM, Matt Edwards wrote:
>> 
>>> Just a guess, but it sounds like you may be having trouble with the
>>> versions of the reference genome indices.  Indices generated by 0.5.*
>>> and 0.6* aren't compatible, and will crash if you try to use them with
>>> the non-matching program.
>>> 
>>> Try running the aln/sampe steps with an index that was generated by
>>> 0.5.8c with 0.5.8c, and see if that works.
>>> 
>>> If you want to use a newer version of bwa, index with 0.6.2 with the
>>> -6 command so that the new index has a different name.  Then try
>>> aln/sampe with 0.6.2, which should use the correct index (*.64.*).
>>> 
>>> Matt
>>> 
>>> On Wed, Aug 22, 2012 at 2:58 PM, Carrie Wessinger <ca...@du...> wrote:
>>>> Dear BWA community,
>>>> 
>>>> I'm having a hard time with my first attempt to use BWA.  I'm running this analysis on the Pittsburgh supercomputer.
>>>> 
>>>> Everything seems well and good after running bwa index and bwa aln on both my forward and reverse reads.  (My .sai files are ~1.5 GB, while each raw read file is 13 GB - hopefully that is normal).
>>>> 
>>>> However, when I try to run sampe, I'm getting one of two different types of errors.
>>>> If I use the bwa0.6.1 that is installed on the supercomputer, I get an immediate segmentation fault.
>>>> 
>>>> If I use any other version of bwa (including 0.5.8c and 0.6.2) that I install myself, again bwa index and aln work fine, but upon running sampe, I get an immediate error stating
>>>> [bns_restore_core] fail to open file '362-3598]'. Abort!
>>>> 
>>>> I have no idea what file the computer is trying to look for and why it might be looking for a file that is named a telephone number.
>>>> 
>>>> Anyone ever experienced this?
>>>> 
>>>> Thanks so much for any help!
>>>> 
>>>> -Carrie Wessinger
>>>> ------------------------------------------------------------------------------
>>>> Live Security Virtual Conference
>>>> Exclusive live event will cover all the ways today's security and
>>>> threat landscape has changed and how IT managers can respond. Discussions
>>>> will include endpoint security, mobile security and the latest in malware
>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>> _______________________________________________
>>>> Bio-bwa-help mailing list
>>>> Bio...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/bio-bwa-help
>>