It doesn't sound like a size limitation - I've certainly indexed much
larger bgzipped VCFs with tabix in the past, including one that weighed in
at over 4*TB* compressed (that one took a while!). I would perhaps try
running something like the GATK's ValidateVariants or whatever the
equivalent is in vcftools to see if you could get more useful feedback on
what's wrong.
-t
On Mon, Aug 25, 2014 at 5:48 PM, Richard Hayes <rdha...@lbl.gov> wrote:
> 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 <la...@ebi.ac.uk> wrote:
>
>> Is your file sorted?
>>
>> thanks
>>
>> Laura
>>
>>
>>
>> On 25 August 2014 20:49, Richard Hayes <rdha...@lbl.gov> 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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>
>
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