[ensembl-dev] VEP offline script: Checking/creating FASTA index fails to find existing index

Will McLaren wm2 at ebi.ac.uk
Mon Oct 20 09:29:09 BST 2014

 Hi Cyriac,

This is not something I've come across before; the FASTA indexing is
performed by code that we do not maintain (the Bio::DB::Fasta module is
part of the BioPerl package).

Which version of BioPerl are you using (there are known issues with 1.2.3,
though not this issue AFAIK, the VEP installs 1.6.0)? And are you using a
single FASTA file or a directory containing multiple FASTA files?

For VEP it is normal that it just generates the .fa.index file; I have
never seen the other two you mention (perhaps they appear with a directory
of files rather than a single .fa).

I'd try removing the indexes and reindexing, or removing the .fa file and
re-downloading/re-generating it.



On 18 Oct 2014 02:33, "Cyriac Kandoth" <kandoth at cbio.mskcc.org> wrote:

> Hi Devs,
> The code to check whether a FASTA index needs to be created, looks for a
> file with extension ".fa.index". However, (and this may be recent) the
> indexes created are files named ".fa.index.dir" and ".fa.index.pag". I
> haven't checked the code to confirm this. I'm assuming this is the case,
> since VEP appears to index the FASTA everytime it runs, unless I create a
> copy of ".fa.index.pag" with extension ".fa.index".
> Cheers!
> ~Cyriac
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