Re: [Bio-bwa-help] segmentation fault in bwa samse with 75 bp SE version 0.7.4-r385

[Mia C. U. <mi...@br...>]

hi,

thanks for the response.
i sent the path to the file to you, heng, about a week ago as i don't think
i can send it on the mailing list.
i am aligning to hg19.
please let me know if you need anything further.

thanks!
mia

On Thu, Oct 9, 2014 at 2:52 PM, Heng Li <lh...@me...> wrote:

> Are you mapping to the human genome? Could you send me the file?
>
> Thanks,
>
> Heng
>
> On Oct 9, 2014, at 9:51 AM, Mia Caplan Uziel <mi...@br...>
> wrote:
>
> > hi,
> >
> > i have been receiving a segmentation fault when running bwa samse
> version 0.7.4-r385 on 75 bp single end reads. this happens consistently
> (and at the same spot) on at least one of the lanes (we have 1 per lane).
> > we have been using this version with the same reference with PE reads
> and shorted SE reads for a long while now, so i do not think the reference
> is the issue.
> > i tried running with version 0.5.9 as well and i get a segmentation
> fault immediately.
> > i have also verified that i have at least 10GB available memory. should
> i be using more?
> > for reads this length - would it be better to use bwa mem? i am somewhat
> reluctant to make changes in our 'pipeline', but if this is preferable - i
> will try that.
> > any help/suggestions will be much appreciated!
> >
> >
> > thanks!
> > mia
> >
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