Hi,
Yes, we're reasonably sure that this file is already sorted.
It's 549 samples, and nearly 400 gigabytes uncompressed. Is it possible
that I'm hitting a limit for file size?
We're going to try working with just the first chromosome to see if that
subset can be indexed.
Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://phytozome.jgi.doe.gov
On Mon, Aug 25, 2014 at 2:22 PM, Laura Clarke <[email protected]> wrote:
> Is your file sorted?
>
> thanks
>
> Laura
>
>
>
> On 25 August 2014 20:49, Richard Hayes <[email protected]> wrote:
> > Hi,
> >
> > I have a VCF file that is 53 Gb after compressing with bgzip. I am having
> > trouble indexing this with tabix version 0.2.5 (r1005). It runs for a
> while
> > but then quits with the message:
> >
> > [ti_index_build2] fail to create the index file.
> >
> > Any advice is appreciated.
> >
> > Thanks,
> >
> > Richard D. Hayes, Ph.D.
> > Joint Genome Institute / Lawrence Berkeley National Lab
> > http://phytozome.jgi.doe.gov
> >
> >
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