Thanks to everyone for the suggestions.
I've gotten an index to completely build at this point. I'm not sure if
this is due to a fresh compile of htslib 0.2.0-rc12 to just random luck in
having enough free RAM on a different server, but all is good now.
Best regards,
Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://phytozome.jgi.doe.gov
On Tue, Aug 26, 2014 at 4:45 AM, Tim Fennell <tfenn...@broadinstitute.org>
wrote:
> 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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