Re: [Vcftools-help] vcftools-help

[Travis C. <tra...@gm...>]

Memory errors can be very difficult to diagnose.  And I haven't been
using vcftools recently.

However, one (maybe remote) possibility is that some of your positions
are too large.  Is this human data with standard chromosome positions?

You should try reducing your input data down to the smallest size that
still gives you the error, and then share that.  One way of starting
to do that would be to delete rows (sites) from the vcf.  It is just a
(possibly compressed) text file.

It may turn out that removing a single entry makes the error go
away... That would be nice for you, but annoying for finding and
fixing the problem.

It may also turn out that a few sites, or maybe just one, is
sufficient to cause the error.  If that is the case, then the
developers (or some users here) will probably be able to help you.

Just edit the vcf and see if you can narrow it down.  Then share the
file which causes vcftools to crash.

Oh, and also tell folks what version of vcftools you are using.  If
you are using an old version, try upgrading it first.


On 8 March 2017 at 08:54, Irina Calic <ic...@ug...> wrote:
> Hi,
>
>
> I tried to run filtering steps in vcftools to improve the SNPs dataset
> quality, however error message was as following:
>
>
> Outputting VCF file...
>
> terminate called after throwing an instance of 'std::bad_alloc'
> what():  std::bad_alloc
> Aborted (core dumped)
>
>
> The dataset contains around 700K sites for 239 individuals. It could be a
> memory problem, and the memory card was previously upgraded, however it is
> not possible to complete filtering steps.
>
> Could you please assist on this?
>
> Thanks,
>
> Irina
>
>
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